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Thermo
TraceFinder
User Guide
Software Version 3.2
Optimized for General Quantitation
XCALI-97597 Revision A
June 2014
© 2014 Thermo Fisher Scientific Inc. All rights reserved.
Aria, Q Exactive, FOCUS, LCquan, ToxID, ExactFinder, Prelude, TSQ 8000, and TriPlus are trademarks, and
Accela, Dionex, Exactive, Thermo Scientific, Trace GC Ultra, TSQ Quantum, TSQ Endura, TSQ Quantiva,
TurboFlow, and Xcalibur are registered trademarks of Thermo Fisher Scientific Inc. in the United States.
NIST is a registered trademark of the National Institute of Standards and Technology in the United States.
The following are registered trademarks in the United States and other countries: Windows, Active Directory,
Excel, and Microsoft are registered trademarks of Microsoft Corporation. Adobe, Acrobat, and Reader are
registered trademarks of Adobe Systems Inc. Agilent is a registered trademark of Agilent Technologies, Inc.
Waters and ACQUITY are registered trademarks of Waters Corporation.
All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries.
Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
product operation. This document is copyright protected and any reproduction of the whole or any part of this
document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.
The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.
This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This
document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of
Sale shall govern all conflicting information between the two documents.
Release history: Revision A, June 2014
Software version: Microsoft Windows 7 Professional; (Thermo) Foundation 3.0 SP2; Xcalibur 2.2 SP1;
LC Devices 2.5 SP2; GC Devices 2.2
For Research Use Only. Not for use in diagnostic procedures.
C
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
License Activation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix
Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii
Thermo Scientific
Chapter 1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
About the TraceFinder Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
TraceFinder Summary of Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
TraceFinder Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Reporting Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Chapter 2
Getting Started. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
Installing the TraceFinder Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Installing the NIST and QED Libraries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Launching the NIST Library Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Launching a Qualitative Explorer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Thermo Scientific FreeStyle. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Thermo Xcalibur Qual Browser. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Converting Legacy Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Version Compatibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Converting Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Converting Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Converting Method Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Converting Batch Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Choosing a Mode or Console . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
TraceFinder Window Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Chapter 3
Using the Configuration Console . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
Specifying Application Defaults. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Specifying Default Peak Detection Parameters . . . . . . . . . . . . . . . . . . . . . . . . . 37
Specifying Adducts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
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Contents
Activating Optional Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Delay Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
User Peak Detection Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Auto Sampler Tray Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Acquisition Submission Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Qualitative Explorer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Screening Libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Multiplexing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Intelligent Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Creating Custom Columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Creating Custom Flags . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Specifying the Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
iv
Chapter 4
Using the Common Features of the Method Development Mode. . . . . . . . . . . . .75
Working with the Compound Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Mass Data Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
Compound Detail Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Grid Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Compound Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Experiment Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
Compound Database Names Mapped to CSV Column Names. . . . . . . . . . 109
Working with Instrument Methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Chapter 5
Using the Method Development Mode for Quantitation Methods . . . . . . . . . . .119
Opening a Master Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Starting a New Master Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
Creating a New Method with Method Forge. . . . . . . . . . . . . . . . . . . . . . . . 125
Importing an Xcalibur Master Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
Creating a Blank Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Selecting Compounds from the Compound Database . . . . . . . . . . . . . . . . . 142
Editing a Master Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
Modifying Retention Times . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
Editing the Acquisition Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
Editing the Processing Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
Editing the Compounds Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
Editing the QAQC Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230
Editing the Groups Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240
Editing the Intelligent Sequencing Page. . . . . . . . . . . . . . . . . . . . . . . . . . . . 243
Editing the Reports Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 248
Saving a Master Method to a New Name . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
Creating a Method Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
Importing Published Master Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265
Exporting Mass Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 266
TraceFinder User Guide
Thermo Scientific
Contents
Thermo Scientific
Chapter 6
Using the Method Development Mode for Screening Methods. . . . . . . . . . . . .267
Opening a Master Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 268
Creating a Master Method. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271
Editing a Master Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 273
Editing the Acquisition Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 273
Editing the Processing Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
Editing the Peak Detection Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295
Editing the Reports Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 306
Saving a Master Method to a New Name . . . . . . . . . . . . . . . . . . . . . . . . . . . . 308
Importing Published Master Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 309
Chapter 7
Using the Acquisition Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .311
Working with Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 312
Opening and Navigating the Acquisition Mode . . . . . . . . . . . . . . . . . . . . . 312
Creating and Submitting Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 314
Real Time Status Pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 348
Acquisition Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 349
Instrument Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351
Devices Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 352
Queues Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 357
Real-Time Trace Display. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 363
Sample Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 365
Chapter 8
Using the Analysis Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .367
Working in the Batch View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 368
Samples Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 369
Auto Samples Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 406
Reference Samples Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 408
Threshold Samples Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 409
Working in Data Review for Quantitation Methods . . . . . . . . . . . . . . . . . . . . 410
Sample View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 411
Compound View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 423
Comparative View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 433
Qualitative View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 441
Features Common to All Data Review Pages . . . . . . . . . . . . . . . . . . . . . . . . 456
Working in Data Review for Target Screening Methods . . . . . . . . . . . . . . . . . 485
Samples Pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 487
Compounds Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 488
Chromatogram Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 502
Spectrum Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 503
Working in the Local Method View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 516
Working in the Report View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 518
Working in the Report Designer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 524
Editing a Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 525
Toolbar Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 533
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Chapter 9
Using the Audit Viewer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .537
Appendix A Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .549
Appendix B Isotopic Pattern Details . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .553
Isotopic Distribution in Exact Mass Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . 553
Isotopic Pattern Score Calculations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 557
Data Set Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 557
Calculating Mass and Intensity Deviations . . . . . . . . . . . . . . . . . . . . . . . . . 560
Calculating Isotopic Pattern Score . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 562
Finding the Noise Value . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 567
Appendix C Using Copy Down and Fill Down . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .569
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .573
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P
Preface
This guide describes how to use the Thermo TraceFinder™ 3.2 application in the Thermo
Scientific™ series of GC/MS and LC/MS analytical software.
Contents
• Related Documentation
• License Activation
• Special Notices
• Contacting Us
Related Documentation
The TraceFinder application includes complete documentation. In addition to this guide, you
can also access the following documents as PDF files from the data system computer:
• TraceFinder User Guide
• TraceFinder Administrator Console User Guide
• TraceFinder Acquisition Quick Reference Guide
• TraceFinder Analysis Quick Reference Guide
• TraceFinder Shortcut Menus Quick Reference Guide
 To view TraceFinder documents using the Start menu
From the Microsoft™ Windows™ taskbar, choose Start > All Programs > Thermo
TraceFinder > Manuals.
Thermo Scientific
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Preface
 To open TraceFinder Help and access related documents from the application
1. Open the TraceFinder application and choose Help > TraceFinder Help.
• To find a particular topic, use the Contents, Index, or Search panes.
• To create your own bookmarks, use the Favorites pane.
2. To view the operator manual, user guide, or one of the quick reference guides, choose
Help > Manuals > PDF file.
Figure 1.
PDF files available from the Help menu
The PDF file of the selected document opens in a new window.
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Preface
License Activation
When you first start the TraceFinder application, a dialog box displays the number of days
remaining in your 120-day free trial. If your free trial has expired, the License Activation
window opens.
Note You can open the License Activation window at any time during your trial period by
choosing Help > License Activation from the TraceFinder menu. If you already have a
permanent license, a message tells you that your product is fully licensed.
Two types of licenses are available:
• 120-Day Evaluation Version (free of charge)
• Full Version Single License
The evaluation version is full-featured and automatically expires 120 days after activation.
Any attempt to set back the system date automatically terminates this version. You can
purchase and then activate the full version of the TraceFinder application at any time, during
or after the free evaluation, without reinstalling the software.
Each activation key is valid only for a single license. Any additional installation generates a
different license and requires a different activation key.
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Preface
 To request an activation key
1. In the License Activation window, enter your information in the User Info area.
As you type, the License Text box creates an XML text string with your information.
2. In the Barcode box, type the barcode printed on the TraceFinder CD.
The form of the barcode number is either xxxx-xxxx-xxxx or xxxx-xxxx-xxxx-xxxx.
Note The barcode might already be filled in for you.
3. When you finish entering all the information, click Copy.
The application copies this XML text to the Clipboard.
If you have not completed all the information, a pop-up box identifies the missing
information.
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4. Paste this XML text in the body of an email and send the email to
[email protected]
You will receive an email response containing the activation key.
 To use your activation key
1. When you receive your activation key, copy it from the email.
2. Choose Help > License Activation from the TraceFinder menu.
The License Activation window opens.
3. Click Paste.
The application pastes the contents of the Clipboard to the License Text box.
4. Click Set.
The application is activated according to the type of authorization your license gives you.
Special Notices
Make sure you follow the special notices presented in this guide. Special notices appear in
boxes.
This guide uses the following types of special notices.
IMPORTANT Highlights information necessary to prevent damage to software, loss of
data, or invalid test results; or might contain information that is critical for optimal
performance of the system.
Note Highlights information of general interest.
Tip Highlights helpful information that can make a task easier.
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Preface
Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need.
For Thermo Scientific™ products
Access by phone, fax, email, or website
Technical Support
(U.S.)
Phone: 1 (800) 532-4752
Fax: 1 (561) 688-8736
Email: [email protected]
Web—for product support, technical documentation, and knowledge bases:
www.thermoscientific.com/support
Customer Service
(Sales and service)
(U.S.)
Phone: 1 (800) 532-4752
Fax: 1 (561) 688-8731
Email: [email protected]
Web—for product information:
www.thermoscientific.com/lc-ms
Web—for customizing your service request:
1. From any Products & Services web page, click Contact Us.
2. In the Contact Us box, complete the information requested, scroll to the
bottom, and click Send.
User Documentation
Web—for downloading documents:
mssupport.thermo.com
1. On the Terms and Conditions web page, click I Agree.
2. In the left pane, click Customer Manuals.
3. To locate the document, click Search and enter your search criteria. For
Document Type, select Manual.
Email—to send feedback directly to Technical Publications:
[email protected]
Web—to complete a survey about this Thermo Scientific document:
www.surveymonkey.com/s/PQM6P62
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1
Introduction
This chapter describes general features of the TraceFinder software.
Contents
• About the TraceFinder Application
• TraceFinder Summary of Features
• TraceFinder Workflow
• Reporting Features
About the TraceFinder Application
The TraceFinder application targets the general quantitation market. It supports a focused
quantification workflow for specific nonbioanalytical laboratory use, instrument control, and
method development functionality. TraceFinder is the primary application for the TSQ
Quantum™ XLS triple quadrupole mass spectrometers.
The TraceFinder application can export mass data in the Acquisition List to XML format so
that other applications, including TSQ 8000, TSQ Quantum™, ISQ, and Q Exactive™, can
import the files into their databases.
The TraceFinder application can import the following file types:
• Sample lists in .csv or .xml format
See “Defining the Sample List” on page 324.
• Processing (.pmd) and instrument (.meth) method files from the Xcalibur data system
For detailed information about creating quantitative processing methods, see Chapter 5,
“Using the Method Development Mode for Quantitation Methods.”
For detailed information about creating target screening processing methods, see
Chapter 6, “Using the Method Development Mode for Screening Methods.”
For detailed information about creating instrument methods, see “Working with
Instrument Methods” on page 113.
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Introduction
About the TraceFinder Application
• Compounds from files that use the database (.xml or .cdb) format
See “Working with the Compound Database” on page 76.
• Batches, methods, or templates from the TraceFinder 2.0, 2.1, 3.0, or 3.1 applications.
See “Converting Legacy Data” on page 18.
The TraceFinder application checks the accuracy and precision of data against systems that
have previously been certified against a standard processing program, such as the Statistical
Analysis System (SAS).
Supported File Types
The TraceFinder application supports the following file types:
• Comma-separated values (.csv): A set of file formats used to store tabular data in which
numbers and text are stored in plain textual form that can be read in a text editor. Lines in
the text file represent rows of a table, and commas in a line separate fields in the tables
row.
• Extensible Markup Language (.xml): A generic framework for storing any amount of text
or any data whose structure can be represented as a tree. The only indispensable
syntactical requirement is that the document has exactly one root element (also called the
document element). This means that the text must be enclosed between a root start-tag
and a corresponding end-tag.
• Instrument method (.meth): A proprietary file format for the Xcalibur software suite with
specific instructions that enable scientific instruments to perform data acquisition.
• Processing method (.pmd): A proprietary file format for the Xcalibur software suite with
specific instructions on processing data that was acquired through the instruments
attached to the system.
• Raw data (.raw): The file type for acquired samples on the system.
• Compound database (.cdb): The file type for TraceFinder or ExactFinder compound
database data.
• Library (.db): A library used for target screening.
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TraceFinder Directory Structure
The TraceFinder application creates folders for batches, methods, and templates in the
…\TraceFinderData directory. Within each batch folder, the application creates folders for
data, methods, and reports.
You can create batches in the TraceFinderData\32\Projects folder, or you can create subfolders
within the Projects folder for your batches. You can create as many subfolders as you want for
your batches, but you cannot create a batch within another batch folder.
IMPORTANT You cannot rename or move the folders created by the TraceFinder
application.
Figure 2.
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Example batch directory structure
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Introduction
TraceFinder Summary of Features
TraceFinder Summary of Features
The TraceFinder system provides a workflow-oriented approach to high-throughput
quantitation, using tools that automate and speed up the processes of method creation,
loading samples, automatically generating data, manually reviewing and editing results, and
finalizing the data review and reporting process.
The TraceFinder software package includes data acquisition, processing, reviewing, and
reporting capabilities designed to assist analysts in general quantitation applications. The
application has a fully automated acquisition mode and a manual data analysis mode. You can
use the data acquisition system to create and submit batches and monitor real-time review of
results.
The TraceFinder application uses a comprehensive processing method to provide improved
handling of ion ratio calculations, reviewing, and reporting. In addition, it can compare the
mass spectra and integrate the processes of data review and reporting.
Key features include the following:
• Role-based authorization for Security, LabDirector, ITAdmin, Supervisor, Technician,
and QAQC (quality assurance) roles
• Administrator Console for user security, role-based permissions, and data repositories
• Configuration console for report configuration, detection and acquisition defaults,
adduct definitions, screening library selection, and customized columns and flags
• Method Development mode for editing instrument methods, setting processing and error
flag parameters, and setting reporting options
• Acquisition mode that guides you in creating batches and running samples
• Analysis mode with batch views, data review, local method views, and reporting views
• Database-capable method development
• Quantification workflows, supporting capabilities present in the LCquan™ and QuanLab
Forms applications
• Target screening workflows
• Spreadsheet-based report designer
Features of the common workflow core include the following:
• Acquisition and processing
• Peak detection
• Quantification to include calibration
• Error analysis and flag setting
• Reporting
• Data persistence
• Raw data file handling
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TraceFinder Workflow
TraceFinder Workflow
The TraceFinder application is structured with a typical laboratory workflow in mind. You
create a batch, and the system injects samples into the instrument, runs the samples, analyzes
the data, and generates a report. You can set up a master method for specific compound
groups or assays that you expect to run in your laboratory. When you are ready to run a
particular type of sample, select the appropriate method and begin.
When using the TraceFinder application, follow these basic steps:
1. Create and save a master method in the Method Development mode.
A master method combines the instrument method and processing method that define
the following:
• How the raw data is acquired and processed
• How the error checking information evaluates the results
• How the results appear in reports
2. Create and submit a batch using the Acquisition wizard.
A batch lists samples for processing and reporting using a specified method. Each row of a
batch represents a unique sample.
3. Monitor the status of the batch in the Real Time Status view.
The real-time display is visible from all the TraceFinder modes. You can begin another
batch while you watch the real-time display of the currently acquiring batch.
Note At any time, you can quickly view the system status by looking in the upper
right corner of the TraceFinder window. This area displays a green, yellow, or red
status light and a description of any activity in the queues, as in this example:
4. Evaluate the data in the Analysis mode.
The Analysis mode includes views where you can review batches, batch data, reports, and
local methods.
5. View and print reports in the Report View of the Analysis mode.
Use the Report View to view or print the reports for the current batch.
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Reporting Features
Reporting Features
The report engine can generate several different types of reports designed to meet the needs of
the laboratory, the laboratory's customers, and key regulatory agencies that might review the
results. The following types of reports meet the requirements of various methods and
worldwide regulatory agencies, helping to track the performance of LC and GC systems and
methods.
Report Types
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•
•
•
•
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•
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Ad Hoc Tune Report
Batch Report
Blank Report
Breakdown Report
Calibration Report
Check Standard Report
Chromatogram Report
Compound Calibration Report
Compound Calibration Report - Alternate
Confirmation Report
Confirmation Report 2
High Density Calibration Report
High Density Internal Standard Report Long
High Density Report
High Density Sample Report 1 Long
Intelligent Sequencing Report
Internal Standard Summary Report
Ion Ratio Failure Report
LCSLCSD Report
Manual Integration Report
Method Detection Limit Report
Method Report
Method Validation Report
MSMSD Report
Quantitation Report
Quantitation Report - 2
Screening Batch Report
SGS Report
Solvent Blank Report
Standard Addition Report
Surrogate Recovery Report
Target Screening Hight Density Sample Report
Target Screening Hight Density Sample Report 2
Target Screening Summary Report
TIC Report
TIC Summary Report
Tune Report
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2
Getting Started
This chapter includes the procedures for getting started with the TraceFinder application.
Contents
• Installing the TraceFinder Application
• Installing the NIST and QED Libraries
• Launching the NIST Library Browser
• Launching a Qualitative Explorer
• Converting Legacy Data
• Choosing a Mode or Console
Installing the TraceFinder Application
To initially install the TraceFinder 3.2 application, follow the instructions in the TraceFinder
Installation Guide. Later, you might need to reinstall the TraceFinder application or other
features on the InstallShield Wizard.
Follow these instructions to reinstall, start, and log in to the TraceFinder application.
 To reinstall the TraceFinder application
1. From the Thermo Foundation Instrument Configuration window, remove all
instruments.
2. From the Windows™ Control Panel, uninstall the TraceFinder application and then
uninstall all Thermo instrument drivers.
3. Insert the TraceFinder CD, and install both the TraceFinder 3.2 application and the
NIST library as follows:
a. Open the TraceFinder launcher and click Next.
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The InstallShield Wizard opens.
b. Click TraceFinder 3.2, and follow the instructions in the InstallShield Wizard.
The installer verifies that you have the appropriate versions of the Thermo
Foundation™ and Thermo Xcalibur™ applications and updates them if necessary.
c. At the prompt, click Yes to completely remove any previously installed TraceFinder
applications.
d. Open the TraceFinder launcher again and click Next.
e. Click TraceFinder 3.2, and follow the instructions in the InstallShield Wizard.
IMPORTANT For the TraceFinder application to properly install, you might be
prompted to uninstall Thermo Foundation™. Do the following:
1. Click Yes, and then when prompted to restart your computer, click OK.
The wizard continues the TraceFinder installation.
2. When prompted to install Thermo Foundation, click Yes, and then when
prompted to restart your computer, click OK.
The wizard continues the installation.
f.
When prompted, choose to install either the GC or LC version of the software.
g. When the installation is complete, open the TraceFinder launcher again and click
Next.
h. If you have not previously installed the NIST library, click NIST Library and follow
the instructions to install the library.
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Installing the TraceFinder Application
i.
(Optional) Click Example Data.
The application installs example compound databases, instrument methods, and
batch data.
4. Install the appropriate device drivers, and configure the instruments in the Thermo
Foundation Instrument Configuration window.
 To start the TraceFinder application
1. Configure your instruments.
You must close the TraceFinder application before you can configure your instruments.
2. Double-click the TraceFinder icon on your desktop, or choose Start > All Programs >
Thermo TraceFinder > TraceFinder.
By default, user security is not activated and the application does not require a password.
To activate user security, refer to the TraceFinder Administrator Console User Guide.
 To log in to the TraceFinder application (when user security is activated)
Note Before you can log in to the TraceFinder application when user security is
activated, a system administrator must set up a user account for you.
1. Enter your user name in the TraceFinder login window. See “TraceFinder login window”
on page 11.
2. Enter your password.
If your user name or password does not match, the system reports this error:
Correct the user name or password, or contact your system administrator.
3. Click Login.
The TraceFinder login window opens. See TraceFinder main window.
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Installing the TraceFinder Application
Figure 3.
TraceFinder main window, showing the Analysis mode
User name available only when
user security is activated
Table 1. TraceFinder main window features (Sheet 1 of 2)
Parameter
Description
Toolbar
See “Toolbar Reference” on page 533.
Application Configuration See Chapter 3, “Using the Configuration Console.”
Acquisition
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See Chapter 7, “Using the Acquisition Mode.”
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2 Getting Started
Installing the TraceFinder Application
Table 1. TraceFinder main window features (Sheet 2 of 2)
Parameter
Description
Analysis
See Chapter 8, “Using the Analysis Mode.”
Method Development
See Chapter 4, “Using the Common Features of the Method Development Mode.”
See Chapter 5, “Using the Method Development Mode for Quantitation Methods.”
See Chapter 6, “Using the Method Development Mode for Screening Methods.”
Figure 4.
TraceFinder login window
Table 2. Login window parameters
Thermo Scientific
Parameter
Description
Domain
The authentication method.
Username
The user’s assigned user name.
Password
The assigned password for the user name.
Login
Verifies the user name and password, and opens the TraceFinder
application.
Exit
Closes the TraceFinder login window.
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Getting Started
Installing the NIST and QED Libraries
Installing the NIST and QED Libraries
When you are using triple quadrupole instruments, such as the TSQ Quantum XLS, follow
these instructions to install the NIST and QED libraries.
 To install the NIST library
1. Open the TraceFinder launcher, and click Next.
2. Click NIST Library.
The NIST 08 MS Search and AMDIS Setup wizard opens.
3. Follow the instructions in the setup wizard.
4. When the wizard prompts you to select a destination folder, select
C:\Program Files\NISTMS.
5. Continue to follow the instructions in the wizard until the setup is complete.
 To install the QED library
1. On your desktop, double-click the Xcalibur icon,
.
The Thermo Xcalibur Roadmap opens.
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Installing the NIST and QED Libraries
2. Choose Tools > Library Manager from the main menu.
The Thermo Library Manager dialog box opens, showing the NIST Libraries list.
3. Click Add.
The Add Library dialog box opens.
4. Click Browse, and locate your QED library in the C:\Thermo folder.
5. Click OK.
The Xcalibur application reports that it has added the library to the NIST application.
6. Click Dismiss to close the message box.
The Xcalibur application adds the QED library to the NIST Libraries list in the Library
Manager dialog box.
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Installing the NIST and QED Libraries
7. Click Exit in the Thermo Library Manager dialog box.
8. To confirm the library installation, do the following:
a. Start the TraceFinder application.
b. Click Method Development in the navigation pane.
c. Click Method View in the Method Development navigation pane.
d. Choose File > New > Method Template from the main menu.
The Method Template Editor displays the QED NIST Library in the Use These
Libraries list.
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Launching the NIST Library Browser
Launching the NIST Library Browser
Use the NIST MS Search tool to search the NIST library.
 To open the NIST library browser
Choose Tools > Launch Library Browser from the TraceFinder main menu.
The NIST MS Search window opens.
For detailed instructions about using the library browser, refer to the Help in the NIST MS
Search window.
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Launching a Qualitative Explorer
Launching a Qualitative Explorer
Use a qualitative explorer application to display chromatograms and spectra, detect
chromatogram peaks, search libraries, simulate spectra, subtract background spectra, apply
filters, add text and graphics, create and save layouts, and view instrument parameters as they
changed during the acquisition.
Your TraceFinder application is configured to use one of the following applications:
• Thermo Scientific FreeStyle
• Thermo Xcalibur Qual Browser
Thermo Scientific FreeStyle
IMPORTANT The FreeStyle™ application is available only when you configure it as your
default qualitative explorer in the Configuration Console. See Chapter 3, “Using the
Configuration Console.”
 To open the FreeStyle window
Choose Tools > Launch Qual Explorer from the TraceFinder main menu.
The Thermo Scientific FreeStyle application opens.
Figure 5.
Freestyle main window
For detailed instructions about using the FreeStyle application, click the Help icon,
the FreeStyle window.
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Launching a Qualitative Explorer
Thermo Xcalibur Qual Browser
IMPORTANT The Qual Browser application is available only when you configure it as
your default qualitative explorer in the Configuration Console. Chapter 3, “Using the
Configuration Console.”
 To open the Qual Browser window
Choose Tools > Launch Qual Explorer from the TraceFinder main menu.
The Thermo Xcalibur Qual Browser application opens.
Figure 6.
Qual Browser main window
For detailed instructions about using the Qual Browser application, refer to the Help in the
Qual Browser window.
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Getting Started
Converting Legacy Data
Converting Legacy Data
Use the Trace Finder Legacy Data Converter to convert methods, batches, method templates,
or batch templates from the source versions to compatible TraceFinder 3.2 target
configurations.
• You can convert legacy data from TraceFinder versions 2.0, 2.1, 3.0, or 3.1.
• You can convert data from TraceFinder 3.2 for general quantitation to another installed
configuration of TraceFinder 3.2.
Version Compatibility
This table shows which source versions of methods, batches, method templates, or batch
templates are compatible with TraceFinder 3.2 target configurations.
Table 3. Version compatibility
Source
TraceFinder 3.2 target
EFS*
Clinical
Research
TraceFinder 3.2 General



TraceFinder 3.1 General



TraceFinder 3.1 EFS

TraceFinder 3.1 Clinical Research


TraceFinder 3.1 Forensic Toxicology




TraceFinder 3.0 Clinical Research


TraceFinder 3.0 Forensic Toxicology




TraceFinder 2.1 Clinical Research


TraceFinder 2.1 Forensic Toxicology






General
TraceFinder 3.0 General

TraceFinder 3.0 EFS
TraceFinder 2.1 General


TraceFinder 2.1 EFS
TraceFinder 2.0 General
TraceFinder 2.0 EFS
TraceFinder 2.0 Clinical Research

Forensic
Toxicology





*
* Environmental and Food Safety
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2 Getting Started
Converting Legacy Data
This section includes the following topics:
• Converting Methods
• Converting Batches
• Converting Method Templates
• Converting Batch Templates
 To open the TraceFinder Legacy Data Converter
Choose Tools > Launch Legacy Data Converter from the TraceFinder main menu.
The TraceFinder Legacy Data Converter window opens.
Note When you open the TraceFinder application, the system checks for any legacy
data and prompts you to open the Legacy Data Converter.
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Converting Legacy Data
Converting Methods
Use the data converter to convert legacy methods to TraceFinder 3.2 methods.
 To convert a method
1. In the Data Type list, select Method.
The TraceFinder Legacy Data Converter displays the interface for converting methods.
The following example shows that you can convert methods from the TraceFinder 3.1
General configuration to the current General configuration. For a complete list of version
compatibilities, see “Converting Methods” on page 20.
2. In the Source Version list, select the version of the method that you will convert.
Note When you select Any Legacy, the Legacy Data Converter examines all possible
methods in the source folder, regardless of version.
The conversion table displays the methods in the Methods folder for the selected source
version. The application verifies that the method file is in the .mmx file format.
3. To convert a method that is not in the default list, do the following:
a. Click Browse and locate a different source method folder.
You can select a specific method folder or a folder that contains multiple methods.
b. Click OK in the Browse for Folder dialog box.
The application displays the selected method folder in the conversion table.
When you select a folder that contains multiple method folders, the application displays
all the methods.
4. In the Target Version list, select the version that you are converting to.
The list displays only TraceFinder configurations with compatible data. See “Converting
Methods” on page 20.
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Converting Legacy Data
5. (Optional) In the Target Name column, change the default new name for each method
that you want converted.
When you populate the conversion table, the application checks each method to see if a
method with this name exists in the target repository.
• If the method name already exists in the target repository, the default new name
appends “_1” to the original name.
• If the method name does not exist in the target repository, the application keeps the
original method name.
IMPORTANT The conversion cannot overwrite an existing file name. If the new name
is identical to an existing method file, the conversion will not work. When you
manually enter a new name, you must verify that the name does not already exist.
6. Select the Convert check box for each method that you will convert, and click
.
The application confirms that all methods to be converted use the .mmx file format.
When the conversion process begins, the application displays a status bar and a Cancel
button. You can cancel pending conversions, but not the method that is currently
converting.
When the Status column reports that a method is successfully converted, the application
writes the converted file to the specified target repository.
Note If a method conversion is unsuccessful, the Status column displays “Conversion
failed.” The log file contains details about the failed conversion.
7. To view a log of the conversion, click View Log.
The application opens a cumulative log file for the session in a Microsoft™ Notepad text
editor window.
Figure 7.
Sample log file for converting a method
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Converting Legacy Data
Converting Batches
Use the data converter to convert legacy batches to TraceFinder 3.2 batches.
 To convert a batch
1. In the Data Type list, select Batch.
The following example shows that you can convert batches from the TraceFinder 3.1
General configuration to the current General configuration. For a complete list of version
compatibilities, see “Converting Methods” on page 20.
2. In the Source Version list, select the version of the batch that you will convert.
Note When you select Any Legacy, the Legacy Data Converter examines all possible
batches in the source folder, regardless of version.
The conversion table displays all batches in the Projects folder for the selected source
version.
3. In the Target Version list, select the version that you are converting to.
The list displays only TraceFinder configurations with compatible data. See “Converting
Methods” on page 20.
4. In the Target Default Project and Subproject boxes, type the name of a project and
subproject, or select the Replicate Original Project/Subproject check box.
5. (Optional) In the New Name column, change the default new name for each batch that
you want converted.
When you populate the conversion table, the application checks each batch to see if a
batch with this name exists in the target repository.
• If the batch name already exists in the target repository, the default new name
appends “_1” to the original name.
• If the batch name does not exist in the target repository, the application keeps the
original batch name.
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Converting Legacy Data
IMPORTANT The conversion cannot overwrite an existing file name. If the new name
is identical to an existing batch folder, the conversion will not work. When you
manually enter a new name, you must verify that the name does not already exist.
6. Select the Convert check box for each batch that you will convert, and click
.
The application confirms that all batches to be converted use the .btx file format.
When the conversion process begins, the application displays a status bar and a Cancel
button. You can cancel pending conversions, but not the batch that is currently
converting.
When the Status column reports that a batch is successfully converted, the application
writes the converted batch to the …\TraceFinderData\32\Projects folder and uses either
the original project and subproject names or the new names that you entered.
Note If a batch conversion is unsuccessful, the Status column displays “Conversion
failed.” The log file contains details about the failed conversion.
7. To view a log of the conversion, click View Log.
Figure 8.
Sample log file for converting a batch
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Converting Legacy Data
Converting Method Templates
Use the data converter to convert legacy method templates to TraceFinder 3.2 method
templates.
 To convert a method template
1. In the Data Type list, select Method Template.
The following example shows that you can convert method templates from the
TraceFinder 3.1 General configuration to the current General configuration. For a
complete list of version compatibilities, see “Converting Methods” on page 20.
2. In the Source Version list, select the version of the method template that you will convert.
Note When you select Any Legacy, the Legacy Data Converter examines all possible
method templates in the source folder, regardless of version.
The conversion table displays the method templates in the Templates folder for the
selected source version. The application verifies that the method template file is in
the .pmtx file format.
3. To convert a method template that is not in the default list, do the following:
a. Click Browse and locate a template folder.
You can select a specific template folder or a folder that contains multiple templates.
b. Click OK in the Browse for Folder dialog box.
The application displays the selected folder in the conversion table.
When you select a folder that contains multiple method template folders, the application
displays all the method templates.
4. In the Target Version list, select the version that you are converting to.
The list displays only TraceFinder configurations with compatible data. See “Converting
Methods” on page 20.
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5. (Optional) In the Target Name column, change the default name for each method
template that you want converted.
When you populate the conversion table, the application checks each method template to
see if a method template with this name exists in the target repository.
• If the method template name already exists in the target repository, the default new
name appends “_1” to the original name.
• If the method template name does not exist in the target repository, the application
keeps the original method template name.
IMPORTANT The conversion cannot overwrite an existing file name. If the new name
is identical to an existing method template file, the conversion will fail. When you
manually enter a new name, you must verify that the name does not already exist.
6. Select the Convert check box for each method template that you will convert, and click
.
The application confirms that all method templates to be converted use the .pmtx file
format.
When the conversion process begins, the application displays a status bar and a Cancel
button. You can cancel pending conversions, but not the template that is currently
converting.
When the Status column reports that the template is successfully converted, the
application writes the converted template to the specified target repository.
Note If a template conversion fails, the Status column displays “Conversion failed.”
The log file contains details about the failed conversion.
7. To view a log of the conversion, click View Log.
The application opens a cumulative log file for the session in a Notepad text editor
window.
Figure 9.
Sample log file for converting a method template
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Converting Legacy Data
Converting Batch Templates
Use the data converter to convert legacy batch templates to TraceFinder 3.2 batch templates.
 To convert a batch template
1. In the Data Type list, select Batch Template.
You can choose either LabForms batch templates or TraceFinder batch templates.
The following example shows that you can convert batch templates from the TraceFinder
3.1 General configuration to the current General configuration. For a complete list of
version compatibilities, see “Converting Methods” on page 20.
2. In the Source Version list, select the version of the batch template that you will convert.
Note When you select Any Legacy, the Legacy Data Converter examines all possible
batch templates in the source folder, regardless of version.
The conversion table displays the batch templates in the Templates folder for the selected
source version.
3. To convert a batch template that is not in the default list, do the following:
a. Click Browse and locate a template folder.
You can select a specific batch template folder or a folder that contains multiple batch
templates.
b. Click OK in the Browse for Folder dialog box.
The application displays the selected folder in the conversion table.
When you select a folder that contains multiple batch template folders, the application
displays all the batch templates.
4. In the Target Version list, select the version that you are converting to.
The list displays only TraceFinder configurations with compatible data. See “Converting
Methods” on page 20.
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Converting Legacy Data
5. (Optional) In the New Name column, change the default new name for each batch
template that you want converted.
When you populate the conversion table, the application checks each batch template to
see if a batch template with this name exists in the target repository.
• If the batch template name already exists in the target repository, the default new
name appends “_1” to the original name.
• If the batch template name does not exist in the target repository, the application
keeps the original batch template name.
IMPORTANT The conversion cannot overwrite an existing file name. If the new name
is identical to an existing batch template file, the conversion will fail. When you
manually enter a new name, you must verify that the name does not already exist.
6. Select the Convert check box for each batch template that you will convert, and click
.
The application confirms that all batch templates to be converted use the .btx file format.
When the conversion process begins, the application displays a status bar and a Cancel
button. You can cancel pending conversions, but not the template that is currently
converting.
When the Status column reports that the template is successfully converted,
the application writes the converted template folder to the
…\TraceFinderData\32\Templates\Batches folder.
Note If a template conversion fails, the Status column displays “Conversion failed.”
The log file contains details about the failed conversion.
7. To view a log of the conversion, click View Log.
The application opens a cumulative log file for the session in a Notepad text editor
window.
Figure 10. Sample log file for a failed batch template conversion
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Getting Started
Choosing a Mode or Console
Choosing a Mode or Console
When user security is activated, the navigation pane displays the modes and consoles available
to the current user’s assigned roles and permissions. The following table shows the available
modes and consoles for each user role.
Table 4. User roles and default access
User role
Method
Development
Acquisition
Analysis
Configuration
Console
Security
LabDirector
Security only






ITAdmin
Supervisor
Administrator
Console

Technician




QAQC



Note When user security is not activated, all modes and consoles are available to all users.
Follow these procedures:
• To choose a mode
• To open the Configuration console
• To open the Administrator Console
• To display a log of instrument errors
• To monitor instrument status
• To watch acquisition and processing in real time
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2 Getting Started
Choosing a Mode or Console
 To choose a mode
In the navigation pane, click the mode where you want to work.
The navigation pane shows only the modes that you have permission to use.
Mode
Description
Acquisition
Opens the Acquisition mode where you can create and review
batches, batch data, reports, and local methods.
See Chapter 7, “Using the Acquisition Mode.”
Analysis
Opens the Analysis mode where you can review batches, batch
data, reports, and local methods.
See Chapter 8, “Using the Analysis Mode.”
Method
Development
Opens the Method Development mode where you can create a
master method or an instrument method.
See Chapter 4, “Using the Common Features of the Method
Development Mode.”
See Chapter 5, “Using the Method Development Mode for
Quantitation Methods.”
See Chapter 6, “Using the Method Development Mode for
Screening Methods.”
 To open the Configuration console
Click the Application Configuration icon,
TraceFinder window.
, in the upper right corner of the
When user security is activated, you must have Configuration permissions to access the
Configuration Console. See Chapter 3, “Using the Configuration Console.”
 To open the Administrator Console
Choose Tools > Administrator Console from the TraceFinder main menu.
When user security is activated, you must have Administrator permissions to access the
Administrator Console. Refer to the TraceFinder Administrator Console User Guide.
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Getting Started
Choosing a Mode or Console
 To display a log of instrument errors
1. Click the status light in the upper right corner of the TraceFinder window.
Status light
The Instrument Log dialog box opens.
The Instrument Log displays all instrument errors that have occurred since the
TraceFinder application started or since the last time that you cleared the message log.
2. Do any of the following:
• Click Refresh to display errors that occur after you open the Instrument Log dialog
box.
• Click Clear Messages to remove messages from the Instrument Log display.
The application clears messages only from the Instrument Log display. These
messages remain in the following log file:
C:\Thermo\TraceFinder\3.2\General\Logs\TraceFinder.log
• Click OK to dismiss the Instrument Log dialog box.
 To monitor instrument status
Look at the status light in the upper right corner of the TraceFinder window.
Green indicates that the instrument is ready.
Yellow indicates that the instrument is in standby mode.
Red indicates that the instrument is turned off or no device is configured.
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2 Getting Started
Choosing a Mode or Console
 To watch acquisition and processing in real time
Click Real Time Status in the upper right corner of the TraceFinder window.
The application displays the Real Time Status pane at the bottom of the window.
For descriptions of all the features of the Real Time Status pane, see “Real Time Status
Pane” on page 348.
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Getting Started
Choosing a Mode or Console
TraceFinder Window Features
A TraceFinder window with user security for a user in the default LabDirector role has these
functions.
Table 5. TraceFinder window parameters
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Parameter
Description
Real Time Status
Opens the Real Time Status pane for the current acquisition. The
acquisition progress is displayed within the current mode window.
CurrentUserName
Displays the name of the current user. This is displayed only when user
security is activated.
Log Off
Logs off the current user and displays the login screen. This function is
available only when user security is activated.
Help
Opens the TraceFinder Help.
Configuration
Console
Opens the Configuration console where you can configure several
options for using the TraceFinder application. See Chapter 3, “Using
the Configuration Console.”
Thermo Scientific
3
Using the Configuration Console
This chapter discusses the features of the Configuration console. When user security is
activated, you must have Configuration permissions to access the features in the
Configuration console.
Contents
• Specifying Application Defaults
• Specifying Default Peak Detection Parameters
• Specifying Adducts
• Activating Optional Features
• Creating Custom Columns
• Creating Custom Flags
• Specifying the Reports
If you are a member of the local administrator’s group and are launching the TraceFinder
application for the first time, by default, you have LabDirector permissions. For information
about groups and permissions, refer to the TraceFinder Administrator Console User Guide.
Using the features on the Configuration console, you can do any of the following:
• Activate features, such as multiplexing, intelligent sequencing, qualitative browsers, and
screening libraries.
• Select the reports that are available to users, the detector types, and the algorithms used
for peak detection.
• Customize adduct definitions, additional sample grid columns, and flags.
 To access the Configuration console
Click the Application Configuration icon,
window.
, in the upper right corner of any
The TraceFinder Configuration console opens.
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Using the Configuration Console
Table 6. Navigation pane functions in the Configuration console
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Function
Description
Defaults
Use the Defaults view to specify the default laboratory and
instrument names, the displayed mass precision, and the intensity
scale to use for reporting. See “Specifying Application Defaults” on
page 35.
Peak Detection
Defaults
Use the Peak Detection Defaults view to specify a peak detection
algorithm and its options and to determine the area under a curve.
See “Specifying Default Peak Detection Parameters” on page 37.
Adducts
Use the Adducts view to specify the adducts that will be available for
use in method development. See “Specifying Adducts” on page 52.
Optional
Features
Use the Optional Features view to enable features, such as quick
acquisition, multiplexing, intelligent sequencing, and screening
libraries. See “Activating Optional Features” on page 55.
Custom
Columns
Use the Custom Columns view to add six additional columns to the
samples list in batches. See “Creating Custom Columns” on
page 63.
Flag
Customization
Use the Flag Customization view to customize error flags and
conditions to indicate compound errors in Data Review for
quantitation batches. See “Creating Custom Flags” on page 66.
Reporting
Use the Reporting view to configure which reports are available to
users. See “Specifying the Reports” on page 72.
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Using the Configuration Console
Specifying Application Defaults
Specifying Application Defaults
Use the Application – Defaults view of the Configuration console to specify the default
laboratory and instrument names, the displayed mass precision, and the chromatogram
intensity scale to use for reporting. When user security is activated, you must have
Configuration – Defaults permission to access these features.
Follow these procedures:
• To open the Defaults view
• To specify a default laboratory name and instrument name
• To specify default mass precision and the intensity scale
 To open the Defaults view
In the navigation pane for the Configuration console, click Defaults.
The Application – Defaults view opens.
 To specify a default laboratory name and instrument name
1. Type the name of your laboratory in the Lab Name box.
When you create a method, the application uses this default laboratory name for the
Laboratory Name value on the Processing page of the Method View. The application uses
this laboratory name in the report headings.
The application does not apply this default laboratory name to previously created
methods. By default, the laboratory name is Default Laboratory.
2. Type the name of your instrument in the Instrument Name box.
When you create a batch, the application uses this default instrument name for the
Instrument Name value. The application uses this instrument name in the report
headings.
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Specifying Application Defaults
3. To save your changes, click Apply.
The application does not apply this default instrument name to previously created
batches. By default, the instrument name is Thermo Scientific Instrument.
 To specify default mass precision and the intensity scale
1. In the Display Mass Precision box, set the decimal value for the mass precision to an
integer from 2 to 6, inclusive.
The default number of digits to display is 2. The TraceFinder application uses this mass
precision value to display mass values in the following locations:
• Reports:
– Blank Report
– Confirmation Report (data spectra, library spectra, quantitation ion display, and
qualitative ion display)
– All High Density reports (m/z values)
– Ion Ratio Failure Report (quantitation ion and qualitative ion)
– Manual Integration Report (m/z value)
– Quantitation Report (QIon)
• All peaks on the Detection pages in the Method Development mode
• The spectrum display in the Analysis mode
• The spectrum display in the Method Forge dialog box
IMPORTANT When you create a method using a raw data file, the application reads
the filter precision value from the raw data file to create scan filters; however, the
TraceFinder application uses the Display Mass Precision value when showing masses
that are not embedded within filter strings and masses that are displayed on spectral
plots.
2. Select either the Relative or Absolute option for the Chromatogram Intensity Scale.
This sets the default display type for both quantitation and qualitative chromatograms
displayed in data review and reports.
3. To save your changes, click Apply.
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3 Using the Configuration Console
Specifying Default Peak Detection Parameters
Specifying Default Peak Detection Parameters
When user security is activated, you must have Configuration – Peak Detection Defaults
permission to access default peak detection parameters for the Genesis, ICIS, or Avalon
detection algorithms.
Use the Peak Detection Defaults view to specify a peak detection algorithm and its options
and to determine the area under a curve. These parameters are available for quantitation
methods only.
This section includes procedures for specifying common peak detection parameters (and the
parameters used for each of the following detection algorithms:
• Genesis Detection Method
• ICIS Detection Method
• Avalon Detection Method
 To open the Peak Detection Defaults view
In the navigation pane for the Configuration console, click Peak Detection Defaults.
The Application – Peak Detection Defaults view opens.
• For parameter information about all detection algorithms, see “Common Peak
Detection Parameters” on page 39.
• For parameter information about the Genesis detection algorithm, see “Genesis
Detection Method” on page 42.
• For parameter information about the ICIS detection algorithm, see “ICIS Detection
Method” on page 45.
• For parameter information about the Avalon detection algorithm, see “Avalon
Detection Method” on page 48.
 To specify common detection parameters
1. In the Detector Type list, select a detector type.
For detailed descriptions of the available detector types, see “Common Peak Detection
Parameters” on page 39.
2. In the Mass Tolerance area, do the following:
a. Select the unit of measure that you want to use (MMU or PPM).
b. In the Value box, specify the number of millimass units or parts per million to use as
the upper limit.
The application applies this mass tolerance to the extracted chromatograms. The default
is 500 MMU.
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Specifying Default Peak Detection Parameters
3. In the Retention Time area, do the following:
a. In the Window box, specify the width of the window (in seconds) to indicate how far
around the expected retention time the system will look for a peak apex.
b. In the View Width box, specify the viewable size (in minutes) of the ion
chromatogram display.
4. In the Ion Ratio Parameters area, do the following:
a. In the Window Type list, select Absolute or Relative as the calculation approach for
determining the acceptable ion ratio range.
b. In the Window box, select the acceptable ion ratio range.
c. In the Ion Coelution box, select the maximum difference in retention time between a
confirming ion peak and the quantification ion peak.
5. In the Peak Detection Parameters area, select one of the detection algorithms: Genesis,
ICIS, or Avalon.
6. Specify the parameters for the selected detection algorithm.
For detailed parameter descriptions, see one of the following:
• Genesis Detection Method
• ICIS Detection Method
• Avalon Detection Method
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3 Using the Configuration Console
Specifying Default Peak Detection Parameters
Common Peak Detection Parameters
All of the detection algorithms use the Detector Type, Mass Tolerance, Retention Time, and
Ion Ratio detection parameters.
Figure 11. Common peak detection areas
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Specifying Default Peak Detection Parameters
Table 7. Common peak detection parameters (Sheet 1 of 2)
Parameter
Description
Detector Type
MS: Mass spectrometer that ionizes sample molecules and then
separates the ions according to their mass-to-charge ratio (m/z).
PDA: Photodiode array detector providing a linear array of discrete
photodiodes on an integrated circuit chip. It is placed at the image
plane of a spectrometer so that a range of wavelengths can be
simultaneously detected.
Analog: Supplemental detectors (for example, FID, ECD). When
you select this detector, any reports that display a QIon value show
the value as Analog and any reports that display spectra show the
spectra as Not Available.
A/D card: If your detector is not under data system control, you can
capture the analog signal and convert it to digital using an interface
box (for example, SS420X) for storage in the raw data file.
UV: A UV spectrophotometer (for variable-wavelength detection) or
photometer (for single-wavelength detection) equipped with a
low-volume flow cell. This detector detects analytes that readily
absorb light at a selected wavelength.
Mass Tolerance
Units
• (Default) MMU (millimass units)
MMU is a static calculation to the extracted mass.
• PPM (parts per million)
PPM is a variable calculation dependent on the actual mass. The
smaller the mass, the narrower the tolerance range. The larger the
mass, the wider the tolerance range.
Value
Upper limit of MMU or PPM.
Default: 500
Range: 0.1 through 50 000
Retention Time
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Window (sec)
Width of the window (in seconds) to indicate how far around the
expected retention time the system will look for a peak apex.
View Width (min)
Viewable size (in minutes) of the ion chromatogram display.
Changing the view width does not affect the process of peak
detection; the TraceFinder application uses it only for graphical
display.
Thermo Scientific
3 Using the Configuration Console
Specifying Default Peak Detection Parameters
Table 7. Common peak detection parameters (Sheet 2 of 2)
Parameter
Description
Ion Ratio
Parameters
Window Type
The absolute or relative calculation approach for determining the
acceptable ion ratio range.
Window (+/-%)
The acceptable ion ratio range.
Ion Coelution (min) The maximum difference in retention time between a confirming ion
peak and the quantification ion peak.
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Specifying Default Peak Detection Parameters
Genesis Detection Method
The TraceFinder application provides the Genesis peak detection algorithm for backward
compatibility with Xcalibur 1.0 studies.
Figure 12. Genesis peak detection
Table 8. Genesis peak detection parameters (Sheet 1 of 3)
Parameter
Description
Detection Algorithm
Specifies the Genesis peak detection algorithm.
Detection Method
Specifies the detection method used for component identification.
Highest peak: Uses the highest peak in the chromatogram for
component identification.
Nearest RT: Uses the peak with the nearest retention time in the
chromatogram for component identification.
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Specifying Default Peak Detection Parameters
Table 8. Genesis peak detection parameters (Sheet 2 of 3)
Parameter
Description
Smoothing
Specifies the degree of data smoothing to be performed on the
active component peak prior to peak detection and integration.
The ICIS peak detection algorithm uses this value.
Default: 1
Range: Any odd integer from 1 through 15 points
S/N threshold
Specifies the current signal-to-noise threshold for peak integration.
Peaks with signal-to-noise values less than this value are not
integrated. Peaks with signal-to-noise values greater than this value
are integrated.
Range: 0.0 to 999.0
Enable Valley
Detection
Uses the valley detection approximation method to detect
unresolved peaks. This method drops a vertical line from the apex
of the valley between unresolved peaks to the baseline. The
intersection of the vertical line and the baseline defines the end of
the first peak and the beginning of the second peak.
Expected Width (sec)
Specifies the expected peak width parameter (in seconds). This
parameter controls the minimum width that a peak is expected to
have if valley detection is enabled.
With valley detection enabled, any valley points nearer than the
expected width/2 to the top of the peak are ignored. If a valley
point is found outside the expected peak width, the TraceFinder
application terminates the peak at that point. The application
always terminates a peak when the signal reaches the baseline,
independent of the value set for the expected peak width.
Range: 0.0 to 999.0
Thermo Scientific
Constrain Peak Width
Constrains the peak width of a component during peak
integration of a chromatogram. You can then set values that
control when peak integration is turned on and off by specifying a
threshold and a tailing factor. Selecting the Constrain Peak Width
check box activates the Peak Height (%) and Tailing Factor
options.
Peak Height (%)
A signal must be above the baseline percentage of the total peak
height (100%) before integration is turned on or off. This text box
is active only when you select the Constrain Peak Width check
box.
Range: 0.0 to 100.0%
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Specifying Default Peak Detection Parameters
Table 8. Genesis peak detection parameters (Sheet 3 of 3)
Parameter
Description
Tailing Factor
Specifies the tailing factor that controls how the TraceFinder
application integrates the tail of a peak. This factor is the
maximum ratio of the trailing edge to the leading side of a
constrained peak. This text box is active only when you select the
Constrain the Peak Width check box.
Range: 0.5 through 9.0
Peak S/N Cutoff
Sets the peak edge to values below this signal-to-noise ratio.
This test assumes it has found an edge of a peak when the baseline
adjusted height of the edge is less than the ratio of the baseline
adjusted apex height and the peak S/N cutoff ratio.
When the S/N at the apex is 500 and the peak S/N cutoff value is
200, the TraceFinder application defines the right and left edges of
the peak when the S/N reaches a value less than 200.
Range: 50.0 to 10000.0
Valley Rise (%)
Specifies that the peak trace can rise above the baseline by this
percentage after passing through a minimum (before or after the
peak). This criteria is useful for integrating peaks with long tails.
This method drops a vertical line from the apex of the valley
between unresolved peaks to the baseline. The intersection of the
vertical line and the baseline defines the end of the first peak and
the beginning of the second peak.
When the trace exceeds rise percentage, the TraceFinder
application applies valley detection peak integration criteria. This
test is applied to both the left and right edges of the peak.
Range: 0.1 to 500.0
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Valley S/N
Specifies a value to evaluate the valley bottom. Using this
parameter ensures that the surrounding measurements are higher.
Default: 2.0
Range: 1.0 to 100.0
# Background Scans
Specifies the number of background scans performed by the
TraceFinder application.
Report Noise As
Determines if the noise used in calculating S/N values is calculated
using an RMS calculation or peak-to-peak resolution threshold.
Options are RMS or Peak To Peak.
Thermo Scientific
3 Using the Configuration Console
Specifying Default Peak Detection Parameters
ICIS Detection Method
The ICIS peak detection algorithm is designed for MS data and has superior peak detection
efficiency at low MS signal levels.
Figure 13. ICIS peak detection
Table 9. ICIS peak detection parameters (Sheet 1 of 3)
Parameter
Description
Detection Algorithm
Specifies the ICIS peak detection algorithm.
Detection Method
Specifies the detection method used for component identification.
Highest peak: Uses the highest peak in the chromatogram for
component identification.
Nearest RT: Uses the peak with the nearest retention time in the
chromatogram for component identification.
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Specifying Default Peak Detection Parameters
Table 9. ICIS peak detection parameters (Sheet 2 of 3)
Parameter
Description
Smoothing
Determines the degree of data smoothing to be performed on the
active component peak prior to peak detection and integration.
The ICIS peak detection algorithm uses this value.
Range: Any odd integer from 1 through 15 points
Default: 1
Area Noise Factor
Specifies the noise level multiplier used to determine the peak edge
after the location of the possible peak. The ICIS peak detection
algorithm uses this value.
Range: 1 through 500
Default: 5
Peak Noise Factor
Specifies the noise level multiplier used to determine the potential
peak signal threshold. The ICIS peak detection algorithm uses this
value.
Range: 1 through 1000
Default: 10
Baseline Window
Specifies that the TraceFinder application looks for a local minima
over this number of scans. The ICIS peak detection algorithm uses
this value.
Range: 1 through 500
Default: 40
Constrain Peak Width
Constrains the peak width of a component during peak
integration of a chromatogram. You can then set values that
control when peak integration is turned on and off by specifying a
peak height threshold and a tailing factor. Selecting the Constrain
Peak Width check box activates the Peak Height (%) and Tailing
Factor options.
Peak Height (%)
Specifies that the signal must be above the baseline percentage of
the total peak height (100%) before integration is turned on or
off. This text box is active only when you select the Constrain Peak
Width check box.
Range: 0.0 to 100.0%
Tailing Factor
Specifies the tailing factor that controls how the TraceFinder
application integrates the tail of a peak. This factor is the
maximum ratio of the trailing edge to the leading side of a
constrained peak. This text box is active only when you select the
Constrain the Peak Width check box.
Range: 0.5 through 9.0
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Specifying Default Peak Detection Parameters
Table 9. ICIS peak detection parameters (Sheet 3 of 3)
Parameter
Description
Noise Method
Specifies the noise method as INCOS or Repetitive.
INCOS: Uses a single pass algorithm to determine the noise level.
The ICIS peak detection algorithm uses this value.
Repetitive: Uses a multiple pass algorithm to determine the noise
level. The ICIS peak detection algorithm uses this value. In
general, this algorithm is more accurate in analyzing the noise than
the INCOS Noise algorithm, but the analysis takes longer.
Min Peak Width
Specifies the minimum number of scans required in a peak. The
ICIS peak detection algorithm uses this value.
Range: 0 to 100 scans
Default: 3
Multiplet Resolution
Specifies the minimum separation in scans between the apexes of
two potential peaks. This is a criteria to determine if two peaks are
resolved. The ICIS peak detection algorithm uses this value.
Range: 1 to 500 scans
Default: 10
Area Tail Extension
Specifies the number of scans past the peak endpoint to use in
averaging the intensity. The ICIS peak detection algorithm uses
this value.
Range: 0 to 100 scans
Default: 5
Area Scan Window
Specifies the number of allowable scans on each side of the peak
apex. A zero value defines all scans (peak-start to peak-end) to be
included in the area integration.
Range: 0 to 100 scans
Default: 0
RMS
Thermo Scientific
Specifies that the TraceFinder application calculate noise as RMS.
By default, the application uses Peak To Peak for the noise
calculation. RMS is automatically selected if you manually
determine the noise region.
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Avalon Detection Method
The Avalon peak detection algorithm is designed for UV data. The Avalon peak detection
algorithm also supports negative peaks. You can edit the Event values from the Avalon Event
List.
Figure 14. Avalon peak detection
Table 10. Avalon peak detection parameters
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Parameter
Description
Detection Algorithm
Specifies the Avalon peak detection algorithm.
Detection Method
Specifies the detection method used for component identification.
Highest peak: Uses the highest peak in the chromatogram for
component identification.
Nearest RT: Uses the peak with the nearest retention time in the
chromatogram for component identification.
Smoothing
Determines the degree of data smoothing to be performed on the
active component peak prior to peak detection and integration.
The ICIS peak detection algorithm uses this value.
Default: 1
Range: Any odd integer from 1 through 15 points
Time/Event/Value
Displays the events specified in the Avalon Event List dialog box.
Initially displays only the default events that cannot be edited or
deleted.
Autocalc Initial Events
Automatically calculates the events in the Event list.
Edit
Opens the Avalon Event List dialog box where you can edit the
Time/Event/Value parameters. See Avalon Event List.
Thermo Scientific
3 Using the Configuration Console
Specifying Default Peak Detection Parameters
Avalon Event List
The event list includes both user-defined and noneditable default events. The application
displays the default events when you choose Avalon sensitivity. You cannot delete these events
or change their time or values. For a detailed list of events and value ranges, see Event types.
Figure 15. Avalon Event List dialog box
Table 11. Avalon Event List dialog box parameters
Thermo Scientific
Parameter
Description
Time (Min)
Specifies the start time of the event.
Event
Specifies the type of event. For a detailed list of events and value
ranges, see “Event types.”
Value
Specifies the value of the event.
Add
Adds a new event to the list with the current Time/Event/Value
parameters.
Delete
Removes the selected Time/Event/Value parameter from the event
list.
Change
Applies the current parameter values.
Cancel
Closes the dialog box without making any changes. Any additions,
deletions, or changes revert to their original state.
Apply
Closes the dialog box.
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Figure 16. Event types
Table 12. Event type descriptions (Sheet 1 of 2)
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Event type
Description
Start Threshold
Specifies the threshold at the start of a peak. The Start Threshold is
directly related to the RMS noise in the chromatogram.
Range: 0 to 999 999 999
End Threshold
Specifies the threshold at the end of a peak. The End Threshold is
directly related to the RMS noise in the chromatogram.
Range: 0 to 999 999 999
Area Threshold
Controls the area cutoff. Any peaks with a final area less than the area
threshold will not be detected. This control is in units of area for the
data.
Range: 0 to 999 999 999
P-P Threshold
Specifies the peak-to-peak resolution threshold controls how much
peak overlap must be present before two or more adjacent peaks
create a peak cluster. Peak clusters have a baseline drop instead of
valley-to-valley baselines. Specified as a percent of peak height
overlap.
Range: 0.1 to 99.99
Negative Peaks
Permits detection of a negative going peak. Automatically resets after
finding a negative peak.
Valid values: On or Off
Bunch Factor
Specifies the number of points grouped together during peak
detection. This event controls the bunching of chromatographic
points during integration and does not affect the final area
calculation of the peak. A high bunch factor groups peaks into
clusters.
Range: 0 to 999
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3 Using the Configuration Console
Specifying Default Peak Detection Parameters
Table 12. Event type descriptions (Sheet 2 of 2)
Thermo Scientific
Event type
Description
Tension
Controls how closely the baseline should follow the overall shape of
the chromatogram. A lower tension traces the baseline to more
closely follow changes in the chromatogram. A high baseline tension
follows the baseline less closely, over longer time intervals.
Range: 0 to 999.99 minutes
Tangent Skim
Specifies that you can tangent skim any peak clusters. By default, it
chooses the tallest peak in a cluster as the parent. You can also
identify which peak in the cluster is the parent. Tangent skim peaks
are detected on either side (or both sides) of the parent peak. Tangent
skim automatically resets at the end of the peak cluster.
Range: 0 to 1
Shoulders On
Allows peak shoulders to be detected (peaks which are separated by
an inflection rather than a valley) Sets a threshold for the derivative.
Shoulders Off
Disables peak shoulder detection.
Range: 0 to 50
Force Cluster On
Forces the following peaks to be treated as a cluster (single peak).
Force Cluster Off
Ends the forced clustering of peaks.
Disable Cluster On
Prevents any peaks from being clustered.
Disable Cluster Off
Permits clusters to occur again.
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Specifying Adducts
Specifying Adducts
An adduct ion is formed from a precursor ion and contains all of the constituent atoms of that
ion and additional atoms or molecules. Adduct ions are often formed in the mass
spectrometer ion source. Adducts can be either positive or negative.
Use the Application – Adducts view to specify the adducts that will be available for you to use
in method development. When user security is activated, you must have
Configuration – Adducts permission to access these features.
Follow these procedures:
• To open the Adducts view
• To add an adduct
• To remove an adduct
 To open the Adducts view
In the navigation pane for the Configuration console, click Adducts.
The Application – Adducts view opens, displaying the default positive and negative
adducts.
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Specifying Adducts
 To add an adduct
1. In the Positive Adducts or Negative Adducts pane, click the Add New Adduct icon,
.
The application adds a new, editable row at the bottom of the Adducts list.
2. Type the formula for the new adduct ion.
The formula syntax is alphanumeric and case sensitive. It can include parentheses and
brackets.
The formula specifies the difference between the neutral molecule and the charged ion
that you expect to see in the results.
For example, a sodium adduct has [M+Na]+ as the expected charged ion (where M is the
neutral molecule), so you would type “Na” for the formula. A water adduct has
[M+H+H2O]+ as the expected charged ion, so you would type “H3O” for the formula.
IMPORTANT When you create an adduct formula, you can type both uppercase and
lowercase letters; however, the TraceFinder application interprets all uppercase input
as single-letter elements and all lowercase input as two-letter elements.
For example, it interprets the string “inau” as In Au and “COSI” as C O S I.
The application displays a type and neutral mass for the adduct formula you entered.
3. Select the default name (New Adduct) and type a name for the adduct.
You cannot change the type or neutral mass, but the application will correctly calculate
these values later.
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Specifying Adducts
4. Press ENTER.
The application adds the adduct to the adducts list and calculates the correct type (Gain
or Loss) and the neutral mass.
These adducts are available for you to select in the Compound Database view of the
Method Development mode when you specify parameter values for target peaks.
 To remove an adduct
1. In the Positive Adducts or Negative Adducts pane, select the adduct that you want to
remove.
2. Press DELETE and confirm that you want to delete the selected adduct.
You can delete only adducts that you added to the adducts list. You cannot delete default
adducts defined by the TraceFinder installation.
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Activating Optional Features
Activating Optional Features
When user security is activated, you must have Configuration – Optional Features permission
to access these features.
Use the Application – Optional Features view to activate the following features:
• Quick Acquisition
• Delay Calibration
• User Peak Detection Settings
• Auto Sampler Tray Configuration
• Acquisition Submission Options
• Qualitative Explorer
• Screening Libraries
• Multiplexing
• Intelligent Sequencing
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Activating Optional Features
 To open the Optional Features page
In the navigation pane for the Configuration console, click Optional Features.
The Application – Optional Features page opens.
Quick Acquisition
The quick acquisition option activates the Quick Acquisition feature in the Acquisition,
Analysis, or Method Development mode.
Note The Quick Acquisition feature is not available when you activate Multiplexing. See
“Multiplexing” on page 61.
 To activate quick acquisition
1. Select the Quick Acquisition Allowed check box.
2. To save your changes, click Apply.
The application immediately applies this feature change.
For a description of the Quick Acquisition features, see Appendix A, “Using Quick
Acquisition.”
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Activating Optional Features
Delay Calibration
You can determine when the application calculates the calibration curve, using the Delay
Calibration option. Delaying the recalibration until the application processes the last
calibration sample in a batch is faster but less responsive than recalibration after each
calibration sample.
 To delay calculation of a calibration curve
1. Select the Delay Calibration check box.
2. To save your changes, click Apply.
The application immediately applies this feature change.
User Peak Detection Settings
Use the User Peak Detection Settings Allowed option to let users modify the method
integration settings for specific compounds in Data Review. For instructions about modifying
the peak detection parameters, see “To modify the peak detection settings” on page 469.
 To allow users to modify peak detection settings
1. Select the User Peak Detection Settings Allowed check box.
2. To save your changes, click Apply.
The application immediately applies this feature change.
Auto Sampler Tray Configuration
By default, the TraceFinder application lets the autosampler automatically determine the tray
configuration. When you are using a Waters™ Acquity™ system, you must make this feature
unavailable and explicitly specify the tray configuration when you create a batch.
 To disallow automatic tray configuration
1. Select the Allow Auto Sampler to Automatically Determine … check box.
2. To save your changes, click Apply.
The application immediately applies this feature change.
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Activating Optional Features
Acquisition Submission Options
To control acquisitions, you can activate either submission option: full-sequence or
single-sample. When you submit batches from the Acquisition mode or Quick Acquisition
batches from any mode, they run in first-in-last-out order. The last batch submitted is the first
batch to run, unless you submit a batch as a priority batch in Acquisition mode.
• When you use Full Sequence Submission, priority batches always run immediately after
the currently acquiring batch is completed.
• When you use Single Sample Submission, priority batches always run immediately after
the currently acquiring sample is completed.
 To specify acquisition submission features
1. Select either the Full Sequence Submission or the Single Sample Submission option:
• Full Sequence Submission: Supports look-ahead features of the autosampler. When
the instrument method specifies the look-ahead feature, the TraceFinder application
functions like a multiplex driver and feeds the autosampler the next vial position.
When you submit a batch, the autosampler begins preparing for all sample injections
when the pre-run condition begins. All samples in the batch must be completed
before other batches (even higher priority batches) can begin.
Note The Full Sequence Submission feature is not available when you activate
Intelligent Sequencing.
• Single Sample Submission: Supports intelligent-sequencing features. When you
submit a batch, the autosampler begins preparing for one sample injection at a time.
Higher priority batches can interrupt the sample sequence in the currently acquiring
batch.
Note The Single Sample Submission feature is not available when you activate
Multiplexing. See “Multiplexing” on page 61.
2. To save your changes, click Apply.
The application immediately applies this feature change.
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Activating Optional Features
Qualitative Explorer
You can use either the FreeStyle application or Qual Browser to display chromatograms and
spectra, detect chromatogram peaks, search libraries, simulate spectra, subtract background
spectra, apply filters, add text and graphics, create and save layouts, and view instrument
parameters as they changed during the acquisition.
 To specify a qualitative explorer
Select either the Thermo FreeStyle or the Xcalibur Qual Browser option.
Note You can access the explorer by choosing Tools > Launch Qual Explorer in the
main TraceFinder menu. See “Launching a Qualitative Explorer” on page 16.
Screening Libraries
Use the screening libraries specified here for both quantitation methods and target screening
methods. For more information about how you can use screening libraries in a quantitation
method, see Screening Libraries in a Quantitation Method. For more information about how
you can use screening libraries in a target screening method, see Screening Libraries in a
Target Screening Method.
When you specify the Library Search Type on the Processing page for a screening method, you
choose either the Library Manager search type or the NIST search type. See “Editing the
Acquisition Page” on page 273.
• When you choose Library Manager as the Library Search Type for the method, the
application uses the Library Manager library file (.db) specified here in the Configuration
console. You can search only one spectral library when you process a sample.
• When you choose NIST as the Library Search Type for the method, the application uses
the NIST libraries specified here in the Configuration console. You can choose to search
multiple NIST libraries when you process a sample.
 To specify a Library Manager screening library
Click Browse and locate the library that you want to use for screening.
Note You can use only one search type when you process a sample. When you select
NIST as the Library Search Type in your method, the application does not use the
screening library that you specify here.
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Activating Optional Features
 To specify a NIST screening library
1. Click Select.
The Select NIST Libraries dialog box opens, listing the libraries you installed for the
application.
2. Select the check box for each NIST library that you want to use for screening and click
OK.
Note You can use only one search type when you process a sample. When you select
Library Manager as the Library Search Type in your method, the application does not
use the NIST libraries that you specify here.
3. To save your changes, click Apply.
The application immediately applies this feature change.
The application searches the specified screening library to identify or confirm a sample
compound, matches the fragment ion spectrum in the library to the compound’s ion
spectrum, and returns the highest score (best match).
The application performs either a forward library search or a reverse library search. A forward
search compares the mass spectrum of an unknown compound to a mass spectral library
entry, while a reverse search compares a library entry to an unknown compound.
Screening Libraries in a Quantitation Method
In a quantitation master method, you can enable library matching and set a score threshold to
minimize poor matches. See “Library” on page 205. To match a compound, the resulting
score from a library search must be higher than the specified threshold value.
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Activating Optional Features
Screening Libraries in a Target Screening Method
In a target screening master method, you can specify the library search to either identify or
confirm library matches and set a score threshold to minimize poor matches. See “Editing the
Processing Page” on page 277.
• Identify or Confirm: The application identifies or confirms the sample compound by
searching the specified search library and returning the highest score (as a percentage
value) for the fragment ion spectrum in that library that matches the compound’s ion
spectrum.
• Score Threshold: To identify or confirm the presence of a compound, the resulting score
from a library search must be higher than the specified threshold value.
IMPORTANT To use a library search for identification or confirmation, the application
requires meeting these conditions:
• The raw data file must contain higher energy collision-induced dissociation (HCD),
source collision-induced dissociation (CID), or all ions fragmentation (AIF) ion
spectra.
• The spectra must exist at a time point within the compound’s elution time range.
Multiplexing
The application uses multiplexing features in the Acquisition mode when you specify
channels for a sample in a batch (see “Defining the Sample List” on page 324) or monitor an
acquisition (see “Devices Page” on page 352).
 To specify multiplexing features
1. Select the Multiplexing check box.
Note Multiplexing is not available when you activate Intelligent Sequencing. See
Intelligent Sequencing.
2. Select the check box for each channel that you want to use for acquisition.
3. To save your changes, click Apply.
The application immediately applies this feature change.
Note When you activate multiplexing, the following optional features are not available:
• Quick Acquisition
• Single Sample Submission
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Activating Optional Features
Intelligent Sequencing
Use Intelligent Sequencing for single-sample submission. When you submit a batch, the
autosampler begins preparing for one sample injection at a time. Higher priority batches can
interrupt the sample sequence in the currently acquiring batch.
 To activate the intelligent sequencing feature
1. Select the Intelligent Sequencing check box.
Note Intelligent Sequencing is not available when you activate Multiplexing. See
“Multiplexing” on page 61.
The Acquisition Submission Options default to Single Sample Submission. The Full
Sequence Submission option is not available when you select the Intelligent Sequencing
option.
2. To save your changes, click Apply.
The application immediately applies this feature change.
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Creating Custom Columns
Creating Custom Columns
Use the Custom Columns page to add six additional columns to the samples list in batches.
The application treats these custom columns the same as other columns when you export data
to a Microsoft Excel™ spreadsheet or to a CSV file.
When user security is activated, you must have Configuration – Custom Columns permission
to access these features.
You can use the Modify Columns dialog box to display and change the order of these columns
in the sample list (see “Column Display” on page 371).
You can use the Field Chooser to display and change the order of these columns in the Data
Review Samples pane (see “Samples Pane” on page 412).
You can use the information in these columns (for example) for temperature control when
you use Aria™ MX for multiplexing or for injector and multiple column module ports when
you use the TurboFlow™ method with the Prelude™ or TLX data systems.
Follow these procedures:
• To open the Custom Columns page
• To add custom columns to new batches
• To create new batches without custom columns
• To control the display of custom columns
 To open the Custom Columns page
Click Custom Columns in the navigation pane.
The Application – Custom Columns page opens.
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Creating Custom Columns
The Enable Custom Columns check box controls both the creation of custom columns on
new batches and the display of custom columns on the Modify Columns dialog box in the
Batch View and the Field Chooser in the Data Review Samples pane.
 To add custom columns to new batches
1. Select the Enable Custom Columns check box.
The application adds six additional columns to the samples list in all new batches that you
create.
2. For each custom column, select the default column name and type your custom name, as
in this example:
3. Click Apply.
The application adds the six custom columns to all new batches that you create.
Note Only new batches include these custom columns. The application does not add
custom columns to previously created batches.
Note If you return to this page and change the custom column names, the
application uses the new names only for future batches.
 To create new batches without custom columns
Clear the Enable Custom Columns check box and click Apply.
When you create new batches, they will not include custom columns, and the application
hides the display of the custom columns for any previous batches that you created with
custom columns enabled.
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 To control the display of custom columns
Do one of the following:
• To make custom columns available for all batches, select the Enable Custom
Columns check box and click Apply.
• To make custom columns not available for batches, clear the Enable Custom
Columns check box and click Apply.
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Creating Custom Flags
Creating Custom Flags
Use the Flag Customization view to customize error flags and conditions that indicate
compound errors in Data Review for quantitation batches. You can edit the priority assigned
to an error condition (flag rule) and the shape and color of the icon used to indicate the error.
You can also delete an error condition or create a new one. When user security is activated,
you must have Configuration – Custom Flags permission to access these features.
 To open the Flag Customization view
Click Flag Customization in the navigation pane.
The Application – Flag Customization view opens.
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Creating Custom Flags
Follow these procedures:
• To edit priority groups
• To create a new priority group
• To edit flag rules
• To create a new flag rule
• To remove all customization
In the Priority Groups area, you can edit the priority, shape, or color of a flag. You can also
delete a flag or create a new one. You cannot change the name of a flag.
 To edit priority groups
1. Do any of the following:
• Select the default Priority value and type a new value.
A priority of 1 is the highest priority. The higher the Priority number, the lower the
priority.
• Double-click the Shape value and select a new shape from the list.
• Click the Color arrow and select a new color from the color palette.
2. When you have completed all your changes, click Apply to save your changes.
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 To create a new priority group
1. In the Priority box, type a value.
You can enter positive or negative numbers. The lower the number, the higher the
priority.
2. In the Name box, type a name for the new priority group.
3. Select a flag shape from the Shape list: Circle, Square, or Flag.
4. Click the Color list and select a color from the color palette.
5. (Optional) Click Advanced and select a color based on RGB, HSL, or CMYK color
palettes. See “Advanced Dialog Box” on page 70.
6. Click Create.
The application adds the new flag to the Priority Groups list, as in this example:
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 To edit flag rules
Note You can edit the description and priority group for a flag rule, and you can
delete a rule. You cannot edit the name or flag type for a rule.
1. Do any of the following:
• In the Description column, select the current text and type a new description.
• Double-click the PriorityGroup value and select a new group from the list.
• Click Delete.
The application immediately removes the flag rule. To restore the deleted rule, click
Undo.
2. When you have completed all your changes, click Apply to save your changes.
 To create a new flag rule
1. In the Name box, type a name for the new rule.
Keep the name short and make it intuitive.
2. In the Description box, type a description for the new flag rule.
This description can be anything you want and use as many characters as you want.
3. From the Flags list, select an error condition.
4. From the PriorityGroup list, select a priority group.
This list includes both the default priority groups and any priority groups that you
created. See “To create a new priority group” on page 68.
5. Click Create.
The application adds your new flag rule to the end of the Flag Rules list.
 To remove all customization
Click Reset to Factory Defaults.
The application removes all new priority groups, new flag rules, and any edits to the
groups or rules.
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Advanced Dialog Box
Use the features on the Advanced dialog box to select custom colors for your flags, using RGB,
HSL, or CMYK color standards.
Figure 17. Advanced RGB colors
With the Red/Green/Blue (RGB) color palette, you can select a color with a specific RGB
value, as displayed on a computer monitor.
Figure 18. Advanced HSL colors
With the Hue/Saturation/Lightness (HSL) color palette, you can select a color with a specific
HSL value, as is commonly used in computer graphics.
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Figure 19. Advanced CMYK Colors
With the Cyan/Magenta/Yellow/Key (CMYK) color palette, you can select a color with a
specific CMYK value, as you might specify in a color printer. The key (K) color used on
printers is always black.
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Specifying the Reports
Specifying the Reports
When user security is activated, you must have Configuration – Reporting permission to
configure a list of reports that are available to all users when they generate reports from the
Method Development, Analysis, or Acquisition modes.
Follow these procedures:
• To open the Application – Reporting view
• To specify which reports are available
 To open the Application – Reporting view
In the Configuration console navigation pane, click Reporting.
The Application – Reporting view opens.
 To specify which reports are available
Select the check box for each report that you want to make available.
• To return the report selections to their original state (when you first opened this
view), click Undo.
• To save your changes, click Apply.
Your report settings are immediately available in the TraceFinder application.
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Specifying the Reports
Reports
The application can generate any of the following reports.
Figure 20. Reports
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Using the Common Features of the Method
Development Mode
This chapter includes method development tasks common to both quantitative and screening
methods.
Contents
• Working with the Compound Database
• Working with Instrument Methods
For information about creating either a quantitation method or a target screening method, see
the appropriate chapter:
• Chapter 5, “Using the Method Development Mode for Quantitation Methods.”
• Chapter 6, “Using the Method Development Mode for Screening Methods.”
 To access the Method Development mode
Click Method Development in the navigation pane.
The Method Development navigation pane opens.
For descriptions of all the features in the Method Development navigation pane for a
quantitation method, see “Opening a Master Method” on page 122 (Chapter 5).
For descriptions of all the features in the Method Development navigation pane for a
screening method, see “Opening a Master Method” on page 268 (Chapter 6).
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Working with the Compound Database
When user security is activated, you must have Method Development permission to manage
compound definitions in the current database from either the Compound Detail Page or the
Grid Page in the Compound Database view. From either of these pages, you can export
compounds to a CSV file or mass list, or you can import compounds from an XML, a CSV,
or a CDB file.
Follow these procedures:
• To export compounds to a CSV file
• To export compounds to a mass list
• To import compounds
In addition to procedures for importing and exporting compound data, this section also
contains the following topics:
• Compound Database Names Mapped to CSV Column Names
• Data Columns with Default Values
 To export compounds to a CSV file
1. Choose Compound Database > Export All Compounds to CSV File from the main
menu.
Note If you have unsaved changes in your current compound database, a message
prompts you to save the changes. Click Yes to save the changes and continue with the
export procedure.
The Export Compounds dialog box opens.
2. (Optional) Click Browse and locate a different folder or file name where you want to
write the exported compound database.
Each parameter in the compound database editor is represented by a column of data in
the spreadsheet. When you export compound data to a CSV file, each parameter is
assigned to a column and each compound is assigned to a row.
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3. Select one of these options:
• Export Only Columns with Data: Writes only columns that contain nondefault
data for at least one compound. This option does not export columns that contain
only default data. See “Data Columns with Default Values” on page 112.
• Export All Columns: Writes all columns to the CSV file, including columns that
contain no data for any compound.
4. Click Export and Overwrite.
The application stores the database as
…\Thermo\TraceFinder\3.2\General\Databases\databaseName.csv
An Excel window opens with the compound data in spreadsheet format.
Figure 21. Compound data in an Excel spreadsheet
Column names in an exported Excel spreadsheet do not always match the parameter names in
the compound database editor. See “Compound Database Names Mapped to CSV Column
Names” on page 109.
You can use the tools in the spreadsheet to edit the data in the compound database and then
import the data in the CSV file back into the TraceFinder application. If you delete a column
from the spreadsheet and then import the CSV file, the TraceFinder application replaces the
data in that column with default values. For a list of default values, see “Data Columns with
Default Values” on page 112.
 To export compounds to a mass list
1. Select the compounds that you want to export.
You can export any experiment type to any instrument format. The application writes the
data to the XML file in a format that is compatible with the specified instrument,
regardless of the original experiment type.
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2. Choose Compound Database > Export Selected Compounds to Mass List from the
main menu.
Note If you have unsaved changes in your current compound database, a message
prompts you to save the changes. Click Yes to save the changes and continue with the
export procedure.
The application writes the mass data for the selected compounds to the following folder,
using a format compatible with your configured instrument:
…\TraceFinderData\32\Methods\Methodname\*.xml
Note If you have neither a TSQ, an ISQ, a Q Exactive, a TSQ Endura™, nor a TSQ
Quantiva™ instrument configured, a message asks which format you want to export:
Triple Quadrupole, Q Exactive, TSQ Quantiva/Endura SIM, or TSQ
Quantiva/Endura SRM.
For examples of exported mass lists, “Mass Data Formats” on page 81.
 To import compounds
1. Choose Compound Database > Import Compounds from the main menu.
Note If you have unsaved changes in your current compound database, a message
prompts you to save the changes. Click Yes to save the changes and continue with the
import procedure.
The Select File to Import into the Current Compound Database dialog box opens.
You can import compounds from the following file types:
• ToxID Exactive CSV
• ToxID™ MS2 CSV
• TraceFinder CSV
• TraceFinder Mass List XML
• TraceFinder 3.1 Legacy CDB
• ExactFinder™ 2.0 CDB
• .include-masses
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IMPORTANT Before you import data from a CSV file, verify that the following
required columns have data for each compound. These columns have no default
values and must have a value before you can import CSV data into the TraceFinder
compound database:
• CompoundName
• ExperimentType
• ProductMass (target peak)
• Confirm Product (confirming peak)
• Fragment
If you delete any of these columns from the spreadsheet and attempt to import the
CSV data into the TraceFinder application, the application warns that it is unable to
parse the file and identifies the missing column.
2. Locate the CDB, CSV, or XML compound database file that you want to import and
click Open.
The Import Compounds to CDB dialog box opens.
Note If the import file is missing required compound information, the application
warns that it is unable to parse the file and identifies the missing columns. For a list of
required columns, see “Compound Detail Page” on page 83.
3. To select a different compound database, click Browse, locate an XML, a CSV, or a CDB
compounds file, and click Open.
4. To select a different target database, do one of the following:
a. Click Browse.
b. Locate an XML, a CSV, or a CDB compounds file.
c. Click Open.
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–or–
a. Click Create.
b. Type a name for a new compound database.
c. Click OK.
5. Confirm that the import file and the target database are correct.
The dialog box reports the total number of compounds in the import file, the number of
compounds with validation errors, and the number of compounds that already exist in
the target database.
6. (Optional) Select one of these options:
• Skip: Imports only those compounds that do not already exist in the target database.
• Overwrite: Replaces compounds that already exist in the target database with the
imported compounds.
7. Click Import.
The TraceFinder application imports the compounds from the imported file, adds them
to any compounds already in the database, and alphabetically sorts them.
The application reports the number of imported compounds.
8. Click OK.
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Mass Data Formats
In the TraceFinder application, you can export the mass data list from the Compound
Database to an XML file that can be read by the TSQ, ISQ, Q Exactive, TSQ Endura, or
TSQ Quantiva applications.
Triple Quadrupole Format
IMPORTANT You can export only SRM or SIM data types to the Triple Quadrupole
format.
The TraceFinder application writes the mass data to the following file:
…\TraceFinderData\32\Methods\Methodname\*.xml
The data in this file matches the TSQ XML data, which you can use in the instrument
method editor of a TSQ application.
Q Exactive Format
IMPORTANT You can export only XIC data types to the Q Exactive format.
The TraceFinder application writes the mass data to the following file:
…\TraceFinderData\32\Methods\Methodname\Methodname.xml.include-masses
The data in this file matches the Exactive XML data, which you can use in the instrument
method editor of a Q Exactive application.
TSQ Quantiva/Endura SIM Format
IMPORTANT You can export only SIM data types to the TSQ Quantiva/Endura SIM
format.
The TraceFinder application writes the mass data to the following file:
…\TraceFinderData\32\Methods\Methodname\Methodname.xml
The data in this file matches the TSQ Endura, TSQ Quantiva, and Xcalibur XML data,
which you can use in the instrument method editors of the associated applications. The
TraceFinder application exports only the following compound parameters to the XML file:
• Compound (as Name in the XML file)
• Product Mass (as Mass in the XML file)
• RT range (as StartTime and StopTime in the XML file)
• Polarity
• Lens (as TubeLens or S-Lens in the XML file)
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TSQ Quantiva/Endura SRM Format
Note You can export only SRM data types to the TSQ Quantiva/Endura SRM format.
The TraceFinder application writes the mass data to the following file:
…\TraceFinderData\32\Methods\Methodname\Methodname.xml
The data in this file matches the TSQ Endura, TSQ Quantiva, and Xcalibur XML data,
which you can use in the instrument method editors of the associated applications. The
TraceFinder application exports only the following compound parameters to the XML file:
• Compound (as Name in the XML file)
• Precursor Mass
• Product Mass
• RT range (as StartTime and StopTime in the XML file)
• Polarity
• Lens (as TubeLens or S-Lens in the XML file)
• Collision Energy
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Compound Detail Page
When you open the Compound Database view, the Compound Detail page is the default.
The compound details are different depending on which experiment type the selected
compound uses.
• Compound Detail page for SRM experiments
• Compound Detail page for SIM experiments
• Compound Detail page for XIC experiments
This section includes the following topics:
• Sorting Compounds in the Database
• Editing Compounds in the Database
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Figure 22. Compound Detail page for SRM experiments
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Figure 23. Compound Detail page for SIM experiments
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Figure 24. Compound Detail page for XIC experiments
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Sorting Compounds in the Database
On the Compound Detail page, you can sort the list of compounds that you want to display.
Follow these procedures:
• To search for compounds by name
• To display compounds by experiment type
• To display truncated compound names
 To search for compounds by name
In the Search box, begin typing any part of a compound name.
As you type, the list of displayed compounds narrows to match the typed text.
For example, you can use this feature in combination with the experiment type list to
display only SIM compounds that begin with the letter “a”.
 To display compounds by experiment type
Select an experiment type from the
list.
The list displays experiment types that each use a different structure for the mass filter.
• SRM: Selected Reaction Monitoring
• XIC: Extracted Ion Chromatogram
• SIM: Single Ion Monitoring
For detailed descriptions of each experiment type, see “Experiment Types” on page 106.
For example, you can use this feature in combination with the text search to display only
SRM compounds that begin with the letter “f ”.
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 To display truncated compound names
Hold your cursor over long, truncated names to display a ToolTip with the entire name.
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Editing Compounds in the Database
In the Compound Detail page of the Compound Database view, you can import compounds
into the database, add or remove compounds from the database, add target or confirming
peaks to a compound, or remove target or confirming peaks from a compound.
Follow these procedures:
• To add a compound to the database
• To remove compounds
• To make a compound editable
• To add a target peak to a compound
• To add a confirming peak to a target peak
• To copy target peaks from one compound to another
• To copy window values from one peak to another
• To add a fragment to a target peak
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 To add a compound to the database
1. Click the Add Compound icon,
.
The application adds a new, empty compound page and highlights the required
parameters in red.
2. Click the Compound box, and type the required Compound name.
3. Select the Experiment type: SRM, SIM, or XIC.
The required parameters are different for each experiment type. See “Experiment Types”
on page 106.
4. In the Target Peaks area, do the following:
• For SRM experiments, enter values for Precursor Mass and Product Mass.
• For SIM or XIC experiments, enter a value for Extracted Mass.
5. In the Confirming Peaks area, do the following:
• For SRM experiments, enter values for Precursor and Product Mass.
• For SIM or XIC experiments, enter a value for Precursor and Extracted Mass.
6. Enter or edit any of the other optional parameters described in the “Compound
Parameters” on page 101.
7. When you have finished your changes, click the Complete Edit icon,
.
Tip You cannot add another new compound or access the menu commands until you
complete the edit,
, or cancel the edit,
.
IMPORTANT After you complete the edits for the compounds, the header in the
Compound Database page marks the database name with an asterisk, indicating that
the database is not saved. To save the database with your compound changes, choose
File > Save Compound Database from the main menu.
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 To remove compounds
1. In the Compound list, select the compounds that you want to delete.
The application supports the following methods to delete multiple compounds:
• CTRL+A to select all compounds
• CTRL+click to select noncontiguous compounds
• SHIFT+click to select contiguous compounds
2. Click the Delete Selected Compounds icon,
.
3. To confirm that you want to delete the selected compounds, at the prompt click OK.
The application removes the selected compounds and all their peak information.
 To make a compound editable
1. In the Compound list, select the compound that you want to edit.
2. Click the Edit Compound icon,
.
The application makes the compound parameters editable and displays the
Add icon,
, so that you can add target peaks, confirming peaks, and fragments to the
compound details.
Note If you are adding a new compound, it is editable by default.
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 To add a target peak to a compound
1. In the Target Peaks header, click the Add Target Peak icon.
Add Target Peak icon
The application adds a new target peak to the compound. A target peak includes
quantitative values for the compound.
Delete Target Peak icon
2. Enter all required parameters.
The required target peak values differ for each experiment type. See “Experiment Types”
on page 106.
For a list of required and optional parameters, see the list of “Compound Parameters” on
page 101.
Tip You cannot add another new target peak or save the compound until you enter all
required peak parameters or delete
the new target peak.
3. Repeat these steps to add as many as six target peaks to the compound.
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 To add a confirming peak to a target peak
1. In the Confirming Peaks header, click the Add Confirming Peak icon.
Add Confirming Peak icon
The application adds a new confirming peak to the target peak.
Delete Confirming Peak icon
2. Type the required values for the confirming peak.
The required confirming peak values differ for each experiment type. See “Experiment
Types” on page 106.
For a list of required and optional parameters, see “Compound Parameters” on page 101.
3. Repeat these steps to add as many as 10 confirming peaks to the target peak.
Tip You cannot add another new confirming peak or save the compound until you
enter all required peak parameters or delete
the new confirming peak.
 To copy target peaks from one compound to another
1. In the compounds list, select the compound whose target peak you want to copy.
Source compound
2. When the target peak includes more than one peak, in the Target Peaks area for the
selected compound, scroll to the peak you want to copy.
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3. In the compounds list, keep the source compound selected and use the SHIFT or CTRL
keys to select the compounds that you want to copy the target peak to.
Source compound
IMPORTANT Be careful to keep the source compound selected.
4. In the Target Peaks area for the selected compound, right-click the target peak area and
choose Add Peak 1 to N Selected Compounds from the shortcut menu.
Right-click the target peak area.
The application reports that the peak was copied to the specified number of compounds.
The application copies the peak information to the selected compounds, adding this peak
to the peaks already defined for the compounds.
5. Click OK.
 To copy window values from one peak to another
1. In the compounds list, select the compound with the window value that you want to
copy.
Source compound
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2. In the Target Peaks area for the selected compound, identify the peak whose window you
want to copy.
3. In the compounds list, keep the source compound selected and use the CTRL key to
select the compounds that you want to copy the window to.
Source compound
IMPORTANT Be careful to keep the source compound selected.
4. In the Target Peaks area for the selected compound, right-click the target peak area and
choose Set the Window for All Peaks of selectedCompounds to windowValue from the
shortcut menu.
Right-click the target peak area.
The application reports that the retention time and window were copied to the specified
number of compounds, including the source compound when it has multiple peaks.
The application copies the retention time and window information to all peaks in the
selected compounds and all additional peaks in the source compound, overwriting the
values for these parameters.
5. Click OK.
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 To add a fragment to a target peak
1. In the Fragments header, click the Add Fragment icon.
Add Fragment icon
The application adds a new fragment to the target peak.
Delete Fragment icon
2. Click the Extracted Mass box, and type a value between 10 and 2999.999.
3. Repeat these steps to add as many fragments as you want.
Tip You cannot save the compound until you enter all required fragment parameters
or delete
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Grid Page
The Grid page of the Compound Database view displays the data in the compound database
as a grid similar to a spreadsheet. The data on the Grid page reflects all populated values on
the Compound Detail page.
• There must be at least one compound in the compound database to view the Grid page.
• There are no empty columns on the Grid page. There must be at least one value for a
parameter in the compound database or that parameter column is not displayed.
Note If a column of interest is not displayed on the Grid page, return to the
Compound Detail page, edit at least one compound to have a value for that
parameter, and then return to the Grid page.
On the Grid page, you can import compounds into the database, add compounds to or
remove compounds from the database, add target or confirming peaks to a compound, or
remove target or confirming peaks from a compound.
 To display the compound database on the Grid page
Click Grid in the Compound Database navigation pane.
The current database opens on the Grid page.
The parameters displayed in the compound database depend on which experiment type the
selected compound uses. For detailed descriptions of all parameters used in the compound
database, see “Compound Parameters” on page 101.
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Follow these procedures:
• To add a compound
• To remove a compound
• To edit values in the compound database grid
• To edit Experiment Type values in the compound database
• To sort the grid on column data
• To organize compounds by column data
 To add a compound
1. Scroll to the bottom of the compound database grid.
There is always one blank row in the grid.
2. In the blank row, type or paste values into the columns.
Note Some columns have dropdown lists from which you can select values.
3. Press ENTER to add another blank row to the grid.
 To remove a compound
1. Click anywhere in a row to select the compound.
2. Press the DELETE key.
Note Do not use CTRL+X to delete a compound. CTRL+X deletes only the
parameter values in the selected cells.
3. At the prompt to confirm that you want to delete the compound, click Yes.
The application removes the compound from the database grid.
 To edit values in the compound database grid
Do either of the following:
• Select the current column value and type a new value.
–or–
• Select single cells or entire columns whose values you want to copy, using a
copy-and-paste operation.
You can use this method to replicate entire columns. Click the column header to
select the entire column, and then use CTRL+C and CTRL+V to replicate the
column values.
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When you edit a value in the Formula column, the application calculates the m/z for the
precursor and product masses.
When you change the charge state, adduct, or polarity for a compound, the application
recalculates the m/z for the precursor and product masses.
Note Do not use CTRL+X to delete a compound. CTRL+X deletes only the
parameter values in the selected cells.
 To edit Experiment Type values in the compound database
1. Select a new experiment type for one compound from the Experiment Type list.
2. Double-click the new type in the cell, and press CTRL+C.
3. Select all Experiment Type cells in all the compounds in the database.
4. Press CTRL+V.
The application pastes the copied experiment to all compounds in the database.
IMPORTANT If you change one experiment type, you must change the experiment
type for all compounds. The Grid page cannot display a database unless all
compounds use the same experiment type.
 To sort the grid on column data
1. Click the header of a column.
The application sorts the grid by ascending column values (alphabetically or numerically).
Note Columns with alphanumeric values sort from 1–n and then A–Z.
2. Click the header a second time to sort by descending column values.
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 To organize compounds by column data
1. In the banner at the top of the column, click the filter icon.
Down arrow
Filter icon
2. Select one of the filtering options, for example, Starts With.
The down arrow
changes to a list box.
3. Click the down arrow and choose one of the column values in the list, for example, EI.
The grid displays only compounds that match the selected filter and data.
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Compound Parameters
The Compound Detail page and the Grid page occasionally use different names for the same
parameter. The Parameter column in Table 13 indicates if the parameter name is different, for
example, “Compound” for the Compound Detail page and “Compound Name” for the Grid
page.
The parameters that are displayed in a compound database on either the Compound Detail
page or the Grid page depend on which experiment type the selected compound uses. The
Description column in the table includes the applicable experiment types.
Table 13. Compound parameters (Sheet 1 of 5)
Parameter
Description
(Compound Detail page) Alphanumeric name assigned to the compound.
Compound
(Grid page)
Compound Name
(Compound Detail page) Experiment type: SRM, XIC, or SIM. For details about the differences, see “Experiment
Types” on page 106.
Experiment
(Grid page)
Experiment Type
Category
(Optional) Alphanumeric identifier.
CAS
The Chemical Abstract Service (CAS) number that the TraceFinder application matched
with the compound.
(Compound Detail page) Chemical formula for the compound. Used to calculate the neutral mass for the
compound.
Formula
(Grid page)
Chemical Formula
Ionization
Alphanumeric identifier.
Valid values: None, ESI, APCI, EI, CI, or APPI
Default: None
Response Threshold
The threshold used to integrate only peaks with a response greater than this value. The
response threshold is a minimum response that must be met to allow peak confirmation.
Used only for target screening methods. Available only for XIC experiments.
Default: 5000
Range: 1000 or greater
Neutral Mass
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Mass calculated from the chemical formula. The neutral mass is the sum of all AMU
elements in the compound. This parameter is informational only; it is not used for peak
detection.
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Table 13. Compound parameters (Sheet 2 of 5)
Parameter
Description
Target Peaks
(Compound Detail page) The mass-to-charge ratio (m/z) of a target peak. The location of the center of a target
precursor ion peak in mass-to-charge ratio units.
Precursor Mass
In confirming peaks, the precursor mass is the same as the target peak precursor mass.
(Grid page)
Default: 0.0
Peak n Precursor Mass
Range: 10.000 to 2999.999
Available for all SRM experiments and for XIC experiments with the MS Order set to
MS2.
For mass values in XIC experiments when the MS Order is set to MS1, see Extracted Mass.
(Compound Detail page) The mass-to-charge ratio of the confirming peak. The location of the center of a target
quan ion peak in mass-to-charge ratio (m/z) units.
Product Mass
Default: 0.0
(Grid page)
Range: 10.000 to 2999.999
Peak n
Available for all SRM experiments and for XIC experiments with the MS Order set to
MS2.
For mass values in XIC experiments when the MS Order is set to MS1, see Extracted Mass.
(Compound Detail page) The mass-to-charge ratio of the confirming peak. The location of the center of a target
quan ion peak in mass-to-charge ratio (m/z) units.
Mass
Available only for SIM experiments.
(Grid page)
Peak n Mass
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Table 13. Compound parameters (Sheet 3 of 5)
Parameter
Description
(Compound Detail page) The mass-to-charge ratio of the target peak. The location of the center of a target quan ion
peak in mass-to-charge ratio (m/z) units.
Extracted Mass
You can enter a value for the Extracted Mass, but when you change the values for Formula,
(Grid page)
Adduct, Polarity, or Charge State, the application recalculates the Extracted Mass value,
Peak n Extracted Mass
overwriting the value you entered.
Default: 0.0
Range: 10.000 to 2999.999
Available only for XIC experiments with the MS Order set to MS1.
For mass values in XIC experiments when the MS Order is set to MS2, see Precursor Mass
or Product Mass.
(Compound Detail page) Positive or Negative
Polarity
(Grid page)
Peak n Polarity
(Compound Detail page) The adducts specified in the configuration file. To add or remove adducts from the default
lists, see “Specifying Adducts” on page 52.
Adduct
(Grid page)
Peak n Adduct
Adducts affect the calculated amount of the extracted mass by adding to or subtracting
from the neutral mass.
Adducts are polarity sensitive. Select the Polarity parameter before selecting the Adduct
value.
Default Positive valid values: Neutral, NH4, H, Na, K
Default Negative valid values: Neutral, H, H3C2O2, HCO2
Default: Neutral
(Compound Detail page) The charge state of the ion (the z value in m/z). For example, a charge state of 2 with a
negative polarity means that the compound has 2 more electrons than protons.
Charge State
(Grid page)
Peak n Charge State
Valid values: 1 through 10
Default: 1
MS Order
The confirming peaks come from the same scan (MS1) or are fragments from an adjacent
scan (MS2).
Available only for XIC experiments.
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Table 13. Compound parameters (Sheet 4 of 5)
Parameter
Description
Time Range Peak
The acquisition time specified as either a window around a specified RT value or as a
retention time range in minutes.
This parameter is visible only when you are editing a compound.
Window (sec)
The Window value used to determine the start and stop time for the acquisition. Available
only when the Time Range Peak option is not selected.
Range: 0.00 to 499.50
Start time = RT – (Window/2)
Stop time = RT + (Window/2)
Start and stop range: 0.00 to 999.00
(Compound Detail page) Retention time. The application uses RT and Window values to determine the start and
stop time for the acquisition. When the Time Range Peak option is selected, the RT value
RT (min)
is specified as a range.
(Grid page)
Range: 0.00 to 999.00
Peak n RT
Start time = RT – (Window/2)
Stop time = RT + (Window/2)
Start and stop range: 0.00 to 999.00
(Compound Detail page) Range: –400 to 400
Lens
(Grid page)
Peak n Lens
(Compound Detail page) The energy used when ions collide with the collision gas.
Available only for SRM experiments.
Collision Energy
(Grid page)
Peak n Collision Energy
Range: –250.00 to 250.00
(Compound Detail page) Range: 0.00 to 200.00
Energy Ramp
(Grid page)
Peak n Energy Ramp
Confirming Peaks
Confirming peak parameters are used only in quantitative methods.
(Compound Detail page) The mass-to-charge ratio of a precursor ion. The location of the center of a target precursor
ion peak in mass-to-charge ratio (m/z) units.
Precursor
Available only for SRM experiments or XIC experiments with the MS Order set to MS2.
(Grid page)
Default: 0.0
Peak n Confirming n
Range: 10.000 to 2999.999
Precursor
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Table 13. Compound parameters (Sheet 5 of 5)
Parameter
Description
(Compound Detail page) The mass-to-charge ratio of the quantitation ion. The location of the center of a target
quan ion peak in mass-to-charge ratio (m/z) units.
Product Mass
Available only for SRM experiments.
(Grid page)
Default: 0.0
Peak n Confirming n
Range: 10.000 to 2999.999
(Compound Detail page) The mass-to-charge ratio of the confirming peak. The location of the center of a target
quan ion peak in mass-to-charge ratio (m/z) units.
Mass
Available only for SIM experiments.
(Grid page)
Peak n Confirming n
Extracted Mass
(Compound Detail page) The mass-to-charge ratio of the target peak. The location of the center of a target quan ion
peak in mass-to-charge ratio (m/z) units.
Extracted Mass
Available only for XIC experiments.
(Grid page)
Default: 0.0
Peak n Confirming n
Range: 10.000 to 2999.999
Extracted Mass
(Compound Detail page) The energy used when ions collide with the collision gas.
Available only for SRM experiments.
Collision Energy
(Grid page)
Peak n Confirming n
Collision Energy
Range: –250.00 to 250.00
(Compound Detail page) Specifies whether the confirming peaks or fragments come from the same scan (MS1) or an
adjacent scan (MS2).
MS Order
Available only for XIC experiments.
(Grid page)
Peak n Confirming n MS
Order
Fragments
Fragment parameters are used for XIC experiment types in target screening methods. The
application uses fragments to define masses that are present in an adjacent scan (MS2).
(Compound Detail page) The mass-to-charge ratio of the target peak. The location of the center of a target quan ion
Extracted Mass
peak in mass-to-charge ratio (m/z) units.
Available only for XIC experiments.
Default: 0.0
Range: 10.000 to 2999.999
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Experiment Types
The TraceFinder application uses three experiment types: SRM, SIM, and XIC.
Each of these experiment types uses a different structure for the mass filter. The target peak
and confirming peak parameters for each experiment type are defined in the “Compound
Parameters” on page 101.
A compound database can include multiple experiment types for a single compound;
however, each compound name and experiment type combination must be unique.
SRM: Selected Reaction Monitoring
The SRM experiment type supports triple quadrupole LC/MS. The mass filter includes
precursor mass and narrow mass ranges to identify product masses. Imported compounds
with no experiment type are treated as SRM data.
Confirming peaks include values for precursor mass, product mass, and collision energy.
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SIM: Single Ion Monitoring
The SIM experiment type supports single quadrupole LC/MS, GC/MS, and Exactive
systems. The mass filter includes narrow mass ranges to identify product masses.
Confirming peaks include an extracted mass value.
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XIC: Extracted Ion Chromatogram
The mass filter is a single, full scan which is post-processed to extract a peak for the ions of
interest.
Confirming peaks include an extracted mass value and a choice of mass order: MS1 or MS2.
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Compound Database Names Mapped to CSV Column Names
Column names in an Excel spreadsheet do not always match the parameter names in the
compound database editor. The following table maps the parameter names for both the
Compound Detail page and the Grid page to the column headings in a CSV spreadsheet.
Table 14. CSV column names for compound parameters (Sheet 1 of 3)
Compound database parameter
CSV column heading
(Compound Detail page)
Compound
CompoundName
(Grid page)
Compound Name
(Compound Detail page)
Experiment
ExperimentType
(Grid page)
Experiment Type
Category
Category
CAS
CAS
Formula
ChemicalFormula
Ionization
Ionization
Response Threshold
ResponseThreshold
(XIC only)
Target Peaks
(Compound Detail page)
Precursor Mass
PrecursorMass
(SRM only)
(Grid page)
Peak n Precursor Mass
(Compound Detail page)
Product Mass
ProductMass
(SRM only)
(Grid page)
Peak n
(Compound Detail page)
Mass
ProductMass
(SIM only)
(Grid page)
Peak n Mass
(Compound Detail page)
Extracted Mass
Extracted Mass
(XIC only)
(Grid page)
Peak n Extracted Mass
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Table 14. CSV column names for compound parameters (Sheet 2 of 3)
Compound database parameter
CSV column heading
(Compound Detail page)
Product Mass
Mass
Extracted Mass
Extracted Mass
(when the Compound Detail page of a compound
database contains any combination of SRM, XIC, and
SIM experiments)
(Compound Detail page)
Adduct
Adduct
(Grid page)
Peak n Adduct
Polarity
Polarity
(Compound Detail page)
Charge State
ChargeState
(Grid page)
Peak n Charge State
Window
Window
(Compound Detail page)
RT (min)
RT
(Grid page)
Peak n RT
(Compound Detail page)
Collision Energy
CollisionEnergy
(SRM only)
(Grid page)
Peak n Collision Energy
(Compound Detail page)
Lens
Lens
(Grid page)
Peak n Lens
Energy Ramp
EnergyRamp
Confirming Peaks
(Compound Detail page)
Precursor
Confirm Precursor
(SRM and XIC only)
(Grid page)
Peak n Confirming n Precursor
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Table 14. CSV column names for compound parameters (Sheet 3 of 3)
Compound database parameter
CSV column heading
(Compound Detail page)
Product Mass
Confirm Product
(SRM only)
(Grid page)
Peak n Confirming n
(Compound Detail page)
Mass
Confirm Product
(SIM only)
(Grid page)
Peak n Confirming n Extracted
Mass
(Compound Detail page)
Extracted Mass
Confirm Extracted
(XIC only)
(Grid page)
Peak n Confirming n Extracted
Mass
(Compound Detail page)
Product Mass
Mass
Extracted Mass
Confirm Extracted
(when the Compound Detail page of a compound
database contains any combination of SRM, XIC, and
SIM experiments)
(Compound Detail page)
Collision Energy
Confirm Energy
(SRM only)
(Grid page)
Peak n Confirming n Collision
Energy
Fragments
Extracted Mass
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Fragment
(XIC only)
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Data Columns with Default Values
When you export compounds to a CSV file with the Export Only Columns with Data
option, the application writes only columns that contain nondefault data for at least one
compound. This option does not export columns that contain only default data.
When you import compounds from a CSV data file that has missing columns, the application
replaces the missing columns and uses default values for all compounds.
Table 15. Default values for compound parameters
CDB parameter
Default value
Compound Detail
Formula
Blank
CAS
Blank
Category
Blank
Ionization
None
Response Threshold
(XIC only)
5000
Target Peaks
Precursor Mass
Blank
Collision Energy
0
Adduct
Neutral
Lens
0
Energy Ramp
0
Confirming Peaks
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0
Collision Energy
Blank
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Working with Instrument Methods
An instrument method is a set of experiment parameters that define the operating settings for
an autosampler, mass spectrometer, and so on. Instrument methods are saved as file
type .meth.
IMPORTANT Do not open the Thermo Foundation Instrument Configuration window
while the TraceFinder application is running.
Follow these procedures:
• To open the Instrument View
• To create a new instrument method
• To create a new multiplexing instrument method
• To open an instrument method
• To import an instrument method
 To open the Instrument View
1. Click Method Development from the navigation pane.
The Method Development navigation pane opens.
2. Click Instrument View.
The Instrument View opens.
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Working with Instrument Methods
 To create a new instrument method
1. Choose File > New Instrument Method from the main menu.
The Thermo Xcalibur Instrument Setup window opens.
Figure 25. Example instrument setup showing multiple configured instruments
2. Click the icon for the instrument that you want to use for the method.
3. Edit the values on the instrument page.
4. From the main menu in the Thermo Xcalibur Instrument Setup window, choose File >
Save As.
The Save As dialog box opens.
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5. Select an instrument method name to overwrite, or type a new name for the instrument
method, and click Save.
The File Summary Information dialog box opens.
6. (Optional) Type a comment about the new instrument method.
7. Click OK.
The TraceFinder application saves the new instrument method in the following folder:
…\Xcalibur\methods
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 To create a new multiplexing instrument method
1. Choose File > New Instrument Method from the main menu.
The Thermo Xcalibur Instrument Setup window opens.
Figure 26. Example instrument setup showing a configured multiplexed instrument
2. Click the icon for the instrument that you want to use for the method.
3. Edit the values for the instrument method.
For information about specifying multiplexing values, refer to the documentation for
your multiplexed instrument.
4. Specify the channels that you want to use for acquisition, as in this example:
5. From the main menu in the Thermo Xcalibur Instrument Setup window, choose File >
Save As.
The Save As dialog box opens.
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6. Select an instrument method name to overwrite or type a new name for the instrument
method, and click Save.
The File Summary Information dialog box opens.
7. (Optional) Type a comment about the new instrument method.
8. Click OK.
The TraceFinder application saves the new instrument method in the following folder:
…\Xcalibur\methods
 To open an instrument method
1. Click Open Instrument Method in the Instrument View navigation pane.
An instrument method browser opens.
2. In the browser, do one of the following:
• Select an instrument method from the list and click Open.
• Click Xcalibur Instrument Method, select a method from the list of recent
methods, and click Open.
The selected method opens in the Thermo Xcalibur Instrument Setup window. You can
edit this method and save the changes, or you can save this method with another name.
Note To open Help for any of your configured instruments, click Help on the
instrument page.
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 To import an instrument method
1. From the main menu, choose Instrument View > Import Published Method.
The Import Published Method dialog box opens. This dialog box lists the master
methods in the Published Master Methods folder. You can import instrument methods
that are associated with these published master methods.
2. Select a method that includes the instrument method that you want to import.
For instructions about importing the master methods for a quantitation method, see
“Importing Published Master Methods” on page 265.
For instructions about importing the master methods for a screening method, see
“Importing Published Master Methods” on page 309.
3. Click Import.
The Save Instrument Method dialog box opens.
4. Do one of the following:
Type a new name for the instrument method and click OK.
–or–
Select an instrument method name to overwrite and click Overwrite.
The application reports that the method successfully imported.
You can use any of the Open Instrument Method commands to open this method just as you
would an instrument method that you created.
5
Using the Method Development Mode for
Quantitation Methods
This chapter includes method development tasks for creating and editing a quantitative
method. When user security is activated, you must have Method Development Access
permission before accessing these features.
Contents
• Opening a Master Method
• Starting a New Master Method
• Editing a Master Method
• Saving a Master Method to a New Name
• Creating a Method Template
• Importing Published Master Methods
• Exporting Mass Data
The TraceFinder application uses a master method to specify the nature and types of
acquisition, processing, and reporting that occur with a batch of samples. When you are
testing for compounds in an assay, you can create a method designed specifically for your
application.
A quantitation master method contains a list of compounds and settings for detecting,
processing, and reporting those compounds.
When you create a master method, the TraceFinder application uses the method to determine
how the software works with a set of samples to provide a set of meaningful results. The
application uses an instrument method to define how raw data is acquired. The rest of the
master method defines how the raw data is processed, how the flags information displays the
results, and how the reporting functionality defines the output for your data and results.
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The TraceFinder application applies your master method to a batch, which is a list of one or
more samples to be processed and reported. Together, the master method and batch provide a
workflow-oriented approach to the data processing and information reporting for batches of
samples.
To speed up the creation of master methods, you can create a method template. Using a
method template helps you to develop methods faster because the TraceFinder application
saves all of your commonly used method settings in a template, such as the number of
confirming ions or the use of data-dependent scans.
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Figure 27. Method Development navigation pane
Available only when you activate the Intelligent Sequencing
option in the Configuration console.
Table 16. Method Development navigation pane commands
Command
Description
Method View
Displays the Method View for the master method.
Acquisition
Displays the Acquisition page of the Method View. See “Editing the Acquisition Page” on
page 146.
Quantitation
Processing
Displays the Processing page of the Method View. See “Editing the Processing Page” on
page 151.
Compounds
Displays the Compounds page of the Method View. See “Editing the Compounds Page” on
page 155.
QAQC
Displays the QAQC page of the Method View. See “Editing the QAQC Page” on page 230.
Groups
Displays the Groups page of the Method View. See “Editing the Groups Page” on page 240.
Intel Seq
Displays the Intelligent Sequencing page of the Method View. See “Editing the Intelligent
Sequencing Page” on page 243. Available only when you activate the Intelligent Sequencing
option in the Configuration console.
Reports
Displays the Reports page of the Method View. See “Editing the Reports Page” on page 248.
Compound
Database
See “Working with the Compound Database” on page 76.
Instrument View
See “Working with Instrument Methods” on page 113.
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Opening a Master Method
Opening a Master Method
Use the TraceFinder application to open a master method that was created and saved in the
current TraceFinder application or converted from previous versions of TraceFinder. To
convert legacy methods, see “Converting Legacy Data” on page 18.
 To open a quantitation method in the Method Development mode
1. Click Method Development in the navigation pane.
The Method Development navigation pane opens.
For descriptions of all the features in the Method Development navigation pane, see
“Starting a New Master Method” on page 124.
2. Choose File > Open > Master Method from the main menu.
Tip You can also open one of your most recently used master method files. Choose
Files > Recent Files > Method.
The Open Master Method dialog box opens, displaying all available methods.
Figure 28. Open Master Method dialog box
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Table 17. Open Master Method dialog box parameters
Parameter
Description
Method
Name of the methods for the selected type.
Type
Type of method: Quan or Screening.
Date Changed
Date the method was last updated.
Size
Size in megabytes.
Domain
TraceFinder domain for which the method was created.
Type
Type of method to display: Quan, Screening, or Any.
Path
Path to the selected method in the
TraceFinderData\32\Methods folder.
3. Select Quan in the Type list.
The method list displays all quantitation methods.
4. Select a quantitation master method and click Open.
The Acquisition page for the selected method opens. For detailed descriptions of all the
features on the Acquisition page, see “Acquisition Page for a Quantitation Method” on
page 149.
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Starting a New Master Method
To create or start a specific method, select as applicable from one of the four different
quantitation method procedures (or techniques) in the Create Master Method dialog box:
• Creating a New Method with Method Forge
• Importing an Xcalibur Master Method
• Creating a Blank Method
• Selecting Compounds from the Compound Database
Then, use the features of the Method View to complete and save the master method.
To open the Create Master Method dialog box, choose File > New > Master Method from
the main menu.
Figure 29. Create Master Method dialog box
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Creating a New Method with Method Forge
With Method Forge, you can create a new master method by manually selecting peaks,
selecting multiple compounds, renaming peaks, or comparing mass spectra from the library
searches. You can also choose to let the TraceFinder application automatically create a master
method for you. For detailed descriptions of all the Method Forge parameters, see “Method
Forge Dialog Box” on page 133.
When the TraceFinder application automatically creates a master method for you, it performs
the following functions:
• Reviews your raw data file and identifies compounds that are present in your sample.
• Uses your mass spectral reference libraries to assign compound names and CAS numbers.
• Uses mass spectral information to select potential quantification and confirming ions and
a reference mass spectrum for the compound.
Note When the identified peak is from an analog trace, the application does not perform
a library search and does not identify any confirming ions.
Follow these procedures:
• To automatically select compounds to create a new method
• To manually select compounds to create a new method
 To automatically select compounds to create a new method
1. From the File menu, choose New > Master Method.
The Create Master Method dialog box opens. To view all available ways to create a master
method, see “Create Master Method dialog box” on page 124.
2. Select the Use Method Forge option and click OK.
The Method Forge dialog box opens. For detailed descriptions of all the features in the
Method Forge dialog box, see “Method Forge Dialog Box” on page 133.
Use Method Forge to create a master method from an existing raw data file or to create a
new raw data file to use for the master method.
Each method requires a processing method template. The application displays all saved
method templates in the template list.
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3. To select a processing method template, do one of the following:
• Click Open Method Template Editor to create and save a new method template.
See “Creating a Method Template” on page 255.
• Select a method template from the template list, and click Open Method Template
Editor to edit and save the method template.
• Select a method template from the template list.
The selected template is now selected by default each time you open the Method Forge
dialog box until you restart the TraceFinder application. To view the parameters for each
available method template, hold your cursor over the template name, as in this example:
4. Select the Name the Master Method check box and type a name for your master method.
You can enter a new method name, or you can enter an existing method name to
overwrite when you create the method. If you do not select this option, the method is
named for the raw data file used to create the method.
Note When the Name the Master Method check box is selected, you must enter a
method name. To let the application name the method with the raw data file name,
clear the Name the Master Method check box.
5. Select the Automatically Create the Master Method check box.
6. Specify a raw data file by doing one of the following:
a. In the Raw File Selection area, select the Use an Existing Raw Data File option.
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b. Click the browse button and locate a raw data file to use for the method.
c. Go to step 8.
–or–
a. In the Raw File Selection area, select the Acquire a New Raw Data File option.
b. From the Instrument method list, select a method (.meth) file to use for acquiring the
data.
c. In the Raw Filename box, type the name of the file where the TraceFinder application
will write the raw data file.
d. In the Path box, type a path or click the browse button and locate a folder where the
application will save the raw data file.
e. (Optional) Type a comment about the acquired sample or the data file.
7. To acquire a new raw data file, do one of the following:
Select the Manual Injection option.
–or–
Specify the autosampler settings:
a. Select the Use Autosampler option.
b. In the Vial Position box, type a vial position.
c. In the Injection Volume box, type an injection volume.
Range: 0.1 to 2000 μL
8. To automatically create the master method, click OK (or Overwrite).
As the Method Forge creates the method, it displays the following status bars:
• For analog peaks, the Method Forge displays the detected peak as [email protected](RT)Analog.
The Method Forge does not perform a library search for peaks found in analog traces.
• For mass spectral peaks, the Method Forge process searches the associated libraries
and displays the identified compound names instead of the peak times.
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When the acquisition is completed, Method Forge performs peak detection, library
searching (except for analog peaks), and identification of characteristic ion and reference
spectra. Method Forge then loads this information into a new master method. This
process occurs immediately if you selected a previously acquired raw data file.
9. From the Instrument Method list, select an instrument method.
10. From the Qualitative Peak Processing Template list, select a method template for
performing peak detection on quantitative samples following target compound analysis.
11. (Optional) From the Background Subtraction Range Option list, select how you want the
background subtraction range determined from one of these options:
• Before Peak: Averages and subtracts a specified number of scans before the apex of
the peak.
• After Peak: Subtracts a specified number of scans following the apex of the peak.
• Both Sides of Peak: Subtracts a specified number of scans from each side of the apex
of the peak.
When you create a reference spectrum with background subtraction, the application uses
the selected method to conduct background subtraction of peak spectra during
quantitative processing and reports the background-subtracted reference spectrum
(indicated with BS in the scan heading) as the last scan for each compound in the
Quantitation Report - 2 report. The application does not use background subtraction
with qualitative processing.
12. In the Stepoff Value box, enter a number.
The TraceFinder application uses this offset value to average and subtract scans that are
not adjacent to the apex of the peak. For example:
If you entered 3 in the Number of Scans To Subtract box and the stepoff value is 5, the
TraceFinder application ignores the first 5 scans to the left of the peak and applies the
averaging and subtraction to the 6th, 7th, and 8th scans to the left of the peak.
13. To save the new method, choose File > Save from the main menu.
For a detailed description of how to modify all the parameters in a master method, see
“Editing a Master Method” on page 144.
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 To manually select compounds to create a new method
1. From the File menu, choose New > Master Method.
The Create Master Method dialog box opens. See “Create Master Method dialog box” on
page 124.
2. Select the Use Method Forge option and click OK.
The Method Forge dialog box opens. For detailed descriptions of all the features in the
Method Forge dialog box, see “Importing an Xcalibur Master Method” on page 135.
Each method requires a qualitative peak processing template. The application displays all
saved method templates in the template list.
3. To select a qualitative peak processing template, do one of the following:
• Click Open Method Template Editor to create and save a new method template.
See “Creating a Method Template” on page 255.
• Select a method template from the template list, and click Open Method Template
Editor to edit and save the method template. The application saves the methods to
the following folder:
…\TraceFinderData\32\Templates\Methods\General folder
• Select a method template from the template list.
The selected template is now selected by default each time you open the Method Forge
dialog box until you restart the TraceFinder application.
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To view the parameters for each available method template, hold your cursor over the
template name, as in this example:
4. Select the Name the Master Method check box and type a name for your master method.
You can enter a new method name, or you can enter an existing method name and
overwrite it when you create the method. If you do not select this option, the method is
named for the raw data file used to create the method.
IMPORTANT When the Name the Master Method check box is selected, you must
enter a method name. To let the application name the method with the raw data file
name, clear the Name the Master Method check box.
5. Ensure that the Automatically Create the Master Method check box is cleared.
6. To select a raw data file, browse to the file location.
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7. To manually create the master method, click OK (or Overwrite).
The method forge results view opens, listing all peaks found in the raw data file.
For each peak listed in the RT column, the application displays a list of possible matches
in the Libraries pane. The TraceFinder application selects the best match, displays the
name in the Compound Name list, and displays the peak spectrum for that compound in
the first Libraries pane.
Figure 30. Method forge results view
Best match compound spectra
Peaks found in raw data file
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8. (Optional) To use a library compound other than the compound chosen by the
TraceFinder application, do the following:
a. Select the peak in the RT column.
b. In the Libraries pane, scroll to the spectrum for the compound that you want to use.
c. Select the check box in the header of the spectrum pane.
Selected
compound
d. Repeat these steps for each peak that you want to replace.
9. In the Compound Name list, use the CTRL or SHIFT keys to select each compound that
you want to include in the method compound.
Note When you select multiple compounds, the method forge results view does not
display any spectrum panes.
10. (Optional) To exit the method forge results view without creating a method, click
Cancel.
The method forge results view closes and the application returns to the Method View
without creating a method.
Note To return to the method forge results view to create a method from the same
results, choose Method View > View Method Forge Results from the main menu.
11. Click Create.
The TraceFinder application uses all selected compounds to create the method and
displays the Acquisition page of the Method View. For detailed descriptions of all the
features on the Acquisition page, see “Acquisition Page for a Quantitation Method” on
page 149.
12. From the Instrument Method list, select an instrument method.
13. To save the new method, choose File > Save from the main menu.
For a detailed description of how to modify a master method, see “Editing a Master
Method” on page 144.
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Method Forge Dialog Box
Use the Method Forge dialog box to create a new master method.
Figure 31. Method Forge dialog box
Table 18. Method Forge dialog box parameters (Sheet 1 of 2)
Parameter
Description
Method template selection
Open Method
Template Editor
Opens the Method Template Editor, where you can edit the currently selected method
template. See “Creating a Method Template” on page 255.
Template
Specifies the method template to use to create this master method. All methods require a
method template. To view the parameters of each template, hold your cursor over the
method name. See the Method Template Parameters example in “To automatically select
compounds to create a new method” on page 125.
Name the Master
Method
Specifies the name for the new master method. If you do not specify a method name, the
application uses the raw data file name for the method.
Automatically Create
the Master Method
Specifies that when acquisition is completed, Method Forge performs peak detection, library
searching, and identification of characteristic ion and reference spectra. This information is
loaded into a new master method. This process occurs immediately when you specify an
existing raw data file.
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Table 18. Method Forge dialog box parameters (Sheet 2 of 2)
Parameter
Description
Raw file selection
Use an Existing Raw
Data File
Activates the Raw Filename box where you can select a raw data file used in creating the
master method.
Acquire a New Raw
Data File
Activates functions to acquire data to create a raw data file used in creating the master
method.
Instrument
Method
Specifies the saved method (.meth) file used for acquiring the data.
Raw Filename
Specifies the file name where the TraceFinder application writes the raw data.
Path
Specifies the location where the TraceFinder application saves the raw data file.
Sample Comment
(Optional) Specifies a comment about the acquired sample or the data file.
Manual Injection
Performs a manual acquisition.
Use Autosampler
Performs an autosampler acquisition.
Vial Position
Specifies the tray vial number used for the autosampler acquisition.
Injection Amount
Specifies the volume (in milliliters) injected by the autosampler acquisition.
Check Instruments
Opens the Submit to Acquisition dialog box that prompts you to prepare the instrument
before you acquire the sample used to create a method. Available only when you select the
Acquire a New Raw Data File option.
Function button
Overwrite
Overwrites the specified master method name. This function is activated only when the
specified master method name already exists.
OK
Creates a master method using the data and parameters that you specified.
Cancel
Closes Method Forge and does not create a master method.
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Importing an Xcalibur Master Method
You can create a new master method from an existing Xcalibur processing method.
 To import an Xcalibur master method
1. Choose File > New > Master Method from the main menu.
The Create Master Method dialog box opens. To view all available ways to create a master
method, see “Create Master Method dialog box” on page 124.
2. Select the Import Xcalibur Processing Method option and click OK.
The Import an Xcalibur Method dialog box opens.
3. For the Xcalibur Method to Import box, browse to the location of the Xcalibur processing
method file, and open the file.
The TraceFinder application imports the compound information from the Xcalibur
method file.
4. (Optional) For the Raw Data File to Associate box, browse to the location of a raw data
file to associate with the method (or select from the list of previously associated raw data
files), and open the file.
To assure that this raw data file is always available to the method (for example, if you
move the method to another system), the application saves the raw data file in the
Methods folder:
…\TraceFinderData\32\Methods\Methodname
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5. (Optional) Change the number of decimal places in the Filter Precision box.
You can set the number of filter precision decimal places to any integer between 2 and 5,
inclusive.
Note When you select a raw data file to associate, the application reads the filter
precision from the file and this feature is not available.
6. (Optional) Change the number of decimal places in the Mass Precision box.
You can set the number of mass precision decimal places to any integer between 2 and 6,
inclusive.
Note When you associate a raw data file, the application reads the filter precision
from the associated file so that you cannot change the Filter Precision value.
7. Click OK.
The TraceFinder application adds all compounds found in the imported Xcalibur method
and displays the Acquisition page of the Method View. For detailed descriptions of the
features on the Acquisition page, see “Acquisition Page for a Quantitation Method” on
page 149.
8. From the Instrument Method list, select an instrument method.
9. To save the new method, choose File > Save from the main menu.
For a detailed description of how to modify a master method, see “Editing a Master
Method” on page 144.
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Creating a Blank Method
You can use the compounds in a previously acquired raw data file to create a new blank master
method.
 To create a blank method
1. From the File menu, choose New > Master Method.
The Create Master Method dialog box opens. To view all available ways to create a master
method, see “Create Master Method dialog box” on page 124.
2. Select the Create Blank Quantitation Method option and click OK.
The Method View for a new, unnamed method opens. This method has no associated
data. You can use the compounds in a previously acquired raw data file to create a new
master method.
3. From the Method View menu, choose Associate a Raw Data File.
The Associate a Raw Data File dialog box opens.
Browse to a data file.
Select a previously associated data file.
4. Browse to a raw data file to associate with the method (or select from the list of previously
associated raw data files) and open the file.
To assure that this raw data file is always available to the method (for example, if you
move the method to another system), the application saves the raw data file in the
Methods folder:
…\TraceFinderData\32\Methods\Methodname
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5. Select the update options to use for creating your method:
• Update Instrument/Trace Selections: Reads the Detector and Trace options from
the associated raw data file. On the Detection page, only detector types and traces
that are defined in the raw data file are available. For detailed descriptions of the
available Detector and Trace values, see “Signal” on page 176.
• Update Target Ion Ratio Values: Reads the ion ratio values from the associated raw
data file.
• Update Scan Filters for All Peaks:
–
Yes, All Peaks updates all peaks to use the scan filters from the associated raw
data file.
–
Yes, Only Peaks Without Filters updates only peaks without scan filters to use
the scan filters from the associated raw data file; it does not override any existing
scan filter.
• Automatically Set Reference Spectrum: Reads a reference spectrum from the
associated raw data file.
When you select Yes, with Background Subtraction, the application uses the
background-subtracted reference spectrum during quantitative processing and
reports the background-subtracted reference spectrum (indicated with BS in the scan
heading) as the last scan for each compound in the Quantitation Report - 2 report.
Note The background subtraction option is available only when you select a
background subtraction method on the Acquisition page in the master method.
See “Editing the Acquisition Page” on page 146.
Options that are set to No use the standard values in the method.
6. Click OK.
The TraceFinder application displays the Acquisition page of the Method View.
7. Click Compounds in the navigation pane.
The method must include at least one compound.
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8. Click the Detection tab.
The Detection page shows an empty Compound list and displays the chromatographic
data for the compounds in the raw data file.
9. Select a filter from the Filter list.
10. Select the peak in the chromatogram that represents the compound that you want to add
to the method.
11. Right-click and choose Add This Peak as New Compound from the shortcut menu.
The TraceFinder application performs a library search for the selected compound. The
application uses the first match it finds as the compound name, the base peak of the mass
spectrum as the quantitative peak, and the second and third largest ions as the confirming
ion peaks.
Note When the peak is from an analog trace, the application does not perform a
library search and does not identify any confirming ions.
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If the name of the first match is already in the library, the Add New Compound dialog
box opens.
12. (Optional) Do the following:
a. To use a compound other than the compound already in the library, scroll to the
spectrum for that compound and select the compound name in the title bar of the
spectrum pane.
Selected
compound
b. In the Type of Compound To Add list, select a compound type.
c. Click OK.
13. Repeat this procedure for each compound that you want to add to the method.
For detailed descriptions of all the features on the Detection page, see “Editing the
Compounds Page” on page 155.
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14. Click Acquisition in the navigation pane.
The Acquisition page for the method opens. For detailed descriptions of all the features
on the Acquisition page, see “Acquisition Page for a Quantitation Method” on page 149.
15. From the Instrument Method list, select an instrument method.
16. To save the new method, choose File > Save from the main menu and name the method.
For a detailed description of how to modify the parameters in a master method, see
“Editing a Master Method” on page 144.
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Starting a New Master Method
Selecting Compounds from the Compound Database
You can select compounds from the compound database to create a new master method.
 To select compounds from the compound database
1. Choose File > New > Master Method from the main menu.
The Create Master Method dialog box opens. To view all available ways to create a master
method, see “Create Master Method dialog box” on page 124.
2. Select the Select Compounds from CDB option and click OK.
The Select Compounds from Database dialog box opens, listing all the compounds
defined in the compound database.
3. Select the check box for each of the compounds that you want to add to the method.
4. To select all compounds in the database, select the Compound check box at the top of
the list.
5. Click Apply.
The TraceFinder application adds the selected compounds to the method.
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6. Click Acquisition in the navigation pane.
The Acquisition page for the method opens. For detailed descriptions of all the features
on the Acquisition page, see “Acquisition Page for a Quantitation Method” on page 149.
7. From the Instrument Method list, select an instrument method.
8. To save the new method, choose File > Save from the main menu and name the method.
For a detailed description of how to modify a master method, see “Editing a Master
Method” on page 144.
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Editing a Master Method
You can open a master method to view or edit the compounds, method instructions, and
reporting options.
This section includes instructions for the following tasks:
• Modifying Retention Times
• Editing the Acquisition Page
• Editing the Processing Page
• Editing the Compounds Page
• Editing the QAQC Page
• Editing the Groups Page
• Editing the Intelligent Sequencing Page
• Editing the Reports Page
Modifying Retention Times
Use the Adjust Retention Times dialog box from any page in the Method View or Local
Method view.
 To modify retention times in a method
1. Do one of the following:
• Choose Method View > Adjust Retention Times from the main menu of the
Method View in the Method Development mode.
• Choose Local Method > Adjust Retention Times from the main menu of the Local
Method view in the Analysis mode.
The Adjust Retention Times dialog box opens.
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2. Do one of the following:
a. Select the Absolute option.
b. Specify a positive or negative value to increase or decrease the expected retention
times.
Valid values: –100.00 through 100.00
c. Click OK.
The application increases or decreases the expected retention times for all compounds
in the method by the specified number of minutes.
–or–
a. Select the Relative option.
b. Specify a positive or negative value to increase or decrease the expected retention
times.
Valid values: –100.00 through 100.00
c. Click OK.
The application increases or decreases the expected retention times for all compounds
in the method by the specified percentage.
–or–
a. Select the By File option.
Note This option is available only from the Local Method view after you have
processed the samples in a batch.
b. Click Select.
The Adjust Retention Time by File dialog box opens, displaying all processed
samples.
c. Select the sample whose retention times you want to use in the method.
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d. Click Select.
e. Click OK.
For each detected peak in the selected, processed sample, the application overwrites
the retention times for the matching compounds in the method. If the method
contains compounds not detected in the selected sample, the retention times for
those compounds are not affected.
Editing the Acquisition Page
The Acquisition page defines basic information about the master method. For detailed
descriptions of all the features, see “Acquisition Page for a Quantitation Method” on
page 149.
Follow these procedures:
• To open the Acquisition page
• To specify Acquisition information for a master method
• To edit an instrument method
 To open the Acquisition page
Click Acquisition in the Method View navigation pane.
Available only when you activate the
Intelligent Sequencing option in
the Configuration console.
 To specify Acquisition information for a master method
1. In the Lab Name box, type the name to be displayed on the top of each printed, saved, or
exported report.
The default name is Default Laboratory.
2. In the Assay Type box, type the assay type to be targeted by the method.
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3. From the Injection Volume box, select an injection volume (between 0.1 and 2000 μL) to
be used for sample injection.
Use the up/down arrows to change the volume in increments/decrements of 1 μL, or use
the keyboard to enter non-integer injection volumes.
IMPORTANT The TraceFinder application uses this injection volume in the master
method, not the injection volume from the instrument method.
4. From the Mass Precision box, select a precision value (between 2 and 6 inclusive) as the
number of decimal places to be used in reports and in peak and spectrum displays.
5. From the Ion Range Calc Method list, select a method for calculating the ion ratio range
windows.
When you select Level, the TraceFinder application displays a Use Level list where you
can choose a calibration level. To define the available calibration levels on the
Compounds page, see “Editing the Compounds Page” on page 155.
 To edit an instrument method
1. From the Instrument Method list on the Acquisition page, select an instrument method.
2. To edit the selected instrument method, click Edit.
The Thermo Xcalibur Instrument Setup dialog box opens. This example of an
instrument setup shows multiple configured instruments.
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Figure 32. Thermo Xcalibur Instrument Setup window
3. Edit the values on the instrument page for your instrument.
4. From the main menu in the Thermo Xcalibur Instrument Setup dialog box,
choose File > Save and then choose File > Exit.
The TraceFinder application returns you to the Acquisition page. See Acquisition Page for
a Quantitation Method.
5. To update any changes that were made to the instrument method after you created this
master method, click Update.
The Update Instrument Method? dialog box opens.
6. Choose one of the following options:
• Send to System Methods: Overwrites the instrument method in the
C:\TraceFinderData\32\Methods folder with the current instrument method.
• Get from System Method: Overwrites the current instrument method with the
instrument method in the C:\TraceFinderData\32\Methods folder.
• Cancel: Makes no changes to the instrument method in the current master method.
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Acquisition Page for a Quantitation Method
Use the features on the Acquisition page to define basic information about the master
method.
Figure 33. Acquisition page for a quantitation method
Table 19. Acquisition page parameters (Sheet 1 of 2)
Parameter
Description
Lab Name
Specifies the laboratory name to be displayed on the top of each
printed, saved, or exported report.
Default: Default Laboratory
To specify this default laboratory name, see “Specifying Application
Defaults” on page 35.
Assay Type
Specifies the name for the analysis type to be targeted by the
method. The assay type associates the method with the analysis of a
compound or specific class of compounds (for example, you might
use an assay type of PAH for the analysis of Polynuclear Aromatic
Hydrocarbons).
Injection Volume
Specifies the system uses the injection volume (in μL) for sample
injection. For a more detailed explanation, refer to the
documentation for the autosampler.
The injection volume in the master method overrides the injection
volume in the instrument method. The injection volume in the
batch overrides the injection volume in the master method.
Range: 0.1 to 2000 μL
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Table 19. Acquisition page parameters (Sheet 2 of 2)
Parameter
Description
Mass Precision
Specifies the number of decimal places used in reports and in peak
and spectrum displays.
Valid values: Integers from 2 to 6, inclusive.
Ion Range Calc
Method
Specifies the selected ion range calc method used to calculate the ion
ratio range windows: Manual (default), Average, Level, or Weighted
average. When you select Level, an additional list is displayed where
you can select a calibration level amount. To define these calibration
levels on the Compounds page, see “Editing the Compounds Page”
on page 155.
Instrument Method
Specifies the instrument method used for acquiring samples.
Edit
Opens the Thermo Xcalibur Instrument Setup dialog box where
you can edit the instrument method.
Update
Specifies one of the following:
Send to System Methods: Overwrites the system method in the
C:\TraceFinderData\32\Methods folder with the current
instrument method.
Get from System Methods: Overwrites the current instrument
method with the system method in the
C:\TraceFinderData\32\Methods folder.
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Editing the Processing Page
The Quantitation – Processing page defines basic information about the master method. For
detailed descriptions of all the features, see “Processing Page for a Quantitation Method” on
page 154.
Follow these procedures:
• To select a qualitative peak processing template
• To set automated background subtraction options
• To specify mass tolerance
• To include data-dependent filters
• To specify a threshold override
 To open the Processing page
Click Processing in the Method View navigation pane.
Available only when you activate the
Intelligent Sequencing option in
the Configuration console.
 To select a qualitative peak processing template
In the Qualitative Peak Processing Template list, select the template that you want to use
to perform peak detection on quantitative samples after compound analysis is complete.
The application uses the libraries in this template to identify compounds for the method.
If there is no library selected in the method template, the application identifies found
peaks as [email protected] on the Compounds page. To specify the libraries that are including in
a qualitative peak processing template, open the template in the Method Template Editor,
and then follow the instructions “To identify the peaks” on page 257.
The application lists all method templates (.pmtx file extensions) in the following folder:
…\TraceFinderData\32\Templates\Methods\General
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 To set automated background subtraction options
1. In the Background Subtraction Range Option list, select how you want the subtraction
range determined from the following options:
• Before Peak: Averages and subtracts a specified number of scans before the apex of
the peak.
• After Peak: Subtracts a specified number of scans after the apex of the peak.
• Both Sides of Peak: Subtracts a specified number of scans from each side of the apex
of the peak.
When you create a reference spectrum with background subtraction, the TraceFinder
application uses the selected method to conduct background subtraction of peak spectra
during quantitative processing. The application then reports the background-subtracted
reference spectrum (indicated with BS in the scan heading) as the last scan for each
compound in the Quantitation Report - 2 report. It does not use background subtraction
with qualitative processing.
2. In the Number of Scans to Subtract box, enter a number.
The TraceFinder application subtracts this number of scans from the background after
averaging. When you select the Both Sides of Peak option, the application subtracts this
number of scans from each side of the peak.
3. In the Stepoff Value box, enter a number.
The TraceFinder application uses this offset value to average and subtract scans that are
not adjacent to the apex of the peak, as in this example:
Before Peak example:
When the Number of Scans to Subtract equals 3 and the Stepoff Value equals 5, the
TraceFinder application ignores the first 5 scans to the left of the peak and applies the
averaging and subtraction to the 6th, 7th, and 8th scans to the left of the peak.
After Peak example:
When the Number of Scans to Subtract equals 3 and the Stepoff Value equals 5, the
TraceFinder application ignores the first 5 scans to the right of the peak and applies the
averaging and subtraction to the 6th, 7th, and 8th scans to the right of the peak.
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Both Sides of Peak example:
When the Number of Scans to Subtract equals 3 and the Stepoff Value equals 5, the
TraceFinder application ignores the first 5 scans to the left of the peak and the first 5 scans
to the right of the peak. Then it applies the averaging and subtraction to both the 6th,
7th, and 8th scans to the left of the peak and the 6th, 7th, and 8th scans to the right of
the peak.
 To specify mass tolerance
1. Select the units of measure that you want to use.
2. Specify the number of millimass units or parts per million to use as the m/z ± tolerance
value.
The application applies this mass tolerance to the extracted chromatograms.
 To include data-dependent filters
Select the Include Data Dependent Filters option.
The application includes data-dependent filters when you specify filters in the method.
See “Signal” on page 176.
Data-dependent filters are indicated with a “d”.
Data-dependent filter
When you process a sample using a data-dependent filter, the application uses the TIC
trace to find all data-dependent full scans, lists them, and performs a library search against
the data-dependent MS/MS or MSn scan.
 To specify a threshold override
1. Select the Threshold Override check box.
2. In the box, type a value for creating a threshold guide to overlay on compounds in the
Comparative View in the Data Review mode.
This threshold value overrides the Threshold value specified on the QAQC – Threshold
page. See “Threshold” on page 237.
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Processing Page for a Quantitation Method
Use the features on the Processing page to define basic information about the master method.
Figure 34. Processing page for a quantitation method
Table 20. Processing page parameters
Parameter
Description
Qualitative Peak
Processing Template
Specifies the template used to perform peak detection on
quantitative samples following compound analysis.
Background Subtraction Specifies the range used for background subtraction.
Range Option
Valid values: None, Before Peak, After Peak, Both Sides of Peak
Default: None
Number of Scans To
Subtract
Valid values: Even numbered integers
Default: 0
Stepoff Value
Offset from the selected peak to the first subtracted peak.
Mass Tolerance
Specifies the upper limit of MMU or PPM.
Default: 500
Range: 0.1 through 50 000
• (Default) MMU (millimass units): MMU is a static
calculation to the extracted mass.
• PPM (parts per million): PPM is a variable calculation
dependent on the actual mass. The smaller the mass, the
narrower the tolerance range. The larger the mass, the wider
the tolerance range.
Include Data Dependent Specifies that the method includes data-dependent filters.
Filters
Available only for quantitation methods.
Threshold Override
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Overrides the Threshold value specified on the QAQC –
Threshold page.
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Editing the Compounds Page
Use the Compounds page to set all parameters for identifying, detecting, and quantifying the
target compound list.
 To open the Compounds page
Click Compounds in the Method View navigation pane.
Available only when you activate the
Intelligent Sequencing option in
the Configuration console.
From the Compounds page of the Method View, you can access the following pages:
Acquisition List
See also Acquisition List.
Identification
See also Identification page parameters.
Detection
See also Detection page panes.
Calibration
See also Calibration page parameters.
Calibration Levels
See also Calibration Levels page parameters.
Chk Std Levels
See also Chk Std Levels page parameters.
Real Time Viewer
See also Real Time Viewer page parameters.
Each page on the Compounds page (except the Acquisition List and Real Time Viewer pages)
uses a right-click shortcut menu. See “Using the Shortcut Menu Commands” on page 225.
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Acquisition List
The Acquisition List page displays all compounds defined for the current method in a display
similar to the Compound Database view. From the Acquisition List page, you can add
additional compounds from the Compound Database or delete compounds from the method.
See Acquisition List page.
For detailed descriptions of all the features in the Compound Database views, see “Working
with the Compound Database” on page 76.
 To remove a compound from the method
1. Select the compound in the Compound list.
2. Click the Remove Compound icon,
.
3. To confirm that you want to delete the selected compound, at the prompt, click OK.
The application removes the selected compound and all its peak information.
4. To remove multiple compounds, use the CTRL or SHIFT keys.
The application confirms that you want to remove the selected compounds.
 To add a compound to the method
1. Click the Add Compound from Compound Database icon,
.
The Select Compounds from Database dialog box opens, listing all the compounds
defined in the compound database. This dialog box is identical to the Compound
Database with the exception that you cannot edit the compound data from here; you can
only choose which compounds you want to include in your method.
2. Select the compounds to add to the method.
You can use the SHIFT or CTRL keys to select multiple compounds.
3. Click Add Selected Compounds to Method.
The TraceFinder application adds the selected compounds to the acquisition list for the
method.
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Figure 35. Acquisition List page
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Identification
The Identification page lists the compounds that are targeted for analysis, reporting, and other
compound-specific values. For descriptions of all values on the Identification page, see
“Identification page.”
 To filter the displayed compounds
From the Show list, select the type of compounds that you want to display in the
compounds list.
Compound type
Description
Quan Compounds
Displays only quantitation compounds, such as target
compounds and internal standards.
Target Compounds
Displays only target compounds.
Internal Standards
Displays only internal standard compounds.
Figure 36. Identification page
Table 21. Identification page parameters (Sheet 1 of 2)
Parameter
Description
RT
Retention time. The time after injection when the compound elutes. The total time that the
compound is retained on the column.
The TraceFinder application uses the RT and Window values to determine the start and
stop time for the acquisition.
Range: 0.00 to 999.00
Start time = RT – (Window/2)
Stop time = RT + (Window/2)
Start and stop range: 0.00 to 999.00
Compound
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A list of identified compounds. To customize the compound names, click the cell and type a
new name. To display a filtered list of compounds, use the Show list.
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Table 21. Identification page parameters (Sheet 2 of 2)
Parameter
Description
Compound Type
Compound types are Target Compound and Internal Standard. The TraceFinder
application uses target compounds and internal standards in quantitative analysis.
Active
Identifies each compound to be included in data review and reporting. By default, all added
compounds are set to active. This active or inactive setting populates the Batch View and
Data Review view in the Analysis mode.
CAS No
The Chemical Abstract Service (CAS) number that the TraceFinder application matched
with each compound. To change or add a number, click the CAS No cell and enter a new
number.
LIMS ID
Laboratory Information Management System identification number.
Use as RT Reference
When performing peak detection with retention time standards, the TraceFinder
application first identifies those compounds identified as retention time standards and then
uses their observed retention times to adjust any associated target compound.
Reference Compound
To be used for retention time adjustment for a compound. This list includes all compounds
that are selected in the Use as RT Reference column.
Shortcut menu
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The Identification page uses a right-click shortcut menu. See “Using the Shortcut Menu
Commands” on page 225.
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Detection
Use the Detection page to customize peak detection and integration for any ions that define
peaks and compounds.
From the Detection page, you can access the following pages:
Times
See also Times page parameters.
Signal
See also Signal page parameters.
Detect
See also Detect page parameters for Genesis.
See also Detect page parameters for ICIS.
See also Detect page parameters for Avalon.
Suitability
See also System Suitability dialog box parameters.
Spectrum
See also Spectrum page shortcut menu commands.
Library
See also Library page parameters.
Isotopes
See also Isotopes page parameters.
Fragments
See also Fragments page parameters.
Ratios
See also Ratios page parameters.
On the Detection page (see “Detection page” on page 172), you can configure how
characteristic ions for targeted compounds are detected and integrated. You can also edit the
list of characteristic ions for a specific compound. Refining these parameters in the master
method for each compound and its ions can reduce the degree of manual integration that
would otherwise be required.
You can change the parameters used to identify a quantitative peak, mass range, or confirming
ion peak. The TraceFinder application automatically uses the first match it finds as the
compound name, the base peak of the mass spectrum as the quantitative peak, and the second
and third largest ions as the confirming ion peaks.
Follow these procedures:
• To filter the displayed compounds
• To change the displayed information for detected peaks
• To add compounds to the method
• To change the compound reference spectrum
• To replace a quantitation mass
• To add a mass to the existing quantitation mass ranges
• To add a quantitative peak
• To add a spectral peak as a new compound
• To replace a quantitative peak with a confirming ion peak
• To set a confirming ion peak as an additional quantitative peak
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• To add a trace to the Real Time Status pane
• To replace a confirming ion peak
• To add a mass as a new confirming ion peak
• To use the cut-and-paste feature on confirming ion peaks
• To save the new method
 To filter the displayed compounds
From the Show list, select the type of compounds that you want to display in the
compounds list.
Compound type
Description
Quan Compounds
Displays only quantitation compounds, such as target
compounds, internal standards, and surrogates.
Target Compounds
Displays only target compounds.
Internal Standards
Displays only internal standard compounds.
 To change the displayed information for detected peaks
1. Right-click the chromatogram plot for any of the quan or confirming peaks and hold the
cursor over Peak Labels.
2. Choose to display labels for the peak area, peak retention time, peak height, or
signal-to-noise.
3. To remove a label, select the label type again and clear it.
The application globally applies these label settings to all quantitative peaks, confirming
peaks, and internal standard peaks in the method.
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 To add compounds to the method
Tip You can add compounds from the current raw data file (begin at step 7), or you
can associate another raw data file and add compounds from that file (begin at step 1).
1. From the main menu, choose Method View > Associate a Raw Data File.
The Associate a Raw Data File dialog box opens.
Browse to a data file.
Select a previously associated data file.
2. Browse to a raw data file to associate with the method (or click the arrow and select from
the list of previously associated raw data files) and open the file.
To assure that this raw data file is always available to the method (for example, if you
move the method to another system), the application saves the file in the Methods folder:
…\TraceFinderData\32\Methods\Methodname
3. To update the target ion ratio values when you associate this raw data file, select the Yes
option.
4. To update the scan filters when you associate this raw data file, select the Yes option.
5. To set a reference spectrum, do one of the following:
Select the Yes option.
–or–
Select the Yes, with Background Subtraction option.
The application uses the background-subtracted reference spectrum during quantitative
processing and reports the background-subtracted reference spectrum (indicated with BS
in the scan heading) as the last scan for each compound in the Quantitation Report - 2
report.
Note This option is available only when you select a background subtraction method
on the Acquisition page in the master method. See “Editing the Acquisition Page” on
page 146.
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6. Click OK.
The TraceFinder application displays the chromatographic and spectrum data for the
compounds in the associated raw data file.
IMPORTANT While the spectra pane displays the associated raw data file, you cannot
display peak information for an original compound in the Compound list. You can
display peak information only for compounds in the associated raw data file. To
return the display functionality for all compounds in the method, save the method.
7. Select a filter from the Filter list.
8. Click to select the peak in the chromatogram that represents the compound that you
want to add to the method.
9. Right-click and choose Add This Peak as New Compound from the shortcut menu.
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The TraceFinder application performs a library search for the selected compound. The
application uses the first match it finds as the compound name, the base peak of the mass
spectrum as the quantitative peak, and the second and third largest ions as the confirming
ion peaks.
• When the name of the first match does not exist in the method, the application adds
this compound to the method and displays the name in the Compound list. You can
now view and edit the parameters for this compound.
• When the name of the first match is already in the method, the Add New Compound
dialog box opens. You cannot overwrite a compound name in the method. If the
selected peak already exists in the method, you must give it a new name to add it to
the method. Or, you can select a different compound to add to the method,
following step 10 through step 12.
Figure 37. Add New Compound dialog box
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10. Do one of the following:
• Type a new name for the first matched compound.
The application displays a red warning when the selected compound name already
exists in the method. You cannot overwrite the compound name, and you cannot
create a duplicate name in the method. You must type a unique name.
–or–
• To use a compound other than the first matched compound, scroll to the spectrum
for that compound and select its corresponding check box in the title bar of the
spectrum pane.
Selected
compound
11. In the Type of Compound To Add list, select a compound type.
12. Click OK.
 To change the compound reference spectrum
1. In the chromatogram pane, click a peak.
The TraceFinder application displays the spectrum for the selected peak in the spectrum
pane.
2. In the spectrum pane, right-click and choose Use This Spectrum for Compound
Reference Spectrum from the shortcut menu.
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 To replace a quantitation mass
1. Click the data pane for the quantitation mass that you want to replace.
2. In the spectrum pane, hold the cursor over a peak.
The red box indicates the selected peak.
3. Right-click and choose Set This Spectral Peak as Quan Value from the shortcut menu.
4. Choose either Don’t Update Ion Ratios or Update Ion Ratios Using This Spectrum.
You can see the updated ion ratios on the Ratios page for the confirming ion peaks. See
“Ratios” on page 213.
 To add a mass to the existing quantitation mass ranges
1. In the spectrum pane, hold the cursor over a peak.
The red box indicates the selected peak.
2. Right-click and choose Add This Spectral Peak to Existing Quan Ranges from the
shortcut menu.
3. Choose either Don’t Update Ion Ratios or Update Ion Ratios Using This Spectrum.
The TraceFinder application adds the selected mass to the existing quantitation mass
ranges to increase the signal.
If you chose to update the ion ratios, you can see the updated ion ratios on the Ratios
page for the confirming ion peaks. See “Ratios” on page 213.
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 To add a quantitative peak
1. In the spectrum pane, hold the cursor over a peak.
The red box indicates the selected peak.
2. Right-click and choose Add This Spectral Peak as New Quan Peak from the shortcut
menu.
The application adds a new quantitative peak to the compound.
You can use the shortcut menu in the spectrum pane for this new quantitative peak to
perform any of the tasks that you would perform on the original quantitative peak.
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 To add a spectral peak as a new compound
1. In the raw data file spectrum pane, hold the cursor over a peak.
The red box indicates the selected peak.
2. Right-click and choose Add This Spectral Peak as New Compound from the shortcut
menu.
The TraceFinder application performs a library search for the selected compound. The
application uses the first match it finds as the compound name, the base peak of the mass
spectrum as the quantitative peak, and the second and third largest ions as the confirming
ion peaks.
When there are multiple matches, the Add New Compound dialog box opens. If the
name of the first match is already in the library, the dialog box opens with the matching
compound selected.
Figure 38. Add New Compound dialog box
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3. (Optional) Make any of the following changes:
• Change the name for the compound in the Name of New Compound box.
• Use a compound other than the compound chosen by the TraceFinder application by
scrolling to the spectrum for that compound and selecting the compound name in
the title bar of the spectrum pane.
Selected
compound
• In the Type of Compound To Add list, select a compound type.
4. Click OK.
 To replace a quantitative peak with a confirming ion peak
1. When you have multiple quantitative peaks, select the quantitative peak that you want to
replace.
2. Right-click the header bar for the confirming ion peak that you want to use as the
quantitative peak, and choose Swap with Quan Peak from the shortcut menu.
The application swaps the quantitative peak and the confirming ion peak. The
application replaces all information for the quantitative peak with information for the
confirming ion. This includes the expected retention time that the confirming ion
inherited from the original quantitative peak. The original quantitative peak replaces the
confirming ion peak. The application recalculates the ratios for all confirming ion peaks.
 To set a confirming ion peak as an additional quantitative peak
Right-click the header bar for the confirming ion peak and choose Promote to Separate
Quan Peak from the shortcut menu.
The application creates a new quantitative peak, using information from the confirming
ion peak. This includes the expected retention time that the confirming ion peak
inherited from the original quantitative peak. The application removes all references to
the confirming ion peak from the method.
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 To add a trace to the Real Time Status pane
Right-click the header bar for the quantitative peak or confirming ion peak that you want
to add to the Real Time Status pane and choose Display in Real Time Viewer from the
shortcut menu.
The application moves the peak to the Traces To Display in Real Time Viewer pane on
the Real Time Viewer page. See “Real Time Viewer” on page 223.
Trace m/z 311.09 added
to Real Time Viewer
When you acquire samples with this method, the application displays the m/z 311.09
trace in addition to the TIC in the Real Time Status pane.
Trace m/z 311.09 added to
Real Time Status display
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 To replace a confirming ion peak
1. Click the pane for the confirming ion peak that you want to replace.
2. In the raw data file spectrum pane, hold the cursor over a peak.
The red box indicates the selected peak.
3. Right-click and choose Set This Spectral Peak as Confirming from the shortcut menu.
The TraceFinder application replaces the confirming ion peak with the selected mass.
 To add a mass as a new confirming ion peak
1. In the spectrum pane, hold the cursor over a peak.
The red box indicates the selected peak.
2. Right-click and choose Add This Spectral Peak as New Confirming from the shortcut
menu.
The TraceFinder application adds the confirming ion peak to the quantitative peak.
You can use the shortcut menu in the spectrum pane for this new confirming ion peak to
perform any of the tasks that you would perform on the original confirming ion peaks.
 To use the cut-and-paste feature on confirming ion peaks
1. Right-click the header bar for the confirming ion peak that you want to remove and
choose Cut Confirming Peak from the shortcut menu.
2. Right-click the header bar for the confirming ion peak that you want to replace and
choose Paste Confirming Peak from the shortcut menu.
The application pastes the confirming ion peak that you removed. You can paste a deleted
peak back to the quantitative peak from which it was removed, or you can paste the
confirming ion peak that was deleted to another quantitative peak for this compound.
 To save the new method
1. Choose File > Save.
The Save Master Method dialog box opens.
2. Type a new name for the master method and click OK, or select a method name to
overwrite and click Overwrite.
The TraceFinder application saves the new method data in the following folder:
…\TraceFinderData\32\Methods
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Detection Page
Use the features on the Detection page to customize peak detection and integration for any
ions that define peaks and compounds.
Figure 39. Detection page
Selected compound data
Chromatogram pane
Spectrum pane
Selected compound
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Table 22. Detection page panes
Pane
Description
Compound
Lists all compounds in the master method. The Compound list uses a right-click shortcut
menu. See “Using the Shortcut Menu Commands” on page 225.
QuanPeakn
Displays a chromatogram for the quantitative peak and its confirming ion peaks. The
quantitative peak and confirming peak panes include additional pages for retention time,
signal, detection, spectrum, and ratio parameters for the selected compound.
Trace
Displays a combination of the Detector and Trace values used for the raw data file.
Do not confuse this Trace parameter with the Trace parameter on the Signal page. This
Trace parameter combines both the Detector and Trace values specified on the Signal page.
See “Signal page for a mass spectrometer detector” on page 181.
Note When you select a detector option other than MS or PDA, the spectrum pane
reports “Not Available.”
Filter
Displays the filter used for the raw data file. Available only when you set the Trace parameter
to MS.
Reference
Chromatogram
and
Spectra
Displays a reference chromatogram and spectra for the raw data file.
When you view an analog trace, there is no spectra display. To close the spectra pane and use
the full width to display the chromatogram, click
.
Additional pages
Times
Defines the retention time and window for a quantitative peak.
See “Times” on page 174.
Signal
Defines the detector and detection parameters used to display each chromatogram trace. See
“Signal” on page 176.
Detect
Defines the peak detection algorithm and its options.
See “Detect” on page 185.
Spectrum
Defines a reference mass spectrum for a quantitative peak or compound. See “Spectrum” on
page 199.
Ratios
Defines the criteria for evaluating, confirming, or qualifying ions. See “Ratios” on page 213.
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Times
Use the Times page to define the expected retention time or a retention time range for a
quantitative peak.
Figure 40. Times page
Parameters for single
RT detection types
Parameters for RT
range detection types
Table 23. Times page parameters (Sheet 1 of 2)
Parameter
Description
Detection Type
Single - Detected: (Default) Specified as a centered retention time window. The application
integrates a distinct peak. In reports, the application displays the expected retention time
and actual retention time values as Method RT and Detected RT, respectively.
Range - Detected: Specified as a retention time start/end range.
Range - Integrated: Specified as a retention time start/end range. The application integrates
all peaks within the specified time range.
Expected RT (min)
Expected retention time for a single peak. Available only for the Single - Detected detection
type.
Window (sec)
Width of the window (in seconds) to indicate how far around the expected retention time
the system looks for a peak apex. Available only for the Single - Detected detection type.
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Table 23. Times page parameters (Sheet 2 of 2)
Parameter
Description
Start/End RT (min)
Beginning and ending retention time window that can encompass multiple peaks. Available
only for the Range - Detected and the Range - Integrated detection types. When you change
from a Single - Detected detection type, these values default to the previous beginning and
ending time calculated from the Expected RT and Window values.
View Width (min)
Viewable size of the ion chromatogram display. Changing the view width does not affect the
peak detection process; the TraceFinder application uses it only for graphical display. When
you select either Range - Detected or Range - Integrated as the detection type, you cannot
select a View Width value less than the retention time range (end time minus start time).
Shortcut menu
Copies the View Width and Window values to all quantitative peaks for the compound and
Set Peak Windows
Settings to All Peaks in updates the compound.
Compound
Available only when a compound has multiple quantitative peaks.
Copies the View Width and Window values to all quantitative peaks for the method and
Set Peak Windows
Settings to All Peaks in updates the method.
Method
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Signal
Use the Signal page to define the detector and filters as you display each chromatogram trace.
For detailed descriptions of all the features on the Signal page, see “Signal Page” on page 181.
The TraceFinder application can use both analog detectors and mass spectrometer detectors.
See “Signal page for a mass spectrometer detector” on page 181 or “Signal page for an analog
detector” on page 182.
Follow these procedures:
• To specify ranges of ions for detection and integration
• To specify an XIC filter
• To specify an MS filter
 To specify ranges of ions for detection and integration
1. Select MS from the Detector list.
2. Select Mass Range from the Trace list.
3. In the Ranges area, click Edit.
Note The parameters in the Ranges area are available only when you set the Detector
parameter to MS and the Trace parameter to Mass Range.
The Edit Mass Ranges dialog box opens where you can define mass ranges using a center
of mass value or start and end values.
Figure 41. Edit Mass Ranges dialog box
4. Enter a value in the Center Mass box and click Add.
A new row with this value opens under Ranges. Center mass values are listed in the Start
m/z column. The application uses a range of one amu that is centered on this value.
5. Enter values in the Start m/z and End m/z columns and click Add.
The application adds a row with these start and end values.
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6. Add as many ranges as you want.
When you process a batch with this method, the application sums the multiple ions
specified by these ranges.
7. Click Apply.
The application applies the parameters to the list of ranges.
 To specify an XIC filter
1. Select MS from the Detector list.
2. Select Mass Range from the Trace list.
3. Select the XIC option.
Note The XIC option is available only when you set the Detector parameter to MS
and the Trace parameter to Mass Range.
4. Click the Filter browse button.
The XIC Filter dialog box opens. See XIC Filter dialog box.
5. Specify your filter options.
6. Click OK.
The application updates the chromatogram data using the specified XIC filter options.
The Filter box indicates the parameters of the specified XIC filter, as in this example:
MassAnalyzerFTMS analyzer
Positive polarity
MS order
Full-scan mode
Data-dependent filter
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Figure 42. XIC Filter dialog box
Table 24. XIC Filter dialog box parameters (Sheet 1 of 2)
Parameter
Description
Mass Analyzer Any: Allows any mass analyzer.
Type
FTMS: Fourier Transform Mass Spectrometer
ITMS: Ion Trap Mass Spectrometer
Sector: Static electric or magnetic sectors, or a combination of the two
SQMS: Single Quad Mass Spectrometer
TOFMS: Time-of-Flight Mass Spectrometer
TQMS: Triple Quad Mass Spectrometer
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MSX
Any: Allows both MSX and non-MSX scans.
On: Allows only MSX scans.
Off: Allows only non-MSX scans.
Data
Dependent
Any: Allows both data-dependent and non-data-dependent filters.
On: Allows only data-dependent filters.
Off: Allows only non-data-dependent filters.
MS Order
Any: Allows any MS order.
MS: Single mass spec stage
MS2-MS3: Multiple mass spec stages
Polarity
Any: Allows both positive and negative.
Positive
Negative
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Table 24. XIC Filter dialog box parameters (Sheet 2 of 2)
Parameter
Description
Scan Mode
Any: Allows any scan mode.
Full: Full-scan mode
SIM: Selective ion monitoring
SRM: Selective reaction monitoring
CRM: Consecutive reaction monitoring
Q1MS: MS using quadrupole 1
Q3MS: MS using quadrupole 3
Activations
Any: Allows any activation method.
CID: Collision-induced dissociation
MPD: Multiple photodissociation
ECD: Electron capture dissociation
PQD: Pulsed dissociation
ETD: Electron transfer dissociation
HCD: Higher energy collision-induced dissociation
This parameter is available only when the MS Order is set to MS2 or MS3.
First Precursor This parameter is available only when the MS Order is set to MS2 or MS3.
Second
Precursor
This parameter is available only when the MS Order is set to MS3.
 To specify an MS filter
1. Select the Filter option.
2. Select MS from the Detector list.
3. Select a trace type from the Trace list.
4. Select a filter from the Filter list.
Filter types can be any of the following:
• MS
• MS2
• MS2 CID
• MS2 HCD
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5. To update the new filter selection, click outside the Signal pane.
As long as the filter is highlighted blue, the new selection is not yet applied.
6. (Optional for quantitative peaks) To apply this same quantitative peak filter to other
peaks, right-click and choose one of the following from the shortcut menu:
• Set Filter Options on All Peaks in This Compound: Applies this filter to all other
peaks in the compound.
• Set Filter Options on All Compounds: Applies this filter to all peaks for all
compounds in the method.
• Set Quan Peak Filter Options on All Compounds: Applies the filter specified for
the quantitative peak to all quantitative peaks for all compounds in the method.
7. (Optional for confirming peaks) To apply this same confirming peak filter to other peaks,
right-click and choose one of the following from the shortcut menu:
• Set Filter Options on All Peaks in This Compound: Applies this filter to all other
peaks in the compound.
• Set Filter Options on All Compounds: Applies this filter to all peaks for all
compounds in the method.
• Set Confirm Peak Filter Options on All Compounds: Applies the filter specified
for the confirming peak to all confirming peaks for all compounds in the method.
• Set Confirm Peak 1 Filter Options on All Compounds: Applies the filter specified
for confirming peak 1 to the first confirming peak for all compounds in the method.
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Signal Page
Use the features on the Signal page to define the detector and filters as you display each
chromatogram trace for either analog detectors or mass spectrometer detectors. For detailed
descriptions of all the parameters on the Signal page, see “Signal page parameters” on
page 182.
• Signal page for a mass spectrometer detector
• Signal page for an analog detector
Figure 43. Signal page for a mass spectrometer detector
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Figure 44. Signal page for an analog detector
Table 25. Signal page parameters (Sheet 1 of 3)
Parameter
Description
XIC
Specifies an Extracted Ion Chromatogram experiment type that uses a single, full-scan mass filter
that is post-processed to extract a peak for the ions of interest.
Filter
Select from the list of mass filters to use for processing the compound.
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Table 25. Signal page parameters (Sheet 2 of 3)
Parameter
Description
Detector
The detection options that are used to create the method determine the available detector options.
The method can use the standard options (all the listed options) or only the detection options used
to acquire an associated raw data file. To specify the available detector options, see “Specifying
Default Peak Detection Parameters” on page 37.
MS: Mass spectrometer that ionizes sample molecules and then separates the ions according to their
mass-to-charge ratio (m/z).
PDA: Photodiode array detector providing a linear array of discrete photodiodes on an integrated
circuit chip. It is placed at the image plane of a spectrometer to allow a range of wavelengths to be
simultaneously detected.
Analog: Supplemental detectors (for example, FID, ECD). When you select this detector, any reports
that display a QIon value show the value as Analog and any reports that display spectra show the
spectra as Not Available.
A/D card: If you have a detector not under data system control, you can capture the analog signal
and convert it to digital using an interface box (for example, SS420X) for storage in the raw data file.
UV: A UV spectrophotometer (for variable-wavelength detection) or photometer (for
single-wavelength detection) equipped with a low-volume flow cell. This detector detects analytes
that readily absorb light at a selected wavelength.
Trace
Represents a specific range of the data. The TraceFinder application uses the trace to identify the
characteristic ions for a compound.
MS detector options: Mass Range, TIC, or Base Peak. When you select Mass Range, you are
prompted to enter the start and end m/z values for the ranges.
PDA detector options: Spectrum Maximum, Wavelength Range, or Total Scan.
Analog detector options: Analog 1, Analog 2, Analog 3, or Analog 4. You can configure these
channel names in your instrument configuration.
A/D Card detector options: AD Card ch1, AD Card ch2, AD Card ch3, or AD Card ch4. You can
configure these channel names in your instrument configuration.
UV detector options: Channel A, Channel B, Channel C, or Channel D. You can configure these
channel names in your instrument configuration.
Filter
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Available only when you select the MS detector. Represents a particular data acquisition channel.
For example, the filter option + c Full ms [35.00-500.00] represents a positive ion centroid signal
acquired in single-stage, full-scan mode from m/z 35 to 500.
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Table 25. Signal page parameters (Sheet 3 of 3)
Parameter
Description
Ranges
Available only when you select the Mass Range trace for an MS detector.
Edit
Opens the Edit Mass Ranges dialog box where you can specify a range of ions for detection and
integration. See “To specify ranges of ions for detection and integration” on page 176.
Start m/z
End m/z
Specifies ranges of ions for detection and integration. The application sums the multiple ions
specified by these ranges.
Ranges specified by a center mass value are listed as a single value in the Start m/z column. The
application uses a range of one amu centered on this value.
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Detect
Use the Detect page to define the peak detection algorithm (sensitivity) and its options and to
determine the area under a curve. There are three sensitivity modes: Genesis, ICIS, and
Avalon. Use the Genesis and Avalon sensitivity modes for mass spectrometry detection. You
use the ICIS sensitivity mode primarily for analog detection.
On this page, you can specify how you want each mode to run. See the following for detailed
descriptions of all the features on the Detect page:
• For Genesis sensitivity, see “Detect page parameters for Genesis” on page 187.
• For ICIS sensitivity, see “Detect page parameters for ICIS” on page 191.
• For Avalon sensitivity, see “Detect page parameters for Avalon” on page 193.
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Figure 45. Detect page for Genesis
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Table 26. Detect page parameters for Genesis (Sheet 1 of 3)
Parameter
Description
Sensitivity
Specifies the Genesis peak detection algorithm.
Detection Method
Highest peak: Uses the highest peak in the chromatogram for component identification.
Nearest RT: Uses the peak with the nearest retention time in the chromatogram for
component identification.
Smoothing
Determines the degree of data smoothing to be performed on the active component peak
prior to peak detection and integration.
Default: 1
Range: Any odd integer from 1 through 15 points
S/N Threshold
Current signal-to-noise threshold for peak integration. Peaks with signal-to-noise values less
than this value are not integrated. Peaks with signal-to-noise values greater than this value
are integrated.
Range: 0.0 to 999.0
Enable Valley
Detection
Uses the valley detection approximation method to detect unresolved peaks. This method
drops a vertical line from the apex of the valley between unresolved peaks to the baseline.
The intersection of the vertical line and the baseline defines the end of the first peak and the
beginning of the second peak.
Expected Width (sec)
The expected peak width parameter (in seconds). This parameter controls the minimum
width that a peak is expected to have if valley detection is enabled.
With valley detection enabled, any valley points nearer than the expected width/2 to the top
of the peak are ignored. If a valley point is found outside the expected peak width, the
TraceFinder application terminates the peak at that point. The application always terminates
a peak when the signal reaches the baseline, independent of the value set for the expected
peak width.
Range: 0.0 to 999.0
Constrain Peak Width
Constrains the peak width of a component during peak integration of a chromatogram. You
can then set values that control when peak integration is turned on and off by specifying a
peak height threshold and a tailing factor. Selecting the Constrain Peak Width check box
activates the Peak Height (%) and Tailing Factor options.
Peak Height (%)
A signal must be above the baseline percentage of the total peak height (100%) before
integration is turned on or off. This text box is active only when you select the Constrain
Peak Width check box.
Range: 0.0 to 100.0%
Tailing Factor
A factor that controls how the TraceFinder application integrates the tail of a peak. This
factor is the maximum ratio of the trailing edge to the leading side of a constrained peak.
This text box is active only when you select the Constrain the Peak Width check box.
Range: 0.5 through 9.0
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Table 26. Detect page parameters for Genesis (Sheet 2 of 3)
Parameter
Description
Min Peak Height (S/N) For the valley detection approximation method to use the Nearest RT Peak Identification
criteria, this peak signal-to-noise value must be equaled or exceeded. For component
identification purposes, the TraceFinder application ignores all chromatogram peaks that
have signal-to-noise values that are less than the S/N Threshold value.
Range: 0.0 (all peaks) through 999.0
Peak S/N Cutoff
The peak edge is set to values below this signal-to-noise ratio.
This test identifies an edge of a peak when the baseline adjusted height of the edge is less
than the ratio of the baseline adjusted apex height and the peak S/N cutoff ratio.
When the S/N at the apex is 500 and the peak S/N cutoff value is 200, the TraceFinder
application defines the right and left edges of the peak when the S/N reaches a value less
than 200.
Range: 50.0 to 10000.0
Valley Rise (%)
The peak trace can rise above the baseline by this percentage after passing through a
minimum (before or after the peak).
This method drops a vertical line from the apex of the valley between unresolved peaks to
the baseline. The intersection of the vertical line and the baseline defines the end of the first
peak and the beginning of the second peak.
When the trace exceeds rise percentage, the TraceFinder application applies valley detection
peak integration criteria.
The TraceFinder application applies this test to both the left and right edges of the peak.
The rise percentage criteria is useful for integrating peaks with long tails.
Range: 0.1 to 500.0
Valley S/N
Specifies a value to evaluate the valley bottom. Using this parameter ensures that the
surrounding measurements are higher.
Default: 2.0
Range: 1.0 to 100.0
# Background Scans
Number of background scans performed by the TraceFinder application.
Report Noise As
Determines if the noise used in calculating S/N values is calculated using an RMS
calculation or a peak-to-peak resolution threshold. Options are RMS or Peak to Peak.
Shortcut menu
Apply to All Peaks in
Method
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Updates all compounds in the method with the current settings on the Detect page. These
updates apply to both quantitative and confirming ion peaks.
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Table 26. Detect page parameters for Genesis (Sheet 3 of 3)
Parameter
Description
Apply to All Peaks with Uses the current settings on the Detect page to update all compounds in the method that
Like Sensitivity Setting use the Genesis sensitivity mode. These updates apply to both quantitative and confirming
ion peaks that use the Genesis sensitivity mode.
Apply to All Peaks in
Compound
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Updates all peaks in the current compound with the current settings on the Detect page.
These updates apply to both quantitative and confirming ion peaks.
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Figure 46. Detect page for ICIS
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Table 27. Detect page parameters for ICIS (Sheet 1 of 2)
Parameter
Description
Sensitivity
Specifies the ICIS peak detection algorithm, used primarily with analog detectors.
Detection Method
Highest peak: Uses the highest peak in the chromatogram for component identification.
Nearest RT: Uses the peak with the nearest retention time in the chromatogram for
component identification.
Smoothing
Determines the degree of data smoothing to be performed on the active component peak
prior to peak detection and integration.
Default: 1
Range: Any odd integer from 1 through 15 points
Area Noise Factor
The noise level multiplier used to determine the peak edge after the location of the possible
peak.
Default: 5
Range: 1 through 500
Peak Noise Factor
The noise level multiplier used to determine the potential peak signal threshold.
Default: 10
Range: 1 through 1000
Baseline Window
The TraceFinder application looks for a local minima over this number of scans.
Default: 40
Range: 1 through 500
Constrain Peak Width
Constrains the peak width of a component during peak integration of a chromatogram. You
can then set values that control when peak integration is turned on and off by specifying a
peak height threshold and a tailing factor. Selecting the Constrain Peak Width check box
activates the Peak Height (%) and Tailing Factor options.
Peak Height (%)
A signal must be above the baseline percentage of the total peak height (100%) before
integration is turned on or off. This text box is active only when you select the Constrain
Peak Width check box.
Range: 0.0 to 100.0%
Tailing Factor
A factor that controls how the TraceFinder application integrates the tail of a peak. This
factor is the maximum ratio of the trailing edge to the leading side of a constrained peak.
This text box is active only when you select the Constrain the Peak Width check box.
Range: 0.5 through 9.0
Min Peak Height (S/N) For the valley detection approximation method to use the Nearest RT Peak Identification
criteria, this peak signal-to-noise value must be equaled or exceeded. For component
identification purposes, the TraceFinder application ignores all chromatogram peaks that
have signal-to-noise values that are less than the S/N Threshold value.
Range: 0.0 (all peaks) through 999.0
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Table 27. Detect page parameters for ICIS (Sheet 2 of 2)
Parameter
Description
Noise Method
The options are INCOS or Repetitive.
INCOS: Uses a single pass algorithm to determine the noise level.
Repetitive: Uses a multiple pass algorithm to determine the noise level. In general, this
algorithm is more accurate in analyzing the noise than the INCOS Noise algorithm, but the
analysis takes longer.
Min Peak Width
The minimum number of scans required in a peak.
Default: 3
Range: 0 to 100 scans
Multiplet Resolution
The minimum separation in scans between the apexes of two potential peaks. This is a filter
to determine if two peaks are resolved.
Default: 10
Range: 1 to 500 scans
Area Tail Extension
The number of scans past the peak endpoint to use in averaging the intensity.
Default: 5
Range: 0 to 100 scans
Area Scan Window
The number of allowable scans on each side of the peak apex. A zero value defines all scans
(peak-start to peak-end) to be included in the area integration.
Default: 0
Range: 0 to 100 scans
RMS
Specifies that the TraceFinder application calculate noise as RMS. By default, the
application uses Peak To Peak for the noise calculation. RMS is automatically selected if you
manually determine the noise region.
Shortcut menu
Apply to All Peaks in
Compound
Updates all peaks in the current compound with the current settings on the Detect page.
These updates apply to both quantitative and confirming ion peaks.
Apply to All Peaks in
Method
Updates all compounds in the method with the current settings on the Detect page. These
updates apply to both quantitative and confirming ion peaks.
Apply to All Peaks with Uses the current settings on the Detect page to update all compounds in the method that
Like Sensitivity Setting use the ICIS sensitivity mode. These updates apply to both quantitative and confirming ion
peaks that use the ICIS sensitivity mode.
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Figure 47. Detect page for Avalon
Table 28. Detect page parameters for Avalon (Sheet 1 of 2)
Parameter
Description
Sensitivity
Specifies the Avalon peak detection algorithm.
Detection Method
Highest Peak: Uses the highest peak in the chromatogram for component identification.
Nearest RT: Uses the peak with the nearest retention time in the chromatogram for
component identification.
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Table 28. Detect page parameters for Avalon (Sheet 2 of 2)
Parameter
Description
Smoothing
Determines the degree of data smoothing to be performed on the active component peak
prior to peak detection and integration.
Default: 1
Range: Any odd integer from 1 through 15 points
Autocalc Initial Events
Automatically calculates the events in the Event list.
Edit
Opens the Avalon Event List dialog box. See “Avalon Event List” on page 49.
Shortcut menu
Apply to All Peaks in
Compound
Updates all peaks in the current compound with the current settings on the Detect page.
These updates apply to both quantitative and confirming ion peaks.
Apply to All Peaks in
Method
Updates all compounds in the method with the current settings on the Detect page. These
updates apply to both quantitative and confirming ion peaks.
Apply to All Peaks with Uses the current settings on the Detect page to update all compounds in the method that
Like Sensitivity Setting use the Avalon sensitivity mode. These updates apply to both quantitative and confirming
ion peaks that use the Avalon sensitivity mode.
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Suitability
Use the Suitability page to determine if the column is degrading and to identify suspicious
peaks eluting at the same time as the target compound. Suspicious peaks caused by highly
retained compounds from a previous injection tend to have a broader than expected peak
profile. Tailing peaks frequently indicate a degrading column.
The Suitability page displays the parameter values to check the suitability of chromatographic
peaks during processing. You can edit these parameters in the System Suitability dialog box.
 To set system suitability parameters
1. Click Edit.
The System Suitability dialog box opens. See “System Suitability dialog box” on
page 197.
2. To perform symmetry testing, do the following:
a. Select the Symmetry Parameters check box.
b. Type a peak height for symmetry testing in the Peak Height box.
c. Type a threshold for symmetry testing in the Symmetry Threshold box.
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3. To carry out classification tests, do the following:
a. Select the Peak Classification Parameters check box.
b. To adjust Xcalibur peak width testing thresholds, type parameters in the Detect Peak
Width area as follows:
• To enter a peak height for the test, type a value in the Peak Height box.
• To enter a minimum peak width threshold, type a value in the Min Peak Width
box.
c. To adjust the Xcalibur peak tailing test, type parameters in the Detect Tailing area:
• To enter a peak height for the test, type a value in the Peak Height box.
• To enter a threshold limit for peak tailing, type a value in the Failure Threshold
box.
d. To adjust the Xcalibur column overload test, type parameters in the Detect Column
Overload area:
• To enter a peak height for the test, type a value in the Peak Height box.
• To enter a threshold limit for peak tailing, type a value in the Failure Threshold
box.
e. To adjust the Xcalibur baseline clipping test, type parameters in the Detect Baseline
Clipping area:
To define the test window, type a value in the Number of Peak Widths for Noise
Detection box.
4. To save your settings, click OK.
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Figure 48. System Suitability dialog box
Table 29. System Suitability dialog box parameters (Sheet 1 of 2)
Parameter
Description
Symmetry Parameters
Determines the symmetry of the left and right sides of the detected peak.
Peak Height
The percentage of the peak height at which to compare the symmetry of the left and
right peak widths.
Left and right widths measured at 30%
and 50% of the peak height
Symmetry Threshold
The minimum percentage difference to be considered symmetrical and pass the
suitability test.
Peak Classification Parameters
Detect Peak Width
Peak Height
Determines the minimum width of each side of the peak measured at the specified
percentage of the peak height.
The percentage of the peak height at which to measure the full peak width.
Full width measured at 30%
and 50% of the peak height
Min Peak Width
Thermo Scientific
Minimum peak width (measured at the specified percentage of the peak height)
required to pass the suitability test.
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Table 29. System Suitability dialog box parameters (Sheet 2 of 2)
Parameter
Max Peak Width
Detect Tailing
Peak Height
Description
Maximum allowed peak width (measured at the specified percentage of the peak
height) to pass the suitability test.
The width of the right side of the peak divided by the width of the left side of the
peak at the specified percentage of the peak height.
The percentage of the peak height at which to measure the left and right sides of the
peak.
Left and right widths measured at 10%
and 30% of the peak height
Failure Threshold
Minimum Detect Tailing value (RHS/LHS) required to pass the suitability test.
Detect Column Overload The width of the left side of the peak divided by the width of the right side of the
peak at the specified percentage of the peak height.
Peak Height
The percentage of the peak height at which to measure the left and right sides of the
peak.
Left and right widths measured at 30%
and 50% of the peak height
Failure Threshold
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Minimum Detect Column Overload value (LHS/RHS) required to pass the
suitability test.
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Spectrum
Use the Spectrum page to store a reference mass spectrum for a quantitative peak or
compound.
For detailed descriptions of all the shortcut menu commands on the Spectrum page, see
“Spectrum Page” on page 204.
Follow these procedures:
• To create a reference spectrum
• To update confirming ion ratios
• To change the quantitation mass used for a quantitative peak
• To add ions together to get an accumulated signal
• To add a quantitative peak to an existing compound
• To add one or more confirming ions to an existing compound
• To zoom in on the chromatogram or spectrum displays
 To create a reference spectrum
1. Click a peak in the quantitative peak chromatogram pane.
The mass spectrum for the peak is displayed in the Spectrum pane.
2. Right-click the Spectrum pane and choose Apply Background Subtraction to Peak and
Set as Reference Spectrum from the shortcut menu.
The application uses the background-subtracted reference spectrum during quantitative
processing and reports the background-subtracted reference spectrum (indicated with BS
in the scan heading) as the last scan for each compound in the Quantitation Report - 2
report.
Note This command is available only when you select a background subtraction
method on the Acquisition page in the master method. See “Editing the Acquisition
Page” on page 146.
 To update confirming ion ratios
1. Click a peak in the quantitative peak chromatogram pane.
The mass spectrum for the peak is displayed in the Spectrum pane.
2. Right-click the Spectrum pane and choose Update Confirming Ion Ratios with This
Spectrum from the shortcut menu.
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 To change the quantitation mass used for a quantitative peak
1. Click a peak in the chromatogram pane.
The mass spectrum for the peak is displayed in the Spectrum pane.
2. In the Spectrum pane, hold the cursor over the mass-to-charge value for an ion.
A red box around the ion’s m/z value indicates that the ion is selected.
3. Right-click and choose one of the following commands from the shortcut menu:
• Set This Mass as Quan Mass > Don’t Update Ion Ratios
• Set This Mass as Quan Mass > Update Ion Ratios Using This Reference Spectrum
The following examples show an original quantitative peak and a quantitative peak with an
updated quantitation mass.
Figure 49. Original quantitative peak mass example
Original quantitative peak mass
The TraceFinder application replaces the original quantitation mass with the selected mass.
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Figure 50. Updated quantitative peak mass example
New quantitative peak mass
 To add ions together to get an accumulated signal
1. Hold the cursor over the m/z value for an ion in the Spectrum pane.
A red box around the ion’s m/z value indicates that the ion is selected.
2. Right-click and choose Add This Mass to Existing Quan Mass Range from the shortcut
menu.
You can now update the ion ratios to adjust the confirming ion comparisons to the new
summed quantitative peak signal.
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 To add a quantitative peak to an existing compound
1. Click the peak in the Quan Peak chromatogram pane.
The mass spectrum for the peak is displayed in the Spectrum pane.
2. In the Spectrum pane, hold the cursor over the m/z value for an ion.
A red box around the ion’s m/z value indicates that the ion is selected.
3. Right-click and choose Set This Mass as New Quan Peak from the shortcut menu.
The TraceFinder application adds this ion as a new quantitative peak.
New quantitative peak mass
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 To add one or more confirming ions to an existing compound
1. Click the quantitative peak in the chromatogram pane.
The mass spectrum for the peak is displayed in the Spectrum pane.
2. In the Spectrum pane, hold the cursor over the m/z value for an ion.
A red box around the ion’s m/z value indicates that the ion is selected.
3. Right-click and choose to Add This Mass as New Confirming Ion from the shortcut
menu.
The TraceFinder application adds the selected mass as a confirming peak for this
quantitative peak.
 To zoom in on the chromatogram or spectrum displays
1. Drag the cursor to delineate a rectangle.
The display zooms in on the specified rectangle.
2. To return to the original display, right-click and choose Reset Scaling from the shortcut
menu.
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Spectrum Page
Use the shortcut menu commands on the Spectrum page to store a reference mass spectrum
for a quantitative peak or compound.
Figure 51. Spectrum page
Table 30. Spectrum page shortcut menu commands
Command
Description
Update Confirming Ion
Updates the confirming ion ratios using the selected peak.
Ratios With This Spectrum
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Set This Mass as Quan
Mass
Adds the quantitation mass of the selected ion to the
quantitation mass used for the quantitative peak. You can
choose to update the ion ratios or not update the ion ratios
using this reference spectrum.
Add This Mass to Existing
Quan Mass Range
Adds the selected mass to your existing quantitation mass
range. You can choose to update the ion ratios to adjust the
confirming ion comparisons to the new summed quantitative
peak signal.
Set This Mass as New
Quan Peak
Adds a new quantitative peak to an existing compound.
Add This Mass as New
Confirming Ion
Adds one or more confirming ion peaks to an existing
compound.
Reset Scaling
Returns the chromatogram or spectrum display to its original
size.
Copy to Clipboard
Copies the graphic display to the Clipboard.
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Library
Use the Library page to define the criteria for library matching. For detailed descriptions of all
the features on the Library page, see Library page.
 To activate library matching
1. Select the Enable check box.
2. From the Library Search Type list, select the type of library to use for matching.
• NIST: Uses the NIST library that you installed with the TraceFinder application. See
“Installing the NIST and QED Libraries” on page 12.
Note Because the NIST library is large, using this library can slow sample
processing.
• Library Manager: Uses the library that you specified in the Configuration console.
See “Screening Libraries” on page 59.
The application searches the library, matches the fragment ion spectrum in the library to
the compound’s ion spectrum, and returns the highest score (best match).
3. Type a threshold value in the Score Threshold box.
To match a compound, the resulting score percentage from a library search match must
be higher than your entered threshold value.
4. (Optional) Select the Use Reverse Library Searching Only check box.
A reverse search compares a library entry to an unknown compound (a forward search
compares the mass spectrum of an unknown compound to a mass spectral library entry).
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Figure 52. Library page
Table 31. Library page parameters
Command
Description
Library Search Type
Specifies the type of library to use for matching.
• NIST: Uses the NIST library that you installed with the
TraceFinder application.
• Library Manager: Uses the library that you specified in the
Configuration console.
Score Threshold (%)
Specifies the minimum score for library matching. To match a
compound, the resulting score percentage from a library search
match must be higher than this threshold value.
Use Reverse Library
Searching Only
A reverse search compares a library entry to an unknown
compound (a forward search compares the mass spectrum of an
unknown compound to a mass spectral library entry).
Shortcut menu
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Set Peak Library Settings
to All Peaks in
Compound
Updates all peaks in the current compound with the current
settings on the Library page. These updates apply to both
quantitative and confirming ion peaks. The application
reprocesses all peaks in the compound and performs a new
library search.
Set Peak Library Settings
to All Peaks in Method
Updates all compounds in the method with the current settings
on the Library page. These updates apply to both quantitative
and confirming ion peaks. When you use this command in the
local method for a processed batch, the application prompts you
to reprocess the batch to update the library settings.
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Isotopes
Use the Isotopes page to define the criteria for identifying an isotope peak. To identify an
isotopic pattern, the application must detect the compound for at least one of its defined
adduct ions. The application identifies the elemental composition to match using the formula
that is associated with the most intense adduct peak. The application then generates an
isotopic pattern score (as a percentage value) for the match between the measured and
expected isotopic patterns of the calculated elemental composition.
For detailed descriptions of all the features on the Isotopes page, see Isotopes page.
 To specify isotope criteria
1. Select the Enable check box to activate the isotopes features.
2. In the Fit Threshold box, type the fit threshold percentage.
The resulting score percentage from isotopic pattern matching must be higher than the
specified fit threshold percentage.
3. In the Allowed Mass Deviation box, type the parts per million to use as the minimum
deviation from the expected m/z.
The isotopic pattern algorithm considers an isotope peak as found if its measured m/z is
less than this amount away from its expected m/z. For best results, set this value to a
number that causes up to 98 percent of all mass deviations to be smaller than the allowed
mass deviation value.
4. In the Allowed Intensity Deviation box, type a value to specify the allowed intensity
deviation of the mass spectrometer relative to the monoisotopic ion, as a percentage of the
base peak height.
The isotopic pattern algorithm considers an isotope peak as not found if its intensity,
relative to the monoisotopic ion’s intensity, is more than the deviation percentage from
the theoretical relative intensity of the isotope ion. For best results, set this value to a
number that causes up to 98 percent of all intensity deviations to be smaller than the
allowed intensity deviation value.
5. To specify that isotopic pattern calculations use internal mass calibration instead of
external mass calibration, select the Use Internal Mass Calibration check box.
With this check box selected, the application applies a requirement that an isotope’s m/z
must be closer to its theoretical value to avoid a score penalty.
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Figure 53. Isotopes page
Table 32. Isotopes page parameters (Sheet 1 of 2)
Parameter
Description
Fit Threshold %
To identify a compound, the resulting score percentage from
isotopic pattern matching must be higher than the specified fit
threshold percentage.
Default: 90%
Allowed Mass Deviation
(ppm)
Specifies the allowed mass deviation in the spectrum data.
Allowed Intensity
Deviation (%)
Specifies the allowed intensity deviation of the mass
spectrometer, relative to the monoisotopic ion, as a percentage
of the base peak height.
The TraceFinder isotopic pattern algorithm considers an isotope
peak as found if its measured m/z is less than this amount away
from its expected m/z. For best results, set this value to a number
that causes up to 98 percent of all mass deviations to be smaller
than the allowed mass deviation value.
Range: 3 to 100 ppm
Default: 3 ppm
The TraceFinder isotopic pattern algorithm considers an isotope
peak as not found if its intensity relative to the monoisotopic
ion’s intensity is more than this deviation percentage from the
theoretical relative intensity of the isotope ion. For best results,
set this value to a number that causes up to 98% of all intensity
deviations to be smaller than the allowed intensity deviation
value.
Default: 10%
Use Internal Mass
Calibration
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Specifies that the application require an isotope’s m/z to be
closer to its theoretical value to avoid a score penalty.
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Table 32. Isotopes page parameters (Sheet 2 of 2)
Parameter
Description
Shortcut menu
Thermo Scientific
Set Peak Isotope Settings
to All Peaks in
Compound
Updates all peaks in the current compound with the current
settings on the Isotopes page. These updates apply to both
quantitative and confirming ion peaks. The application
reprocesses all peaks in the compound and performs a new
library search.
Set Peak Isotope Settings
to All Peaks in Method
Updates all compounds in the method with the current settings
on the Isotopes page. These updates apply to both quantitative
and confirming ion peaks. When you use this command in the
local method for a processed batch, the application prompts you
to reprocess the batch to update the library settings.
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Fragments
Use the Fragments page to define the criteria for identifying a fragment ion.
To use fragment ions, the application requires the following conditions:
• The selected compound databases contain the charged mass for each defined fragment
ion of interest for the compounds in the target list.
• The HCD (higher energy collision-induced dissociation), source CID (source
collision-induced dissociation), or AIF (all ions fragmentation) ion spectra exist at a time
point within the compound’s elution time range.
For detailed descriptions of all the features on the Fragments page, see Fragments page.
 To specify fragment ion options
1. Select the Enable check box.
2. To ignore the Fragment Ions options when no fragment is defined in the compound
database, select the Ignore If Not Defined check box.
When the compound database does not define fragments for a compound, the
application does not include the results for fragment ions in the results.
• When the Ignore If Not Defined option is selected, the application does not perform
filtering for the Fragment Ions and, in the Data Review view, the FI column is blank.
• When the Ignore If Not Defined option is not selected, the application considers that
this target compound is not identified. The Fragment Ions filter fails.
3. In the Min. # of Fragments box, type the minimum number of fragments required to
identify a compound.
The application uses the number of fragment masses defined in the compound database
when it processes a sample for fragment ions. The value you specify for Min. # of
Fragments cannot be greater than the number of fragments defined in the compound
database.
4. In the Intensity Threshold box, type the intensity threshold value.
The intensity of a fragment must be above this threshold for the application to identify it.
5. In the Mass Tolerance box, type a mass tolerance value and then select ppm or mmu for
the mass tolerance units.
This mass tolerance value indicates the number of millimass units or parts per million to
use as the m/z ± tolerance value for the fragment ions. It is separate from the mass
tolerance value specified for the parent peak.
Note When using ion trap data, the application uses 300 mmu regardless of the
value you enter here.
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Figure 54. Fragments page
Table 33. Fragments page parameters (Sheet 1 of 2)
Parameter
Description
Ignore If Not Defined
Ignores the values you specify when no fragment is defined in the
compound database, and does not include the results for fragment
ions in the Data Review results.
Min. # of Fragments
Specifies the minimum number of fragments required to find the
compound.
Range: 1 to 5
Default: 1
Intensity Threshold
Specifies the minimum height of a fragment ion peak. The peak of
a fragment ion must be above this intensity threshold for the
application to find it.
Range: 1 to 1e9
Default: 10 000
Mass Tolerance
Specifies the number of millimass units or parts per million to use
as the m/z ± tolerance value for the fragment ions and is separate
from the mass tolerance specified for the parent (see “Editing the
Acquisition Page” on page 146).
Range: 0 to 500
Default: 5 ppm
Unit: mmu or ppm
Note When using ion trap data, the application uses 300 mmu
regardless of the value you enter here.
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Table 33. Fragments page parameters (Sheet 2 of 2)
Parameter
Description
Shortcut menu
Set Fragment Settings
to All Peaks in
Compound
Updates all peaks in the current compound with the current
settings on the Fragments page. These updates apply to both
quantitative and confirming ion peaks. The application
reprocesses all peaks in the compound and performs a new library
search.
Set Fragment Settings Updates all compounds in the method with the current settings
to All Peaks in Method on the Fragments page. These updates apply to both quantitative
and confirming ion peaks. When you use this command in the
local method for a processed batch, the application prompts you
to reprocess the batch to update the library settings.
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Ratios
Use the Ratios page to define the criteria for evaluating the confirming or qualifying ions. The
TraceFinder application detects compounds that have confirming ion values outside their
acceptable window and flags them in the Acquisition mode and in reports.
For detailed descriptions of all the features on the Ratios page, see Ratios page.
 To specify ion ratio criteria
1. Select the Enable check box to activate the confirming ion.
2. In the Target Ratio box, select the theoretical ratio of the confirming ion’s response to the
quantification ion’s response.
3. In the Window Type list, select Absolute or Relative as the calculation approach for
determining the acceptable ion ratio range.
4. In the Window (+/-%) box, select the acceptable ion ratio range.
5. In the Ion Coelution box, select the maximum difference in retention time between a
confirming ion peak and the quantification ion peak.
In the following example, the target ratio is expected to be 61.02% and the window is
Absolute 20%, so the acceptable window for this confirming ion peak is 41.02–81.02%.
However, if the window type is Relative, the plus or minus value is 20% of 61.02% (or
12.20%), so the acceptable window for this confirming ion peak is 48.82–73.22%.
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Figure 55. Ratios page
Table 34. Ratios page parameters
Parameter
Description
Enable
Makes the ion ratio criteria available.
Target Ratio (%)
The theoretical ratio of the confirming ion’s response to the
quantification ion’s response.
Window Type
The absolute or relative calculation approach for determining the
acceptable ion ratio range.
Window (+/-%)
The acceptable ion ratio range.
Ion Coelution (min)
The maximum difference in retention time between a confirming
ion peak and the quantification ion peak.
Shortcut menu commands
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Set Ion Ratio to All
Confirming Peaks in
Compound
Copies the Window Type, Window, and Ion Coelution values to
all confirming ion peaks for the compound and updates the
compound.
Available only when a compound has multiple confirming ion
peaks.
Set Ion Ratio to All
Confirming Peaks in
Method
Copies the Window Type, Window, and Ion Coelution values to
all quantitative peaks for the method and updates the method.
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Calibration
Use the Calibration page to set or edit the mathematical model used for preparing the initial
calibration evaluation for one or more calibration standards.
Each target compound can have its own initial calibration settings, independent of the other
compounds. You can modify the calibration approach on this page or in Acquisition mode
when you view the results of an actual calibration batch.
Typically, general quantitation uses a measured response (area or height) to determine the
amount of a compound contained in a sample. The application compares the response of an
unknown, target compound to the response of a calibration sample that contains a known
amount of the compound by building a calibration curve to interpolate the amount in the
target compound.
To use a semi-quantitative process, you specify the compound’s standard type as Estimated
and then identify another compound as the linked compound. Instead of using the target
compound to create a calibration curve, the application uses a calibration curve from the
linked compound to calculate the amount in the target compound.
To use a real sample for the calibration procedure, you specify the compound’s standard type
as Std Addition. The autosampler divides the sample into multiple portions (one unspiked
portion and at least two spiked portions). To maintain consistent conditions across all
samples, the autosampler adds selected amounts of standard into the vials and adds a volume
of a solvent calculated to maintain constancy in the total volume of liquid in each vial.
For detailed descriptions of all the features on the Calibration page, see “Calibration Page” on
page 217.
Follow these procedures:
• To specify an internal standard type for a compound
• To specify an estimated standard type for a compound
• To specify a standard addition standard type for a compound
 To specify an internal standard type for a compound
1. On the Identification page, specify at least one compound in the method as an internal
standard compound type. See “Identification” on page 158.
2. On the Calibration page, do the following:
a. In the Standard Type column, select Internal.
b. In the ISTD column, select the compound that you want to use as the internal
standard for this compound.
The application lists only compounds specified as internal standards on the
Identification page.
To view the internal standard peak in the Analysis mode, see “Compound Details” on
page 465.
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 To specify an estimated standard type for a compound
1. In the Standard Type column, select Estimated.
2. In the Linked Compound column, select any other compound in the method that you
want to link to this compound.
The Estimation Method value defaults to Ext Curve and is read-only.
The Compound Results in Data Review display the Calculated Amt value as N/F (not
found) highlighted in green.
 To specify a standard addition standard type for a compound
In the Standard Type column, select Std Addition.
• The Curve Type column value defaults to Linear and is read-only.
• The Origin column value defaults to Ignore and is read-only.
• The Weighting column value defaults to Equal and is read-only.
When you process this sample, the application divides the sample into multiple portions:
one portion is not spiked and at least two portions are spiked. The application calculates
the analyte concentration as intercept/slope, where intercept is the y-intercept of the
regression line and slope is the slope of the regression line.
When you use the Std Addition calibration, the y-intercept on the calibration curve might
not be at 0, as shown in the following figure:
The Compound Results in Data Review display the following:
• The Calculated Amt value is the spiked amount from the calibration curve.
• The Theoretical Amt value is the level defined in the method.
• The Sample Amt value is the actual amount in the standard spike plus the spiked
amount in each standard.
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Calibration Page
Use the features on the Calibration page to define the mathematical model used for preparing
the initial calibration evaluation for one or more calibration standards.
Figure 56. Calibration page
Table 35. Calibration page parameters (Sheet 1 of 2)
Parameter
Description
RT
Retention time. The time after injection when the compound elutes. The total time that the
compound is retained on the column.
Compound
The compound name.
Compound Type
Displays the compound type as a Target Compound or an Internal Standard.
Standard Type
Specifies Internal, External, Estimated, or Std Addition standards.
Response Via
The use of area or height. When you set the standard type to Estimated, this column is
inactive.
Curve Type
Specifies Linear, Quadratic, or AverageRF curve types. When you set the standard type to
Estimated, this column is inactive. When you set the standard type to Std Addition, this
column value defaults to Linear and is read-only.
Origin
The origin treatment is Ignore, Include, or Force. The Origin and Weighting columns are
available only when you use Linear or Quadratic curve types. When you set the standard
type to Estimated, this column is inactive. When you set the standard type to Std Addition,
this column value defaults to Ignore and is read-only.
Weighting
Specifies the weighting as Equal, 1/X, 1/X^2, 1/Y, or 1/Y^2. When you set the standard
type to Estimated, this column is inactive. When you set the standard type to Std Addition,
this column value defaults to Equal and is read-only.
Units
The units to be displayed with the calculated values.
ISTD
The internal standard (ISTD) for a target compound or surrogate. The list displays all
compounds with the compound type of Internal Standard. This column is available only
when you set the standard type to Internal.
Amount
The amount of the internal standard for ISTD compounds. When you set the standard type
to Estimated, this column is inactive.
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Table 35. Calibration page parameters (Sheet 2 of 2)
Parameter
Description
Linked Compound
This column is available only when the standard type is set to Estimated. The list of
available compounds to be linked does not include any compounds whose standard type is
set to Estimated.
Estimation Method
This column is unavailable for editing when the standard type is set to Estimated.
• When the compound type for the associated linked compound is Target Compound,
the estimation method is automatically set to Ext Curve.
• When the compound type for the associated linked compound is Internal Standard, the
estimation method is automatically set to Ratio.
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The Calibration page uses a right-click shortcut menu. See “Using the Shortcut Menu
Commands” on page 225.
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Calibration Levels
On the Calibration Levels page for a master method, you can define the standards for
calibration. You can edit calibration levels and concentrations for master methods only. The
contents of this page are read-only when you are editing a local method.
For detailed descriptions of all the features on the Calibration Levels page, see Calibration
Levels page.
You can use the copy-and-paste functions in the shortcut menu to copy calibration levels from
one column to another or from one master method to another. For detailed instructions, see
“Copying and Pasting Column Values” on page 226.
 To specify calibration levels and concentrations
1. Select the compound whose calibration levels and concentrations you want to define.
2. In the Manage Calibration Levels area, type a value for the first calibration level.
The application adds a new, empty calibration level row beneath the edited row.
3. Continue adding calibration levels.
When you finish adding calibration levels, you can specify the concentrations for each
compound at each level.
4. To enter the concentrations in the table, do the following:
a. Select the first calibration level table cell.
b. Click the cell again to make it editable.
c. Type a concentration value.
5. Repeat Step 4 for all calibration levels associated with the first compound.
6. To specify the same concentration values for all compounds, select the value that you
want to copy, right-click, and choose Copy Down from the shortcut menu.
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Figure 57. Calibration Levels page
Table 36. Calibration Levels page parameters
Parameter
Description
RT
Retention time. The time after injection when the compound
elutes. The total time that the compound is retained on the
column.
Compound
The compound name.
CalLevel_1–CalLevel_n
User-defined calibration levels for the compound. The names
you enter here become the column headers for the calibration
levels.
Manage Calibration Levels Defines values for each of the calibration level values for the
selected compound.
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The Calibration Levels page uses a right-click shortcut menu.
See “Using the Shortcut Menu Commands” on page 225.
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Chk Std Levels
Use the Chk Std Levels page for a master method to define the standards for Chk Std levels.
You can edit Chk Std levels for master methods only. The contents of this page are read-only
when you are editing a local method. Chk Std Levels page, see “Chk Std Levels page” on
page 222.
You can use the copy-and-paste functions in the shortcut menu to copy Chk Std levels from
one column to another or from one master method to another. For detailed instructions, see
“Copying and Pasting Column Values” on page 226.
 To specify Chk Std levels and concentrations
1. Select the compound whose Chk Std levels, percentage test values, and concentrations
you want to define.
2. In the Manage Chk Std Levels area, type a name for the first Chk Std level.
The TraceFinder application adds a new, empty Chk Std level row beneath the edited row.
3. Type a value for the % Test.
The % Test is the acceptable difference (as a percentage) between the known amount and
the calculated (measured) amount of each Chk Std level.
4. Continue adding Chk Std levels and values for the percentage test.
When you finish adding Chk Std levels, you can specify the concentrations for each level
for each compound.
5. To enter the concentration values in the table, do the following:
a. Select the first Chk Std level table cell.
b. Click the cell again to make it editable.
c. Type a concentration value.
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6. Repeat step 5 for all Chk Std levels associated with the first compound.
7. To specify the same concentration values for all compounds, select the value that you
want to copy, right-click, and choose Copy Down from the shortcut menu.
Figure 58. Chk Std Levels page
Table 37. Chk Std Levels page parameters
Parameter
Description
RT
Retention time. The time after injection when the compound
elutes. The total time that the compound is retained on the
column.
Compound
The compound name.
Level_1–Level_n
User-defined quality control levels for the compound.
Manage Chk Std Levels
Level
User-defined quality control level names. The names you enter
here become the column headers for the Chk Std levels.
% Test
A value for the acceptable difference (as a percentage) between the
known amount and calculated (measured) amount of each Chk
Std level.
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“Using the Shortcut Menu Commands” on page 225.
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Real Time Viewer
Use the Real Time Viewer page to specify which traces display in the Real Time Status pane
when you perform acquisition in the Acquisition mode. See “Real Time Status Pane” on
page 348.
Figure 59. Real Time Viewer page
Table 38. Real Time Viewer page parameters (Sheet 1 of 2)
Parameter
Description
Show Quan Peaks
Only
Displays only quantitative peaks in the compounds list. Quantitative peaks are indicated
with a black dot in the Quan Peak column.
Displayable Traces
Quan Peak
Dots indicate quantitative peak traces. Unmarked traces indicate confirming ion peaks.
Compound Name
Names of all compounds in the method.
Trace
Lists the simple mass or precursor mass for all traces—both quantitative peak and
confirming ion peak—for each compound.
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Table 38. Real Time Viewer page parameters (Sheet 2 of 2)
Parameter
Description
Moves the selected trace to the Traces to Display in Real Time Viewer pane.
Moves the selected trace to the Displayable Traces pane.
Moves all traces to the Displayable Traces pane.
To move multiple traces to the Traces to Display... pane, hold down the SHIFT key, select
multiple traces, and then click
.
Traces to Display in
Real Time Viewer (n/25)
List the traces to be displayed and the display order used in the real-time display in the
Acquisition mode. See “Real-Time Trace Display” on page 363.
Maximum number of traces is 25.
Move to Top
Moves the selected trace to the top of the Traces to Display... list and the second position in
the real-time display. The TIC is always the first position in the real-time display in the
Acquisition mode.
Move Up
Moves the selected trace up one position in the list.
Move Down
Moves the selected trace down one position in the list.
Move to Bottom
Moves the selected trace to the bottom of the list.
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Using the Shortcut Menu Commands
Each page on the Compounds page (except the Acquisition List and Real Time Viewer pages)
uses right-click shortcut menu commands to display or hide the retention column, remove
compounds from the method, copy and paste data, or save the compound list to a CSV file.
Table 39. Compounds page shortcut menu commands (Sheet 1 of 2)
Command
Description
Copy Down
Copies the value in the selected row to all rows below it. This
command is available only when you have selected a value that
can be copied down. See Appendix C, “Using Copy Down and
Fill Down.”
Display Retention Time Displays or hides the RT column in the compound list.
Column
Delete Compound From Removes the selected compound from the current master
Method
method.
Thermo Scientific
Copy
Copies the data in the selected rows or columns to the Clipboard.
Use this command to copy compound information to a text
editor or spreadsheet application. You cannot paste this data back
into the method development compound list.
Copy With Headers
Copies the data in the selected rows or columns and the
associated column headers to the Clipboard. Use this command
to copy sample information to a text editor or spreadsheet
application. You cannot paste this data back into the method
development compound list.
Paste
Pastes a single column of copied data from a text editor or
spreadsheet application into the selected column. The pasted
data must be valid data for the selected column.
Undo Last Paste
Removes the last pasted item in the method development
compound list.
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Table 39. Compounds page shortcut menu commands (Sheet 2 of 2)
Command
Description
Export to CSV File
Opens the Save As dialog box where you can save the current
compound list to a CSV file.
Sort by Compound
Name
Sorts the compounds alphabetically from A to Z.
Sort by Retention Time
Sorts the compounds from shortest retention time to longest
retention time.
Copying and Pasting Column Values
You can use the copy-and-paste functions in the shortcut menu to copy column values within
a master method or from one master method to another. You can use these copy-and-paste
techniques on any pages with grids of data in the Compounds and QAQC views.
After you copy grid values to the Clipboard, you can paste them into a text application such as
Notepad, an email, a spreadsheet, other grid cells in the same master method, or into another
master method.
Tip When copying data into an application other than a TraceFinder master method grid,
use the Copy with Headers command instead of the Copy command in the shortcut
menu to preserve the column headers.
Following these procedures:
• To copy a value from one cell to another cell
• To copy all values in a column to another column
• To copy multiple columns
• To copy an entire grid to another master method
 To copy a value from one cell to another cell
1. Select a cell value to copy to the Clipboard.
You can select either an entire table cell or just a cell value.
Cell is selected.
Cell value is selected.
2. Right-click and choose Copy from the shortcut menu.
The application copies either the selected cell value or the selected cell to the Clipboard.
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3. In this or another master method, select the cell value or table cell that you want to
overwrite.
• If you copied a cell value, you can select the cell value or simply click in the cell.
• If you copied an entire cell, you must select a table cell to overwrite.
4. Right-click and choose Paste from the shortcut menu.
The application replaces the selected value with the value copied to the Clipboard.
 To copy all values in a column to another column
1. Use the SHIFT key to select the column to copy.
2. Right-click and choose Copy from the shortcut menu.
3. In this or another master method, use the SHIFT key to select the column to overwrite.
4. Right-click and choose Paste from the shortcut menu.
The application overwrites the selected cells with the cells that you copied to the
Clipboard.
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 To copy multiple columns
1. Use the SHIFT key to select the columns to copy.
2. Right-click and choose Copy from the shortcut menu.
3. In this or another master method, use the SHIFT key to select the columns to overwrite.
4. Right-click and choose Paste from the shortcut menu.
The application overwrites the selected cells with the cells that you copied to the
Clipboard.
 To copy an entire grid to another master method
1. Use the SHIFT key to select all the columns in the grid.
2. Right-click and choose Copy from the shortcut menu.
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3. In another master method, use the SHIFT key to select the columns to overwrite.
4. Right-click and choose Paste from the shortcut menu.
The application overwrites the selected cells with the cells that you copied to the
Clipboard.
Note When the Clipboard contains more cells of data than there are selected target
cells for the paste operation, the application overwrites the selected cells and reports
that the Clipboard contents were truncated to fit the grid.
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Editing the QAQC Page
Use the QAQC page to set limits and ranges so that the TraceFinder application can review
the data and results as an aid to final approval.
On most QAQC pages, you can use the copy-and-paste functions in the shortcut menu to
copy grid values from one column to another or from one master method to another. For
detailed instructions, see “Copying and Pasting Column Values” on page 226.
 To open the QAQC page
Click QAQC in the Method View navigation pane.
Available only when you activate the
Intelligent Sequencing option in
the Configuration console.
From the QAQC page of the Method View, you can access these additional pages:
• Limits
• Calibration
• Chk Std
• Matrix Blank
• ISTD
• Solvent Blank
• Threshold
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Limits
Use the Limits page to define levels of review for quantified results. Quantified results appear
in printed and electronic reports. You can also define when a quantified value is reported
instead of reporting less than a particular limit.
Figure 60. Limits page
Table 40. Limits page parameters
Parameter
Description
RT
Retention time. The time after injection when the compound elutes. The total time that the
compound is retained on the column.
Compound
The compound name.
LOD
(Detection Limit)
Limit of detection. The lowest amount that can be detected. Usually derived from a method
detection limit (mdl) study.
LOQ
(Quantitation Limit)
Limit of quantitation. The lowest amount that can be confidently and accurately
quantitated. This is usually the lowest calibration amount.
LOR
Limit of reporting. Also called cutoff in some industries. This is the lowest amount that can
be reported, as determined by each laboratory’s standard operating practices.
ULOL
(Linearity Limit)
Upper limit of linearity. This is usually the highest calibrator amount.
Carryover Limit
The highest amount of a substance that does not leave a residual amount in the instrument.
If a substance has a carryover limit of 5, amounts higher than 5 usually dirty the instrument
and leave residue behind, tainting the following sample. A carryover limit of less than 5 does
not leave any residual amounts of the substance.
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Calibration
Use the Calibration page to define acceptable criteria for initial calibration. The TraceFinder
application compares the initial calibration results for each compound found in the sample to
the values defined on this page.
In the Calibration report, the application flags the calculated values for internal standard
compounds that exceed these limits.
Figure 61. Calibration page
Table 41. Calibration page parameters
Parameter
Description
RT
Retention time. The time after injection when the compound elutes. The total time that the
compound is retained on the column.
Compound
The compound name.
R^2 Threshold
The minimum correlation coefficient (r2) for an acceptable calibration (when in linear or
quadratic mode).
Max RSD (%)
The maximum relative standard deviation (RSD) for an acceptable calibration (when in
average RF mode).
Note This RSD value is not the same value used in Data Review or the Compound
Calibration Report. The application uses this RSD value when you select AverageRF as
the curve type for the method. See “Calibration Page” on page 217.
Min RF
The minimum average response factor (RF) for an acceptable calibration (when in average
RF mode).
Max Amt Diff (%)
The maximum deviation between the calculated and theoretical concentrations of the
calibration curve data points (when in linear or quadratic mode).
CV Test (%)
Coefficient of Variance test. The coefficient of variance percentage is the standard deviation
of the multiple samples of one level, multiplied by 100, and then divided by the average of
the multiple samples of that level. This calculation is based on the areas of the peaks.
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Chk Std
Use the Chk Std page to review the calibration on an ongoing basis. The TraceFinder
application compares the quality check standard results for each compound in the sample to
the initial calibration using values defined on this page.
In the QC Standard report, the TraceFinder application flags the calculated values for internal
standard compounds that exceed these limits.
For linear and quadratic modes, the maximum difference for the calculated concentration in
the QC Std sample versus the theoretical value is set on the QC Levels page of the
Compounds page.
Figure 62. Chk Std page
Table 42. Chk Std page parameters
Thermo Scientific
Parameter
Description
RT
Retention time. The time after injection when the compound
elutes. The total time that the compound is retained on the
column.
Compound
The compound name.
Max RF Diff (%)
The maximum deviation between the response factor (RF) of the
QC Std sample and the average response factor from the
calibration (when in average RF mode).
Min RF
The minimum response factor for the QC Std sample (when in
average RF mode).
CV Test (%)
Coefficient of Variance test. The coefficient of variance percentage
is the standard deviation of the multiple samples of one level,
multiplied by 100, and then divided by the average of the multiple
samples of that level. This calculation is based on the areas of the
peaks.
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Matrix Blank
Use the Matrix Blank page to define acceptable levels of target compounds in blank samples.
The TraceFinder application compares the calculated concentration for each compound in the
sample to the maximum concentration defined on this page. You can enter the maximum
concentration as a percentage of a flag value or as a specified value.
For detailed descriptions of all the features on the Matrix Blank page, see Matrix Blank page
parameters.
In the Matrix Blank report, the application flags the calculated values for target compounds
that exceed these limits.
 To specify the maximum concentration as a percentage
1. From the Method column list, select one of the following methods:
• % of LOD
• % of LOQ
• % of LOR
2. In the Percentage column, type a percentage value.
 To specify the maximum concentration
1. From the Method column list, select Concentration.
2. In the Max Conc column, type an absolute value.
Figure 63. Matrix Blank page
Table 43. Matrix Blank page parameters
Parameter
Description
RT
Retention time. The time after injection when the compound elutes. The total time that the
compound is retained on the column.
Compound
The compound name.
Method
The evaluation process used for comparing the calculated concentration. You can specify no
maximum, a specific concentration, or a percentage of the LOR, LOD, or LOQ.
Percentage
The percentage of the LOR, LOD, or LOQ if you are using the percentage approach.
Max Conc
The maximum concentration if you are using an absolute value.
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ISTD
Use the ISTD page to review the response and retention time of internal standards (when
available). The TraceFinder application compares the area and retention time results for each
internal standard compound in the sample to a specified range.
If all of your target compounds are set to external calibration mode or if you have not
identified any compounds as internal standards, this page does not show any values.
Figure 64. ISTD page
Table 44. ISTD page parameters
Parameter
Description
RT
Retention time. The time after injection when the compound elutes. The total time that the
compound is retained on the column.
Compound
The compound name.
Min Recovery (%)
The minimum and maximum percent recoveries for the internal standards to define an
acceptable range. For check standards, the TraceFinder application compares the response of
each internal standard in each sample to a range around the average of the responses of that
compound in all of the calibration standards. For all other samples, the application calculates
the comparison range around the check standard responses if a check standard is available in the
batch. If no check standard is available, the application tests against the initial calibration.
Max Recovery (%)
Min RT (–min)
Max RT (+min)
CV Test (%)
Thermo Scientific
The minimum and maximum drift (in minutes) for the internal standards to define an
acceptable range. For check standards, the TraceFinder application compares the retention time
of each internal standard in each sample to a range around the average of the retention times of
that compound in all of the calibration standards. For all other samples, the application
calculates the comparison range around the check standard retention times if a check standard
is available in the batch. If no check standard is available, the application tests against the initial
calibration.
Coefficient of Variance test. The coefficient of variance percentage is the standard deviation of
the multiple samples of one level, multiplied by 100, and then divided by the average of the
multiple samples of that level. This calculation is based on the areas of the peaks.
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Solvent Blank
Use the Solvent Blank page to view or edit QC values for solvent reporting. The application
compares the calculated response for each compound in the sample to the maximum response
defined on this page.
In the Solvent Blank report, the TraceFinder application flags the calculated values for target
compounds that exceed these limits.
Figure 65. Solvent Blank page
Table 45. Solvent Blank page parameters
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Parameter
Description
RT
Retention time. The time after injection when the compound
elutes. The total time that the compound is retained on the
column.
Compound
The compound name.
Method
The evaluation process to use as a response for the quantitation ion
only (Quan Ion RT) or as a summed response for the quantitation
ion and any confirming ions (All Ion RT). To deactivate the
solvent blank test for a specific compound, select None.
Upper Limit
Specifies an upper limit for each compound in the sample when
you select an evaluation process. These values are not
concentrations; they are raw response values.
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Threshold
Use the Threshold page (see “Threshold page” on page 238) to specify how to create a
threshold guide to overlay on compounds in the Comparative View in the Data Review mode.
For each compound, you can specify an absolute value or you can specify a percentage of the
peak height. The application uses the selected threshold method and the specified amount to
create a threshold guide in the Comparative View chromatograms. See “Comparative View”
on page 433.
When you create a batch, you can group samples and then specify a sample in the group as the
threshold sample to use in the Comparative View. For instructions about specifying a
threshold sample, see “Threshold Samples Page” on page 409.
In the following figures, the threshold for the dibutyl phthalate compound is 50 percent of
the peak height in the threshold sample, the samples Benzo26473, Benzo25557, and
Benzo26154 are members of groupB, and the threshold sample for the group is Benzo26473.
In the Comparative Data view, you can easily see that the peak height of dibutyl phthalate in
the other samples in the group is less than 50 percent of the peak height in the threshold
sample.
Figure 66. QAQC page in Method View
Threshold method
Threshold at 50% of the
peak height in the threshold
sample
Figure 67. Samples page in Batch View
Samples belong to the same group
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Figure 68. Threshold Samples page in Batch View
Benzo26473 selected as the
threshold sample for groupb
Figure 69. Comparative View in Data Review
Threshold sample
Threshold percentage - 50%
Figure 70. Threshold page
Table 46. Threshold page parameters (Sheet 1 of 2)
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Parameter
Description
RT
Retention time. The time after injection when the compound
elutes. The total time that the compound is retained on the
column.
Compound
The compound name.
Method
Specifies the threshold method as a specific peak height value
(Threshold) or as a percentage of the peak height in the threshold
sample (% of Threshold Sample).
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Table 46. Threshold page parameters (Sheet 2 of 2)
Parameter
Description
Threshold
Specifies the absolute peak height value to use when you select the
Threshold method. This value represents the default threshold
value to use when you do not specify a Threshold Sample for a
group of samples.
Default: 1.000
Percentage
Specifies the percentage of the peak height value to use when you
select the % of Threshold Sample method. This value represents a
percentage of the actual peak height in the Threshold Sample you
select for a group of samples. For instructions about specifying a
Threshold Sample, see “Threshold Samples Page” on page 409.
Default: 0.1
Range: 0.1 to 100.1
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Editing the Groups Page
Use the Groups page of the Method View to organize compounds into functional or logical
groups. You can use these groups for creating a subset of target compounds. For detailed
descriptions of all the features on the Groups page, see “Groups Page.”
For quantitative processing, the TraceFinder application processes all compounds in the
method and stores the complete result set, but only those in the selected group are visible in
the Acquisition mode. Limiting the displayed compounds to those in the selected group can
be useful when working with a master method containing a large list of compounds, only
some of which are required for analysis in certain samples. In that case, the application
requires only a single method and can reduce the results. To display only those compounds to
be used in quantitative processing, select Quan Compounds from the Show list.
You can create multiple groups and include the same compound in more than one group.
 To open the Groups page
Click Groups in the Method View navigation pane.
Available only when you activate the
Intelligent Sequencing option in
the Configuration console.
 To create a group
1. At the bottom of the Groups area, click Add Group.
The Add a New Group dialog box opens.
2. Type a name for the new group and click OK.
The new group appears in the Groups area.
3. Drag a compound from the Compounds area onto a group name (as if you were moving
files into a folder).
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4. To remove all the compounds from a group, rename the group, or delete it, right-click the
group name and choose from the shortcut menu.
5. To remove a single compound, right-click the compound name in the group and choose
Remove from Group from the shortcut menu.
Groups Page
Use the features on the Groups page to organize compounds into functional or logical groups.
Figure 71. Groups page
Table 47. Groups page parameters (Sheet 1 of 2)
Thermo Scientific
Parameter
Description
Compounds
Lists all available compounds.
Groups
Lists all available groups.
Add Group
Opens the Add a New Group dialog box where you can create a
new group.
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Table 47. Groups page parameters (Sheet 2 of 2)
Parameter
Description
Shortcut menu
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Empty Group
Removes all compounds from the selected group.
Rename Group
Changes the name of the selected group.
Delete Group
Removes the selected group and all the compounds in it.
Remove From Group
Removes the selected compound from its group.
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Editing the Intelligent Sequencing Page
Use the Intelligent Sequencing page to specify the actions you want the application to take
when there are acquisition failures with each sample type. The Intelligent Sequencing page is
available only when you activate the Intelligent Sequencing option in the Configuration
console. See “Intelligent Sequencing” on page 62.
 To open the Intelligent Sequencing page
Click Intel Seq in the Method View navigation pane.
The Intelligent Sequencing page opens.
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 To specify actions for sample acquisition failures
1. In the Sample Types list, select a sample type.
Each sample type has a specific set of failure flags. See “Sample-Specific Failure Flags” on
page 247.
2. For each failure flag, select a failure action.
The failure action choices are the same for each failure flag except flags for Solvent or
Matrix Blank sample types. The Solvent and Matrix Blank sample types do not have Auto
Sample or Auto Sample and Reinject failure actions.
Each Failure Action requires one or more of the following values:
• Sample Type
• Priority
• Max Action Count
• Failure Continuation
For a detailed description of each of these parameters, see “Actions” on page 246.
3. Select a sample type to use for the failure action.
This value is available only for Auto Sample and Auto Sample and Reinject failure
actions. When you create your samples list on the Auto Samples page, you must include
at least one sample with this sample type for the autosampler to use when it encounters
this error condition. See “Auto Samples Page” on page 406.
4. In the Priority column, type a priority value for this action.
The priority value can be any positive or negative integer.
• The application performs the failure action for the highest priority failure it
encounters and ignores all others.
• When you assign the same priority to two or more failures, the application performs
the failure action for the first failure it encounters and ignores all others.
5. In the Max Action Count column, type a value for the maximum number of times the
application should repeat a sample.
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6. In the Failure Continuation column, do one of the following:
• Select the check box to skip this sample and continue to the next sample when this
sample exceeds the Max Action Count value.
• Clear the check box to stop the batch when this sample exceeds the Max Action
Count value.
Example
The following example shows the actions that the TraceFinder application uses when the
acquisition for a sample fails.
2
1
3
4
5
6
1. The acquisition encounters an Ion Ratio Failure error on a sample.
2. The application runs a Solvent sample.
3. The application reinjects the original sample.
4. This action is priority 0 in the Acquisition queue.
5. The application repeats this autosample and reinject process two times.
6. After repeating the failure action two times, the application skips the sample and
continues to the next sample.
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Actions
Use the Actions pane to specify what action the application takes when it encounters a
submission failure for the type of failure flag associated with each sample type.
Table 48. Actions parameters (Sheet 1 of 2)
Parameter
Description
Flag
Flag (error) types specific to each sample type. See Sample-Specific
Failure Flags. Each flag type has a set of user-specified actions that
the application follows when it encounters this error.
Failure Action
In the event of a failed sample, the application does one of the
following:
• Continue: Continues to the next sample in the batch.
• Stop: Stops the batch.
• Auto Sample: Injects the sample type specified for the Auto
Sample Type parameter and continues to the next sample.
• Reinject: Reinjects the current sample by inserting a “reinject”
sample in the batch.
• Auto Sample and Reinject: Injects the sample type specified
for the Auto Sample Type parameter and then reinjects the
failed sample.
Sample Type
Specifies either a Solvent or Matrix Blank sample type to use for
the auto sample injection.
Default: Solvent
Priority
The priority value can be any positive or negative integer.
When two or more failures have the same priority, the application
performs the failure action for the first failure it encounters and
ignores all others.
The application performs the failure action for the highest priority
failure and ignores all others.
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Table 48. Actions parameters (Sheet 2 of 2)
Parameter
Description
Max Action Count
Specifies the maximum number of times the application should
repeat a sample before it continues to the next sample or stops the
sequence, as determined by the value in the Failure Continuation
parameter.
Default: 1
Failure Continuation
When this check box is selected, samples that exceed the value
specified for the Max Action Count parameter cause the
application to skip the sample and continue to the next sample.
Default: Selected
When this check box is cleared, samples that exceed the value
specified for the Max Action Count parameter cause the
application to stop the batch.
Sample-Specific Failure Flags
Each sample type has a specific set of failure flags.
Sample Type
Thermo Scientific
Flag
Matrix Blank
• Blank
Cal Std
• Out of Range
• Ion Ratio Failure
• Carryover
QC Std
• Ion Ratio Failure
• Carryover
• Out of Range
Solvent
• Solvent Flag
Unknown
• Ion Ratio Failure
• Carryover
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Editing the Reports Page
Use the Reports page to specify how you want to save or print your reports. For detailed
descriptions of the features on the Reports page, see Reports Page.
For the quantitation report types, you can modify quantitation limits flags, user interface
options, and quantitation flag options on the Quan Report Settings page.
This section includes instructions for the following tasks:
• Specifying Report Formats
• Specifying Quan Report Settings
Specifying Report Formats
For each report type, you can create a hard-copy printout, a PDF file, or an XML file.
 To open the Reports page
Click Reports in the Method View navigation pane.
Available only when you activate the
Intelligent Sequencing option in
the Configuration console.
The Reports page opens with a list of all configured reports.
To configure which reports are available when you create a master method or which
reports create a batch-level report, see “Specifying the Reports” on page 72.
 To specify report types and output formats
1. To edit the Report Title, double-click the name and type your new custom title.
The TraceFinder application uses this title for all reports that use this master method. You
cannot edit the Report Title from other report views.
2. To specify the type of report output to create for each report type, select the check box in
the appropriate column.
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3. To duplicate an output type for all reports, click the cell to select it, and then right-click
and choose Copy Down from the shortcut menu.
All check boxes in the column below the selected cell duplicate the selected or cleared
state of the selected cell. This action applies only to reports where this output format is
available. By default, all report types are cleared.
Reports Page
Use the features on the Reports page to specify how you want to save or print your reports.
Figure 72. Reports page
Table 49. Reports page parameters
Parameter
Description
Report list columns
Thermo Scientific
Report
The name of a report.
Print
Sends reports to the default printer.
Create PDF
Saves reports as PDF files.
Create CSV
Saves reports as CSV files.
Create Excel
Saves reports as Excel files.
Found
Indicates that the report template is identified in the
C:\TraceFinderData\32\Templates\ReportTemplates folder.
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Specifying Quan Report Settings
Use the options on the Quan Report Settings page to choose parameters for flagging values
and displaying information in reports. See “Quan Report Settings Page” on page 252.
Follow these procedures:
• To specify quantitation limits
• To specify user interface options
• To specify quantitation flag options
 To specify quantitation limits
1. To report the calculated concentration at all times or only when the quantified value
exceeds LOD, LOQ, or LOR, choose the appropriate value from the Report
Concentration list.
For a description of concentration limits, see “Editing the QAQC Page” on page 230.
2. To select the number of decimal places to report for calculated concentrations, set the
value in the Decimal Places to be Reported box.
3. To include a chromatogram of the sample in the Quantitation Report, select the Show
Chromatogram on Quantitation Report check box.
4. To display only valid compounds, select the Display Compounds Above Set Limit
check box.
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 To specify user interface options
1. To shade a compound row in any of the reports if a value fails one of the criteria used for
evaluation, select the Shade Row when Sample is Outside of Evaluation Criteria
check box.
2. To separate the ion overlay pane from the confirming ion plots, select the Separate Ion
Overlay Display check box.
3. To use an alternate format for the Calibration Report designed to print more concisely
and limit the report to a maximum of seven calibration standards, select the Use
Alternate Calibration Report Format check box.
 To specify quantitation flag options
Select the values that you want to display in the report.
Values are above or below the limits defined on the Quan page.
These flags appear in a variety of reports and are defined in “Quan Report Settings page
parameters” on page 252.
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Quan Report Settings Page
Use the features on the Quan Report Settings page to specify parameters for flagging values
and displaying information in reports.
Figure 73. Quan Report Settings page
Table 50. Quan Report Settings page parameters (Sheet 1 of 2)
Parameter
Description
Quan Limits Flags
Report Concentration
Reports the concentration at all times or only when the quantified value exceeds either the
limit of detection (LOD), the limit of quantitation (LOQ), or the limit of reporting (LOR).
Report concentration: Always, >LOD, >LOQ, or >LOR.
Decimal Places to be
Reported
Number of decimal places to be included in the report. Maximum value is 6.
Show Chromatogram
on Quantitation
Report
Displays a chromatogram (TIC trace) of the sample in the quantitation report.
Display Compounds
Above Set Limit
Prints reports for only the compounds that are found in a sample. If a compound is above
the specified Quan Flag Options limits, the TraceFinder application reports the compound.
This prevents generating “empty” reports for the compounds that are not found.
User Interface Options
Shade Row When
Sample is Outside of
Evaluation Criteria
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Shades a compound row in any of the reports if a value fails one of the criteria used for
evaluation.
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Table 50. Quan Report Settings page parameters (Sheet 2 of 2)
Parameter
Description
Separate Ion Overlay
Display
Separates the ion overlay pane from the confirming ion plots in an analysis.
Use Alternate
Calibration Report
Format
Uses an alternate format for the Calibration Report that is designed to print more concisely
(this report is limited to a maximum of seven calibration standards).
Quan Flag Options
Values that are above or below limits defined on the Limits page. These flags appear in a
variety of reports.
Flag Values Below
LOD
Flags values below the limit of detection (LOD).
Flag Values Below
LOQ
Flags values below the limit of quantitation (LOQ).
Flag Values Above
LOR
Flags values above the limit of reporting (LOR).
Flag Values Above
ULOL
Flags values above the upper limit of linearity (ULOL).
Flag Values Above
Carryover
Flags values above the carryover limit.
Flag Values Between
LOD and LOQ
Flags values between the limit of detection and the limit of quantitation known as the J flag.
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Saving a Master Method to a New Name
Saving a Master Method to a New Name
You can save any method to a new name, or you can use the current method data to overwrite
an existing method. The new method contains all the data of the saved method.
 To save a method to a new name
1. From the main menu, choose File > Save As.
The Save Master Method As dialog box opens, displaying all available methods.
Table 51. Save Master Method As dialog box parameters
Parameter
Description
Method
Name of the methods for the selected type.
Type
Type of method: Quan or Screening.
Date Changed
Date the method was last updated.
Size
Size in megabytes.
Domain
TraceFinder domain for which the method was created.
New Method
Name of the new method to create.
Path
Path to the selected method in the Methods folder.
2. Do one of the following:
• In the New Method box, type a name for the new method.
The application enables the Save button.
• In the Method column, select a method to overwrite.
The application enables the Overwrite button.
3. Click Save or Overwrite.
The application saves all the method data using the specified name and opens the
Acquisition page of the new method.
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Creating a Method Template
Creating a Method Template
In the TraceFinder application, you can create a processing method using a method template
that contains common settings. You can create a method template that specifies peak
detection criteria, screening libraries, confirming ion criteria, compound calibration, and
qualitative peak processing. For a complete description of the features in the Method
Template Editor, see “Method Template Editor” on page 261.
The application uses the settings in the method template to identify the data to display in the
Qualitative View. See “Qualitative View” on page 441.
Only quantitation methods use method templates.
Follow these procedures:
• To open the Method Template Editor
• To specify peak criteria
• To identify the peaks
• To specify confirming ions
• To calibrate the compounds
• To save the method template
 To open the Method Template Editor
1. Click Method Development in the navigation pane.
The Method Development navigation pane opens.
2. Click Method View.
3. From the main menu, choose File > New > Method Template.
The Method Template Editor opens. See “Method Template Editor” on page 261.
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 To specify peak criteria
Note Parameters in the Find the Peaks* area might also be used for qualitative peak
processing.
1. In the Find the Peaks area, select a sensitivity level.
In selecting the degree of sensitivity, you define how extensively the peak detector
algorithm searches for low-level peaks.
• The Genesis peak detection algorithm provides backward compatibility with
Xcalibur 1.0 studies.
• The ICIS peak detection algorithm is designed for MS data and has superior peak
detection efficiency at low MS signal levels.
• The Avalon peak detection algorithm is designed for integrating UV/Vis and analog
chromatograms.
2. To look for peaks only in a certain range of the entire chromatogram, select the Limit the
Retention Time Range check box and specify a retention time (RT) range.
3. To indicate whether to select peaks by relative height or area and the percentage of the
highest peak that results in compound selection, select the Enable Peak Threshold check
box.
To consider a peak for a processing method, the TraceFinder application uses the Enable
Peak Threshold filter to determine which peaks meet the specified percentage of the
height or area of the largest peak.
4. To display a specific number of the largest peaks by height or area, select the Only Select
Top Peaks check box and enter the number of peaks to display.
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 To identify the peaks
Note Parameters in the Identify the Peaks* area might also be used for qualitative
peak processing.
1. In the Use these Libraries box, select the libraries that you want to search.
All libraries loaded on your instrument are displayed in the Use these Libraries box.
2. To limit the number of hits returned when the system searches a spectrum against the
selected libraries, set a value in the Limit Library Hits box.
3. To specify how to sort the library searches, select a value from the Best Match Method
list.
 To specify confirming ions
1. To set the number of confirming ions, select the Include Confirming Ions check box
and enter a value in the Number of Confirming Ions box.
This value is the number of other ions in the spectrum whose ratio is compared to the
quantitation ion. Using this ratio, you can then determine if it is the target compound or
something else. You can set this value to integers from 1 to 10, inclusive. This value
defaults to 2 because you typically perform a 3-ion experiment with one quantitation
mass and two confirming ions.
The system selects the most intense ion to use as the quantitation mass and uses this mass
for the mathematical operations.
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2. To define the criteria for evaluating confirming or qualifying ions, select the Specify
Default Ion Ratio Ranges check box and set the following values:
a. To specify the maximum difference in retention time between a confirming ion peak
and the quantification ion peak, set a value in the Ion Coelution (min) box.
b. To specify an absolute or relative calculation approach for determining the acceptable
ion ratio range, select Absolute or Relative from the Window Type list.
c. To specify the acceptable ion ratio range, set a value in the Window (+/– %) box.
3. To include the peak spectrum in the processing method, select the Include Compound
Peak Spectrum as Reference Spectrum check box.
 To calibrate the compounds
1. From the Calibration Method list, select Internal or External.
2. From the Curve Type list, select one of the following:
• Linear: All other settings are available with this exception: When you select Include
in the Origin list, the Weighting parameter is unavailable.
• Quadratic: All other settings are available with this exception: When you select
Include in the Origin list, the Weighting parameter is unavailable.
• Average RF: The Weighting and Origin parameters are unavailable.
3. From the Origin list, select one of the following:
• Ignore: Specifies that the origin is not included as a valid point in the calibration
curve when the curve is generated. When you select Ignore, the calibration curve
might or might not pass through the origin.
• Force: Specifies that the calibration curve passes through the origin of the data point
plot when the calibration curve is generated.
• Include: Specifies that the origin is included as a single data point in the calculation
of the calibration curve. When you select Include, the calibration curve might or
might not pass through the origin.
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4. From the Weighting list, select one of the following:
• Equal: Specifies that the origin is included as a single data point in the calculation of
the calibration curve. When you select Equal, the calibration curve might or might
not pass through the origin.
• 1/X: Specifies a weighting of 1/X for all calibration data points during the
least-squares regression calculation of the calibration curve. Calibrants are weighted
by the inverse of their quantity.
• 1/X^2: Specifies a weighting of 1/X^2 for all calibration data points during the
least-squares regression calculation of the calibration curve. Calibrants are weighted
by the inverse of the square of their quantity.
• 1/Y: Specifies a weighting of 1/Y for all calibration data points during the
least-squares regression calculation of the calibration curve. Calibrants are weighted
by the inverse of their response (or response ratio).
• 1/Y^2: Specifies a weighting of 1/Y^2 for all calibration data points during the
least-squares regression calculation of the calibration curve. Calibrants are weighted
by the inverse of the square of their response (or response ratio).
5. From the Response Via list, select Area or Height.
• Area: Specifies that the TraceFinder application use this area value in response
calculations.
• Height: Specifies that the application use this height value in response calculations.
 To specify qualitative peak processing
1. Select the Use Genesis Algorithm for Qual Processing check box and specify a value for
internal standard matching.
The application uses the Genesis algorithm to match internal standards in a range
plus/minus the value that you specify. For additional information about the Genesis
algorithm, see “Genesis Detection Method” on page 42.
This parameter is available only when you set the Sensitivity parameter in the Find the
Peaks area to ICIS or Avalon. When you select the Use Genesis Algorithm for Qual
Processing check box, the application ignore the Sensitivity parameter in the Find the
Peaks area.
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2. Select or clear the Exclude Matching Quan Peaks check box and specify a value for the
exclusion window.
The application excludes quantitative peaks in a range plus or minus the value that you
specify.
3. To process samples that include data-dependent scans, select the Use Data Dependent
Scans check box.
When you process a sample using this feature, the application uses the TIC trace to find
all data-dependent full scans, lists them, and performs a library search against the
data-dependent MS/MS or MSn scan.
This option constrains the Data Review to only data-dependent scan spectra. See
“Working in the Local Method View” on page 516.
In addition to the peak information, the TIC Report and TIC Summary Report display
information about the data-dependent filtered data.
4. To indicate whether to select peaks above a minimum percentage of the nearest internal
standard peak that results in compound selection, select the Enable ISTD Threshold
check box and specify a minimum percentage.
To consider a peak for a processing method, the TraceFinder application uses the Enable
ISTD Threshold filter to determine which peaks meet the specified percentage of the
height of the nearest internal standard peak.
When you select the Enable ISTD Threshold parameter, the method ignores values set for
the Enable Peak Threshold and Only Select Top Peaks parameters. See “To specify peak
criteria” on page 256.
Note When you create a method with the Method Forge, the application ignores the
parameters in the Qualitative Peak Processing area.
 To save the method template
1. Choose File > Save from the Method Template Editor menu.
The Save Method Template dialog box opens.
2. Do one of the following:
Type a new name for the master method and click OK.
–or–
Select a method name to overwrite and click Overwrite.
The TraceFinder application saves the new method template in the following folder:
…\TraceFinderData\32\Templates\Methods\General
Saved method templates are available when you create a method using Method Forge. See
“Creating a New Method with Method Forge” on page 125.
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Method Template Editor
Use the features in the Method Template Editor to specify peak detection criteria, screening
libraries, confirming ion criteria, compound calibration, and qualitative peak processing.
Figure 74. Method Template Editor dialog box
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Table 52. Method Template Editor dialog box parameters (Sheet 1 of 3)
Parameter
Description
Find the peaks
Sensitivity
Defines how extensively the peak detector algorithm searches for low-level peaks.
Limit the Retention
Time Range
Min RT specifies the beginning of the range. Max RT specifies the end of the range.
Enable Peak Threshold
Specifies whether to select peaks by relative height or area and the percentage of the highest
peak that results in compound selection.
Only Select Top Peaks
Displays a specific number of the largest peaks by height or area.
Identify the peaks
Use These Libraries
Lists the libraries that you can search.
Limit Library Hits
Specifies the number of hits returned when the system searches a spectrum against the
selected libraries.
Best Match Method
Specifies how to sort the library searches.
Valid values: Search Index, Reverse Search Index, Match Probability
Handle confirming ions
Include Confirming
Ions/
Number of Confirming
Ions
Specifies the number of confirming ions, which are other ions in the spectrum whose ratio
is compared to the quantitation ion to identify the compound.
This value defaults to 2 because you typically perform a 3-ion experiment with one
quantitation mass and two confirming ions.
Range: Integers from 1 to 10, inclusive.
Specify Default Ion
Ratio Ranges
Enables the ion ratio range features.
Ion Coelution specifies the maximum difference in retention time between a confirming
ion peak and the quantification ion peak.
Window Type specifies an Absolute or Relative calculation approach for determining the
acceptable ion ratio range.
Window (+/-%) specifies the acceptable ion ratio range.
Include Compound
Peak Spectrum as
Reference Spectrum
Includes the peak spectrum in the processing method. Use this setting to perform a spectra
comparison in Data Review.
Calibrate the compounds
Calibration Method
Specifies an internal or external calibration method.
Curve Type
Specifies a linear, quadratic, or average RF curve type.
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Table 52. Method Template Editor dialog box parameters (Sheet 2 of 3)
Parameter
Description
Origin
Specifies that the origin is ignored, forced, or included in the generated calibration curve.
• Ignore: Specifies that the origin is not included as a valid point in the calibration curve
when the curve is generated. When you select Ignore, the calibration curve might or
might not pass through the origin.
• Force: Specifies that the calibration curve passes through the origin of the data point
plot when the calibration curve is generated.
• Include: Specifies that the origin is included as a single data point in the calculation of
the calibration curve. When you select Include, the calibration curve might or might
not pass through the origin.
Weighting
Specifies the weighting for the calibration data points.
• Equal: Specifies that the origin is included as a single data point in the calculation of
the calibration curve. When you select Equal, the calibration curve might or might not
pass through the origin.
• 1/X: Specifies a weighting of 1/X for all calibration data points during the least-squares
regression calculation of the calibration curve. Calibrants are weighted by the inverse
of their quantity.
• 1/X^2: Specifies a weighting of 1/X^2 for all calibration data points during the
least-squares regression calculation of the calibration curve. Calibrants are weighted by
the inverse of the square of their quantity.
• 1/Y: Specifies a weighting of 1/Y for all calibration data points during the least-squares
regression calculation of the calibration curve. Calibrants are weighted by the inverse
of their response (or response ratio).
• 1/Y^2: Specifies a weighting of 1/Y^2 for all calibration data points during the
least-squares regression calculation of the calibration curve. Calibrants are weighted by
the inverse of the square of their response (or response ratio).
Response Via
Specifies if the TraceFinder application uses area or height in response calculations.
• Area: Specifies that the application use this peak area value in response calculations.
• Height: Specifies that the application use this peak height value in response
calculations.
Qualitative Peak Processing
Use Genesis Algorithm
For Qual Processing
The application uses the Genesis algorithm to match internal standards.
ISTD Matching
Excludes all the target compounds found in the method and does not list these compounds
in the TIC Report or in the Qual Mode view in the Data Review.
Exclude Matching Quan Compares the retention time of the internal standard in the method to the found retention
time of the internal standard in the library search and excludes peaks outside the Exclusion
Peaks
Window range.
Exclusion Window
Thermo Scientific
Defines a range plus/minus the Exclusion Window value that you specify.
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Table 52. Method Template Editor dialog box parameters (Sheet 3 of 3)
Parameter
Description
Use Data Dependent
Scans
Constrains the Data Review to only data-dependent scan spectra. See “Working in the
Local Method View” on page 516. In addition to the peak information, the TIC Report
and TIC Summary Report display information about the data-dependent filtered data.
Enable ISTD Threshold Specifies that, when identifying a peak, qualitative peak processing use the minimum
threshold specified as a percentage of the nearest internal standard peak, rather than the
threshold specified in the Enable Peak Threshold and Only Select Top Peaks parameters.
See Enable Peak Threshold or Only Select Top Peaks in this parameter table.
% of Internal
Standard
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Percentage of the nearest internal standard peak to use as the minimum threshold for
identifying a peak.
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Importing Published Master Methods
Importing Published Master Methods
In the TraceFinder application, you can import published methods to use for detecting,
processing, and reporting. The TraceFinder installation provides the following folder of
published methods:
…\Thermo\TraceFinder\3.2\General\Published Master Methods
 To import a published master method
1. Choose Method View > Import Published Method from the main menu.
The Import Published Method dialog box opens.
2. Select a method to import.
3. Click Import.
The application reports that the method successfully imported and saves the method in
the following folder:
…\TraceFinderData\32\Templates\Methods\General
You can use any of the Open Method commands to open this method just as you would a
method that you created.
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Exporting Mass Data
Exporting Mass Data
You can export the mass data list from the Compounds page to an XML file that can be read
by the TSQ, ISQ, Q Exactive, TSQ Endura, or TSQ Quantiva applications. You can export
mass data only from quantitation methods.
 To export mass data list to an XML file
1. Open the master method whose mass data list you want to export.
If you make changes to the method, you must save it before you can export the mass data
list.
2. To view a list of your mass data, click the Acquisition List tab on the Compounds page.
You do not have to display the Acquisition List to export the data, but the compounds in
the Acquisition List must contain at least one experiment type appropriate to the export
file format. For information about displaying the Acquisition List, see “Acquisition List”
on page 156. For information about editing the experiment type for a compound, see
“Editing Compounds in the Database” on page 89.
3. Choose Method View > Export Mass List from the main menu.
IMPORTANT If you have neither a TSQ, an ISQ, a Q Exactive, a TSQ Endura, nor
TSQ Quantiva instrument configured, a message asks which format you want to
export: Triple Quadrupole, Q Exactive, TSQ Quantiva/Endura SIM, or TSQ
Quantiva/Endura SRM.
The application writes the mas data in the Acquisition List to the following folder, using a
format compatible with your configured instrument:
…\TraceFinderData\32\Methods\Methodname
For examples of exported mass lists, see the following:
• “Triple Quadrupole Format” on page 81
• “Q Exactive Format” on page 81
• “TSQ Quantiva/Endura SIM Format” on page 81
• “TSQ Quantiva/Endura SRM Format” on page 82
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Using the Method Development Mode for Screening
Methods
This chapter includes method development tasks for creating and editing screening master
methods. When user security is activated, you must have Method Development Access
permission before accessing these features.
Contents
• Opening a Master Method
• Creating a Master Method
• Editing a Master Method
• Saving a Master Method to a New Name
• Importing Published Master Methods
The TraceFinder application uses a master method to specify the nature and types of
acquisition, processing, and reporting that occur with a batch of samples. When you are
testing for compounds in an assay, you can create a method designed specifically for that type
of application.
When you create a master method, the TraceFinder application uses the method to determine
how the software works with a set of samples to provide a set of meaningful results. The
application uses an instrument method to define how raw data is acquired. The rest of the
master method defines how the raw data is processed, how the flags information displays the
results, and how the reporting functionality defines the output for your data and results.
The TraceFinder application applies your master method to a batch, which is a list of one or
more samples to be processed and reported. Together, the master method and batch provide a
workflow-oriented approach to the data processing and information reporting for batches of
samples.
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Opening a Master Method
Opening a Master Method
A target screening master method contains compound databases, identification and
confirmation criteria used in detecting and processing, and settings for reporting compounds.
When you open a target screening master method, the Method View navigation pane displays
the available pages for screening methods. For descriptions of all the features in the Method
Development navigation pane, see “Method Development navigation pane” on page 270.
 To open a screening method in the Method Development mode
1. Click Method Development in the navigation pane.
The Method Development navigation pane opens.
2. Choose File > Open > Master Method from the main menu.
The Open Master Method dialog box opens, displaying all available methods.
Figure 75. Open Master Method dialog box
Table 53. Open Master Method dialog box parameters (Sheet 1 of 2)
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Parameter
Description
Method
Name of the methods for the selected type.
Type
Type of method: Quan or Screening.
Date Changed
Date the method was last updated.
Size
Size in megabytes.
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Table 53. Open Master Method dialog box parameters (Sheet 2 of 2)
Parameter
Description
Domain
TraceFinder domain for which the method was created.
Type
Type of method to display: Quan, Screening, or Any.
Path
Path to the selected method in the
TraceFinderData\32\Methods\General folder.
Tip You can also open one of your most recently used master method files. Choose
Files > Recent Files > Method.
3. Select Screening in the Type list.
The method list displays only target screening methods.
4. Select a master method and click Open.
The Acquisition page for the selected method opens. To edit the master method, see
“Editing a Master Method” on page 273.
The navigation pane displays the available pages for screening methods. For descriptions
of all the features in the Method Development navigation pane, see Method
Development navigation pane.
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Figure 76. Method Development navigation pane
Table 54. Method Development navigation pane commands
Command
Description
Method View
Acquisition
Displays the Acquisition page of the Method View. Use the
features on the Acquisition page to define basic information about
the master method. See “Editing the Acquisition Page” on
page 273.
Screening
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Processing
Displays the Processing page of the Method View. Use the features
on the Processing page to specify peak filter settings, screening
databases, and identification and confirmation settings for a
screening method. See “Editing the Processing Page” on page 277.
Peak Detection
Displays the Peak Detection page of the Method View. Use the
features on the Peak Detection page to specify any of the following
peak detection algorithms: Genesis, ICIS, or Avalon. See “Editing
the Peak Detection Page” on page 295.
Reports
Displays the Reports page of the Method View. See “Editing the
Reports Page” on page 306.
Compound Database
See “Working with the Compound Database” on page 76.
Instrument View
See “Working with Instrument Methods” on page 113.
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Creating a Master Method
Creating a Master Method
The following procedure includes the minimum parameters you must define to create and
save a master method. For a detailed description of how to modify all parameters in a master
method, see “Editing a Master Method” on page 273.
 To create a new method
1. Choose File > New > Master Method from the main menu.
The Create Master Method dialog box opens.
2. Select the Create Screening Method option and click OK.
The Method View for a target screening method includes the Acquisition, Processing,
Peak Detection, and Reports pages.
The Acquisition page for the method opens.
3. From the Instrument Method list, select an instrument method.
4. Click Processing in the Method View navigation pane.
The Processing page for the method opens. The application lists the compound databases
(.cdb) that are stored in the following folder:
…\Thermo\TraceFinder\3.2\General\Databases
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5. Select the Enabled check box for at least one compound database.
You must select at least one compound database before you can save the method. The
target screening method uses only the target list of compounds in the selected compound
databases to identify the compounds in the samples.
6. To save the new method, choose File > Save from the main menu.
7. In the Save Master Method dialog box, type a name for the method and click OK.
For a detailed description of how to modify a master method, see Editing a Master
Method.
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Editing a Master Method
You can open a master method to specify method instructions, reporting options, peak filter
settings, screening databases, identification and confirmation settings, and peak detection
parameters.
This section includes instructions for the following tasks:
• Editing the Acquisition Page
• Editing the Processing Page
• Editing the Peak Detection Page
• Editing the Reports Page
Editing the Acquisition Page
Use the features on the Acquisition page to define basic information about the master
method.
 To edit the parameters on the Acquisition page
1. Click Acquisition in the Method View navigation pane.
The Acquisition page for the method opens. See “Acquisition Page” on page 275.
2. In the Lab Name box, type the name to be displayed on the top of each printed, saved, or
exported report.
The default name is Default Laboratory.
3. In the Assay Type box, type the assay type to be targeted by the method.
4. From the Injection Volume box, select the injection volume (in μL) to be used for sample
injection.
Range: 0.1 to 2000 μL
Use the up/down arrows to change the volume in increments/decrements of 1.0 μL, or
use the keyboard to enter non-integer injection volumes.
IMPORTANT The TraceFinder application uses this injection volume in the master
method, not the injection volume in the instrument method.
5. From the Mass Precision box, select the number of decimal places to be used in reports
and in peak and spectrum displays.
Valid values: Integers from 2 to 6, inclusive
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6. From the Instrument Method list, select an instrument method.
7. To edit the instrument method, click Edit.
The Thermo Xcalibur Instrument Setup dialog box opens. The following example of an
instrument setup shows multiple configured instruments.
Figure 77. Thermo Xcalibur Instrument Setup window
8. Edit the values on the instrument page for your instrument.
9. From the main menu in the Thermo Xcalibur Instrument Setup dialog box,
choose File > Save and then choose File > Exit.
The TraceFinder application returns you to the Acquisition page of the Method View.
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Acquisition Page
Use the features on the Acquisition page to define basic information about the master
method.
Figure 78. Acquisition page for a screening method
Table 55. Acquisition page parameters (Sheet 1 of 2)
Parameter
Description
Lab Name
The laboratory name to be displayed on the top of each printed,
saved, or exported report.
Default: Default Laboratory
To specify this default laboratory name, see “Specifying
Application Defaults” on page 35.
Assay Type
The name for the analysis type to be targeted by the method. The
assay type associates the method with the analysis of a compound
or specific class of compounds (for example, you might use an
assay type of PAH for the analysis of Polynuclear Aromatic
Hydrocarbons).
Injection Volume
The system uses the injection volume (in μL) for sample injection.
For a more detailed explanation, refer to the documentation for
the autosampler.
The injection volume in the master method overrides the injection
volume in the instrument method.
The injection volume in the batch overrides the injection volume
in the master method.
Range: 0.1 to 2000 μL
Mass Precision
Thermo Scientific
Number of decimal places used in reports and in peak and
spectrum displays.
Valid values: Integers from 2 to 6, inclusive
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Table 55. Acquisition page parameters (Sheet 2 of 2)
Parameter
Description
Instrument Method
Instrument method used for acquiring samples.
Edit
Opens the Thermo Xcalibur Instrument Setup dialog box where
you can edit the instrument method.
Update
Choose one of the following:
• Send to System Methods: Overwrites the instrument method
in the C:\TraceFinderData\32\Methods folder with the
current instrument method.
• Get From System Methods: Overwrites the current
instrument method with the instrument method in the
C:\TraceFinderData\32\Methods folder.
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Editing the Processing Page
Use the features on the Processing page to specify peak filter settings, screening databases, and
identification and confirmation settings for a master method.
This section includes instructions for the following tasks:
• To open the Processing page
• To specify peak filter settings
The Peak Filter Settings pane displays parameters for limiting the display of unwanted
data.
• To specify compound databases
The Compound Databases pane displays all available compound databases.
• To specify identification and confirmation settings
The Identification and Confirmation Settings pane displays parameters for how
compounds are identified or confirmed. For additional information about the
confirmation and identification process, see “Understanding the Identification and
Confirmation Process” on page 288.
 To open the Processing page
Click Processing in the Method View navigation pane.
The Processing page for the method opens. See “Processing Page” on page 283.
 To specify peak filter settings
1. To set a retention time range that excludes searching for peaks outside the range, do the
following:
a. Select the Use RT Limits check box.
The application activates the Search From and To options.
b. In the Search From box, enter the lower limit; in the To box, enter the upper limit.
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2. To use one or more matrix blank samples for subtraction to filter the resulting peaks, do
the following:
a. Select the Use Matrix Blank check box.
The application activates the Amplifier option.
During automatic processing, the TraceFinder application subtracts the areas of the
peaks in the matrix blank samples from the matching areas in the unknown samples.
To determine the pair of peaks to subtract from each other, the application selects the
two peaks with the mass and the retention time that are closest to each other (as
defined in the compound database), within the mass tolerance specified in the
method.
When the same compound peak (same mass and retention time within the
predefined tolerance windows) is in multiple selected matrix blank samples, the
application subtracts only the one with the highest area.
When a compound peak in one matrix blank sample has the same primary ion as
another peak in a different matrix blank sample but has different adducts, the
application uses all the adducts from both these peaks for subtraction purposes. For
example, if a compound has the M+H and M+Na ions in one matrix blank sample,
and this same compound has the M+H and M+NH4 ions in another matrix blank
sample, the application uses for subtraction the area that results from all of these ions.
When no matrix blank sample exists in the sequence, or if one or more matrix blank
samples exist but you do not select the Use Matrix Blank check box, then subtraction
does not occur. If subtraction occurs and the subtracted area is less than 0, the
application sets the subtracted area to 0.
b. In the Amplifier box, type an amplifier value.
Use the up/down arrows to change the value in increments/decrements of 1 unit, or
use the keyboard to enter non-integer values.
The TraceFinder application multiplies a matrix blank area by this value before
performing subtraction. The larger the amplifier value, the more peaks the
application filters from the final results.
In the Batch View for sequences created with this method, you can select which matrix
blank samples to use for subtraction. See “Blank Subtraction in Target Screening Batches”
on page 374.
3. In the Chromatogram View Width box, type a value to define the chromatogram viewing
range in the Data Review view.
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4. To use source CID scans for target screening confirmation (fragment ion or library
search), select the Use Source CID Scans check box.
When you select this check box, the TraceFinder application uses the source CID scans
when they are available in the data file. If they are not available, then the application uses
AIF or MS/MS scans when available.
5. To display all compounds from the compound databases in the Data Review display
(regardless of whether there is a match in the samples), select the Show All Compounds
check box.
 To specify compound databases
1. Select the Enabled check box for at least one compound database.
The Compound Databases pane displays all compound databases stored in the
…\Thermo\TraceFinder\3.2\General\Databases folder.
2. (Optional) To edit a database, click Open and do the following:
a. Edit the database.
See “Editing Compounds in the Database” on page 89.
b. When you finish editing the database, click Processing in the Method View
navigation pane to return to the Processing page.
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 To specify identification and confirmation settings
1. To set a target threshold override and include only peaks with areas above this designated
threshold, do the following:
a. Select the Threshold Override check box.
b. In the associated box, type the threshold as an area value.
This threshold overrides the Response Threshold value set in the compound
database. The application ignores the peaks with areas below your specified threshold.
c. To include only peaks with signal-to-noise ratios (S/Ns) that are above a specified
value, in the S/N Ratio Threshold box, type the threshold as a ratio value.
The application ignores the peaks with S/Ns that are below the specified threshold.
2. In the Mass Tolerance box, type a mass tolerance value and then select ppm or mmu for
the mass tolerance units.
The application applies this mass tolerance to the extracted chromatograms.
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3. To specify the Retention Time option, do the following:
a. Select either the Identity or Confirm check box.
b. Select the Window Override check box and type the window value.
This window overrides the RT Window value that was set in the compound database
and includes only peaks within this designated window. The application identifies or
confirms the presence of a compound only when its measured retention time matches
the target compound’s expected retention time within the specified Window
Override retention time.
For additional information about how the application identifies retention time, see
“Retention Time” on page 290.
4. To specify the Fragment Ions option, do the following:
a. Select either the Identity or Confirm check box.
b. To ignore the Fragment Ions options when no fragment is defined in the compound
database, select the Ignore if Not Defined check box.
When the compound database does not define fragments for a compound, the
application does not include the results of identification or confirmation for fragment
ions in the target screening results.
c. In the Min. # of Fragments box, type the minimum number of fragments required to
identify or confirm the presence of a compound.
d. In the Intensity Threshold box, type the intensity threshold value.
The intensity of a fragment must be above this threshold to be identified or
confirmed.
e. In the Mass Tolerance box, type a mass tolerance value and then select ppm or mmu
for the mass tolerance units.
This mass tolerance value indicates the number of millimass units or parts per million
to use as the m/z ± tolerance value for the fragment ions. It is separate from the mass
tolerance value specified for the parent peak.
Note When using ion trap data, the application uses 300 mmu regardless of the
value you enter here.
For additional information about how the application identifies fragment ions, see
“Fragment Ions” on page 291.
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5. To specify the Isotopic Pattern option, do the following:
a. Select either the Identity or Confirm check box.
b. In the Fit Threshold box, type the fit threshold percentage.
To identify or confirm the presence of a compound, the resulting score percentage
from isotopic pattern matching must be higher than the specified fit threshold
percentage.
c. In the Allowed Intensity Deviation box, type a value to specify the allowed intensity
deviation of the mass spectrometer relative to the monoisotopic ion, as a percentage
of the base peak height.
The TraceFinder isotopic pattern algorithm considers an isotope peak as not found if
its intensity, relative to the monoisotopic ion’s intensity, is more than the deviation
percentage from the theoretical relative intensity of the isotope ion. For best results,
set this value to a number that causes up to 98% of all intensity deviations to be
smaller than the allowed intensity deviation value.
d. To specify that isotopic pattern calculations use internal mass calibration instead of
external mass calibration, select the Use Internal Mass Calibration check box.
When this check box is selected, the application applies a requirement that an
isotope’s m/z must be closer to its theoretical value to avoid a score penalty.
For additional information about how the application calculates isotopic pattern scores,
see “Isotopic Pattern” on page 292.
6. To specify the Library Search option, do the following:
a. Select either the Identity or Confirm check box.
b. Select a Library Search Type, either NIST or Library Manager.
c. Type the threshold value in the Score Threshold box.
The resulting score percentage from a library search match must be higher than your
entered threshold value to identify or confirm the presence of a compound.
d. To compare a library entry to an unknown compound, select the Use Reverse
Library Searching Only check box.
A forward search compares the mass spectrum of an unknown compound to a mass
spectral library entry.
For additional information about how the application performs library searches, see
“Library Search” on page 292.
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Processing Page
Use the features in the Settings pane to specify peak filter settings.
Use the features in the Target Screening Settings pane to specify screening databases and
identification and confirmation settings.
Figure 79. Settings pane on the Processing page
Table 56. Settings pane parameters
Parameter
Description
Peak Filter Settings
Use RT Limits
Specifies a lower and upper limit for searches.
Ranges: 0.00 to 999.99 minutes
Default: 0.00 minutes for lower limit; 999.00 minutes for upper
limit
Use Matrix Blank
Specifies that during automatic processing, the TraceFinder
application subtracts the areas of the peaks in the selected matrix
blank samples from the matching areas in the unknown samples.
Amplifier
The application multiplies a matrix blank area by this value before
performing subtraction. The larger the amplifier value, the more
peaks the application filters from the final results.
Range: .01 to 1000.00
Default: 1.00
Chromatogram View Specifies a a window width to define the chromatogram viewing
Width
range in the Data Review view.
Range: 0.10 to 999.00 minutes
Default: 0.75 minutes
Thermo Scientific
Use Source CID
Scans
Specifies that the application use the source CID scans when they
are available in the data file. If they are not available, then the
application uses AIF or MS/MS scans when available.
Show All
Compounds
Displays results for all compounds in the method, regardless of
whether they are found in any samples.
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Figure 80. Target Screening Settings pane on the Processing page
Table 57. Target Screening Settings pane parameters (Sheet 1 of 4)
Parameter
Description
Compound Databases
Enabled
Specifies databases to use for target screening processing.
Database Name
Lists available databases in the Databases folder.
Identification and Confirmation Settings
Peaks
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Specifies that the application use the mass-to-charge ratio (m/z) for
filtering compound peaks.
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Table 57. Target Screening Settings pane parameters (Sheet 2 of 4)
Parameter
Description
Threshold Override
This threshold overrides the Response Threshold value set in the
compound database. The application ignores the peaks with areas
below this specified threshold.
Range: 1000 to 1 000 000 000
Default: 5000
S/N Ratio Threshold
Includes only peaks with signal-to-noise ratios (S/Ns) above the
specified value.
Range: 1.0 to 100 000
Default: 5.0
Retention Time
Specifies either the Identify or Confirm option for a retention time
search. To identify a compound, the application searches the
specified RT window for a match. To confirm a compound, the
application searches the entire raw data file.
Ignore if Not
Defined
Ignores the values you specify for Retention Time options when
no retention time is defined in the compound database, and does
not include the results of identification or confirmation for
retention time in the Data Review target screening results.
Window Override
Specifies the number of seconds to override the RT Window value
set in the compound database and include only peaks within this
designated window. The application identifies or confirms the
presence of a compound only when its measured retention time
matches the target compound’s expected retention time within the
specified Window Override retention time.
Range: 0 to 999 seconds
Default: 30 seconds
Fragment Ions
Thermo Scientific
Specifies either the Identify or Confirm option for a fragment ion
match. To identify a fragment, the application searches the
specified RT window for a match. To confirm a fragment, the
application searches the entire raw data file.
Ignore if Not
Defined
Ignores the values you specify for Fragment Ions options when no
fragment is defined in the compound database, and does not
include the results of identification or confirmation for fragment
ions in the Data Review target screening results.
Min. # of
Fragments
Specifies the minimum number of fragments required to identify
or confirm the presence of a compound.
Range: 1 to 5
Default: 1
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Table 57. Target Screening Settings pane parameters (Sheet 3 of 4)
Parameter
Intensity
Threshold
Description
Specifies the minimum height of a fragment ion peak. The peak of
a fragment ion must be above this intensity threshold to be
identified or confirmed.
Range: 1 to 1e9
Default: 10 000
Mass Tolerance
Specifies the number of millimass units or parts per million to use
as the m/z ± tolerance value for the fragment ions and is separate
from the mass tolerance specified for the parent (see “Editing the
Acquisition Page” on page 273).
Range: 0 to 500
Default: 5
Unit: mmu or ppm
Note When using ion trap data, the application uses 300 mmu
regardless of the value you enter here.
Isotopic Pattern
Specifies either the Identify or Confirm option for an isotopic
pattern match. To identify a compound, the application searches
the specified RT window for a match. To confirm a compound,
the application searches the entire raw data file.
Fit Threshold
To identify or confirm the presence of a compound, the resulting
score percentage from isotopic pattern matching must be higher
than the specified fit threshold percentage.
Default: 90%
Allowed Mass
Deviation
Specifies the allowed mass deviation in the spectrum data.
The TraceFinder isotopic pattern algorithm considers an isotope
peak as found if its measured m/z is less than this amount away
from its expected m/z. For best results, set this value to a number
that causes up to 98 percent of all mass deviations to be smaller
than the allowed mass deviation value.
Range: 3 to 100 ppm
Default: 3 ppm
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Table 57. Target Screening Settings pane parameters (Sheet 4 of 4)
Parameter
Allowed Intensity
Deviation
Description
Specifies the allowed intensity deviation of the mass spectrometer,
relative to the monoisotopic ion, as a percentage of the base peak
height.
The TraceFinder isotopic pattern algorithm considers an isotope
peak as not found if its intensity relative to the monoisotopic ion’s
intensity is more than this deviation percentage from the
theoretical relative intensity of the isotope ion. For best results, set
this value to a number that causes up to 98% of all intensity
deviations to be smaller than the allowed intensity deviation value.
Default: 10%
Use Internal Mass
Calibration
Library Search
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Specifies that the application require an isotope’s m/z to be closer
to its theoretical value to avoid a score penalty.
Specifies either the Identify or Confirm option for a library search.
To identify a compound, the application searches the specified RT
window for a match. To confirm a compound, the application
searches the entire raw data file.
Library Search
Type
NIST or Library Manager
Score Threshold
The resulting score percentage from a library search match must
be higher than your specified threshold value to identify or
confirm the presence of a compound.
Default: 80%
Use Reverse
Library Searching
Only
Compares a library entry to an unknown compound (a forward
search compares the mass spectrum of an unknown compound to
a mass spectral library entry). This option is available for both
NIST and Library Manager searches.
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Understanding the Identification and Confirmation Process
By default, the TraceFinder application uses the mass-to-charge ratio (m/z) for filtering
compound peaks. In the Identification and Confirmation Settings area, you can select
additional criteria to help increase confidence using either of the following:
• Compound identification for identifying a sample compound as a minimum requirement
for a match to be displayed in the results.
To identify a compound, the application searches within the specified RT window (or the
RT window override if specified in the method) and compares the measured m/z of the
sample peak against the expected m/z of the target compound. When the sample peak’s
m/z is within the default ±5 ppm tolerance of the target compound’s m/z, the application
considers that this target compound is identified.
• Compound confirmation for confirming a sample compound and to increase confidence
in the match results.
To confirm a compound, the application searches the entire raw data file and compares
the measured m/z of the sample peak against the expected m/z of the target compound.
When the sample peak’s m/z is within the tolerance of the target compound’s m/z, the
application considers that this target compound is confirmed.
The TraceFinder application processes identification and confirmation settings in a specific
order. When a compound passes identification at each point in the order of processing, the
application continues to the next automatic or selected identification or confirmation test.
Note When you select the Ignore if Not Defined option and the related data is not
defined in the compound databases, the application skips that criteria test.
When a compound fails identification at a point in the processing, the application skips the
testing of all remaining criteria, even when they are selected, and the flags for those criteria are
blank.
The TraceFinder application processes identification and confirmation settings in the
following order:
1. m/z and Retention Time
The application automatically identifies the mass to charge ratio for all compounds.
When you select the Retention Time settings, the compound must pass this criteria first.
When a compound fails the m/z or the Retention Time identification test, the application
does not perform identification or confirmation testing for any other selected criteria
lower in the processing order.
For additional information about the m/z and Retention Time parameters, see “Mass to
Charge (m/z)” on page 289 and “Retention Time” on page 290.
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2. Threshold
The application automatically identifies the default area threshold (5000) for the
compound after the compound passes the m/z and Retention Time criteria. When you
specify a Threshold Override, the application uses the specified threshold value instead.
When a compound fails the Threshold identification test, the application does not
perform the selected Fragment Ions or Library Search testing for identification or
confirmation.
For additional information about the Threshold parameter, see Threshold.
3. Isotopic Pattern
For additional information about the Isotopic Pattern parameter, see “Isotopic Pattern”
on page 292.
4. Fragment Ions
For additional information about the Fragment Ions parameter, see “Fragment Ions” on
page 291.
5. Library Search
For additional information about the Library Search parameter, see “Library Search” on
page 292.
Mass to Charge (m/z)
The application automatically uses the m/z and mass tolerance values to identify each
compound, using the mass tolerance value you specified on the Acquisition page. See “Editing
the Acquisition Page” on page 273.
The application compares the measured m/z of the sample peak against the expected m/z of
the target compound. When the measured m/z is within the mass tolerance of the expected
m/z, the application considers that this target compound is found and the m/z criteria passes.
On the Target Screening page in Data Review, the MZ column in the Compounds table
indicates whether this criteria passes or fails. The Flag column indicates whether the target
compound is identified, fully confirmed, or both. For details, see “Compounds Pane” on
page 424.
The Compounds table also displays the m/z Expected, m/z Measured, and m/z Delta values for
each compound.
Threshold
The application automatically uses the area and threshold values defined in the selected
compound database to identify each sample compound.
In the Identification and Confirmation Settings pane, you can specify a threshold override to
use instead of the area threshold defined in the compound database.
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The application compares the area of the sample peak against the defined area thresholds.
When the sample peak’s area is greater than or equal to the corresponding area threshold from
the compound database or the override area threshold, the target compound is identified.
On the Target Screening page in Data Review, the Flag column in the Compounds table
indicates whether this criteria passes or fails. The Flag column indicates whether the target
compound is identified, fully confirmed, or both. For details, see “Compounds Pane” on
page 424.
The Compounds table also displays Measured Area column displays the area value in green to
indicate that the peak’s area is greater than or equal to the area threshold; otherwise, this
column displays the area value in red.
Retention Time
The application uses the expected retention time and retention time window values defined in
the selected compound database to identify or confirm each sample compound.
In the Identification and Confirmation Settings pane, you can set an override value to use for
the retention time window instead of using the retention time window that is specified in the
compound database.
When the compound database defines an expected retention time for a compound, it uses the
following process to identify or confirm the compound.
• Identify: the application searches within the specified retention time window (or the
retention time window override) and compares the measured m/z of the sample peak
against the expected m/z of the target compound. When the measured m/z is within
the mass tolerance of the expected m/z, this target compound is identified.
• Confirm: the application searches the entire raw data file and compares the measured
m/z of the sample peak against the expected m/z of the target compound. When the
measured m/z is within the specified mass tolerance of the expected m/z, the target
compound is confirmed.
When the compound database does not define an expected retention time for a compound,
the application cannot identify or confirm the compound. If you select the Ignore if Not
Defined option, the application does not perform testing for the retention time and the RT
flag is blank on the Target Screening page in Data Review.
On the Target Screening page in Data Review, the RT column in the Compounds table
indicates whether this criteria passes or fails. The RT column indicates whether the target
compound is identified, fully confirmed, or both. For details, see “Compounds Pane” on
page 424. The Compounds table also displays the RT Expected, RT Measured, and RT Delta
values for each compound.
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Fragment Ions
To use fragment ions for identification or confirmation, the application requires the following
conditions:
• The selected compound databases contain the charged mass for each defined fragment
ion of interest for the compounds in the target list.
• The HCD (higher energy collision-induced dissociation), source CID (source
collision-induced dissociation), or AIF (all ions fragmentation) ion spectra exist at a time
point within the compound’s elution time range.
When no fragment is defined in a compound database for a target compound, the following
apply:
• When the Ignore if Not Defined option is selected in the method, the application does
not perform filtering for the Fragment Ions. In the Data Review view, the FI column is
blank.
• When the Ignore if Not Defined option is not selected in the method, the application
considers that this target compound is not identified. The Fragment Ions filter fails.
The application uses the number of fragment masses defined in the compound database when
it processes a sample for fragment ions. The value you specify for Min. # of Fragments cannot
be greater than the number of fragments defined in the compound database.
For example, if a compound has three fragment ion masses defined in a compound database,
any of the following scenarios can occur:
• You enter “2” in the Min. # of Fragments box of the method, and the application finds at
least two out of the three defined fragment ions. The Fragment Ions filter passes.
• You enter “4” in the Min. # of Fragments box of the method, and the application finds
only the three defined fragment ions. The Fragment Ions filter fails.
• You enter “2” in the Min. # of Fragments box of the method, but the application finds
only one of the three defined fragment ions. The Fragment Ions filter fails.
The application repeats the following process for each of the fragment ions:
1. When the mass of the parent (plus or minus half of the isolation window value from the
acquired raw data file) is not within the mass range of the extracted ion chromatogram
shown in the Chromatogram pane of the Data Review view, the application considers the
fragment ion as not found and the application fails the Fragment Ions filter; otherwise,
the application continues.
2. The application inspects the processed fragment ion scan closest to the target compound’s
expected retention time and locates the MS/MS spectrum closest to the compound’s apex.
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Within this spectrum, the application finds the intensity for the tallest fragment whose
mass is within the mass tolerance of an entered fragment ion mass. When this intensity is
not found or when it is less than the intensity threshold defined in the method, the
application determines that the entered fragment ion is not found; otherwise, it
determines that the fragment ion is found.
Isotopic Pattern
You can choose to either identify or confirm the isotopic patterns for all compounds in a
batch. The TraceFinder application calculates an isotopic pattern score (as a percentage value),
using the target compound’s formula.
For the isotopic pattern filter, enter the isotopic pattern parameters, including a fit threshold
value, in the processing method. To identify or confirm the presence of a compound, the
resulting score from isotopic pattern matching must be higher than the fit threshold.
To identify or confirm an isotopic pattern, the application must detect the compound for at
least one of its defined adduct ions. The application identifies the elemental composition to
match using the formula that is associated with the most intense adduct peak. The application
then generates an isotopic pattern score (as a percentage value) for the match between the
measured and expected isotopic patterns of the calculated elemental composition.
• For profile data, the application calculates the measured isotopic pattern using the average
of all scans (within the allowed intensity deviation of the spectrum closest to the
compound’s apex retention time). In the Data Review view, the application displays both
the expected and measured spectra.
• For centroid data, the application calculates the measured isotopic pattern using the apex
scan. In the Data Review view, the application displays the expected spectra.
A high isotopic pattern score (approaching 100 percent) occurs when the measured isotope
patterns, the expected isotope patterns, and the intensities are almost identical using the
scoring parameters specified in the processing method. When the patterns are not similar, the
score is closer to 0 percent. When the score is greater than or equal to the specified fit
threshold and the number of isotopes matched is not 1 out of 1, this filter passes.
When you view results in the Data Review view, the IP column displays a green or red flag to
indicate whether the compound passed or failed based on the criteria specified in the method.
Library Search
For a target screening analysis, you can select the Library Search criterion for either
identification or confirmation in the processing method. The TraceFinder application
identifies or confirms the sample compound by searching the selected library and returning
the library entry with the highest score (as a percentage value) for the fragment ion spectrum
in that library that matches the compound’s ion spectrum.
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For this criterion, you enter a score threshold value in the processing method. The resulting
score from a library search match must be higher than your entered threshold value, and the
library entry must match a compound’s name, a compound’s formula, or both to identify or
confirm the presence of the compound.
The application uses the following logic to determine when a match is successful:
• When a formula is available in the library entry and the formula matches the target
compound formula:
–
The criteria passes when the library score is higher than or equal to the score
threshold.
–
The criteria fails when the library score is lower than the score threshold.
• When a formula is available in the library entry and the name in the library entry matches
the target compound name but the formula does not match the target compound formula
(or it is not available):
–
The criteria passes when the library score is higher than or equal to the score
threshold.
–
The criteria fails when the library score is lower than the score threshold.
• When neither the formula nor the library entry name match the target compound, the
criteria fails and the Lib Match Name, Library Score, and Library Match Rank columns
display N/A in black text.
Note When the compound is identified, but no MS/MS scan has been performed,
the Lib Match Name, Library Score, and Library Match Rank columns display N/A
in red text.
• When an MS/MS scan has been performed and both the library entry and the formula
match the target compound:
–
The criteria passes when the library score is higher than or equal to the score
threshold. The Lib Match Name, Library Score, and Library Match Rank columns
display their values in green text.
–
The criteria fails when the library score is lower than the score threshold. The Lib
Match Name, Library Score, and Library Match Rank columns display their values in
red text.
To use a library search for identification or confirmation, the TraceFinder application requires
that the data meet these conditions:
• The raw data file contains HCD (higher energy collision-induced dissociation), source
CID (source collision-induced dissociation), or AIF (all ions fragmentation) ion spectra.
• The spectra exist at a time point within the compound’s elution time range.
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The application performs either a forward library search or a reverse library search. A forward
search compares the mass spectrum of an unknown compound to a mass spectral library
entry, while a reverse search compares a library entry to an unknown compound.
When a parent-selected MS/MS spectrum does not exist, the application performs a reverse
library search because the compound scan contains a mixture of fragments from all co-eluting
parents. A forward search with such a mixture biases the results toward the strongest parent
because its fragments would be dominant, and a forward search also takes more time because
the application must search every spectrum in the library.
When a parent-selected MS/MS spectrum exists, the application performs a forward library
search because the scan usually contains fragments of only one or two parents, so matching
this spectrum against the library is faster and more accurate. When you select the Use Reverse
Library Searching Only check box in the processing method, the application performs only a
reverse library search.
When you use profile data, the application uses the averaged spectrum of the unknown peak
as the input spectrum for the library search. This averaged spectrum is based on the average of
all scans within 10 percent of the spectrum closest to the peak’s apex retention time. When
you use centroid data, the application uses the apex scan as the input spectrum for the library
search.
When the application locates a match, it generates a score percentage for the matching library
entry. This library search can result in multiple matches with different scores.
After searching based on the m/z in the input spectrum, the application performs another
search for only the matches from the first library search, but this time based on the name, and
then the formula, of the target compound. If at least one match is found, the application
displays the highest scoring match from the second search for data review. If no match is
found from the second search, the application displays the highest scoring match from the
first search.
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Editing the Peak Detection Page
Use the features on the Peak Detection page to specify any of the following peak detection
algorithms: Genesis, ICIS, or Avalon.
 To specify peak detection parameters
1. Click Peak Detection in the Method View navigation pane.
The Peak Detection page for the method opens.
2. In the Peak Detection Parameters area, select one of the detection algorithms: Genesis,
ICIS, or Avalon.
• The Genesis peak detection algorithm provides backward compatibility with
Xcalibur 1.0 studies. For detailed descriptions of the Genesis method parameters, see
Genesis Detection Method.
• The ICIS peak detection algorithm is designed for MS data and has superior peak
detection efficiency at low MS signal levels. For detailed descriptions of the ICIS
method parameters, see “ICIS Detection Method” on page 299.
• The Avalon peak detection algorithm is designed for integrating UV/Vis and analog
chromatograms. For detailed descriptions of the Avalon method parameters, see
“Avalon Detection Method” on page 302.
3. Specify the parameters for the selected detection algorithm.
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Genesis Detection Method
The TraceFinder application provides the Genesis peak detection algorithm for backward
compatibility with Xcalibur 1.0 studies.
Figure 81. Genesis peak detection
Table 58. Genesis peak detection parameters (Sheet 1 of 3)
Parameter
Description
Detection Algorithm
Specifies the Genesis peak detection algorithm.
Detection Method
Highest peak: Uses the highest peak in the chromatogram for
component identification.
Nearest RT: Uses the peak with the nearest retention time in the
chromatogram for component identification.
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Table 58. Genesis peak detection parameters (Sheet 2 of 3)
Parameter
Description
Smoothing
Determines the degree of data smoothing to be performed on the
active component peak prior to peak detection and integration.
The ICIS peak detection algorithm uses this value.
Default: 1
Range: Any odd integer from 1 through 15 points
S/N threshold
Current signal-to-noise threshold for peak integration. Peaks with
signal-to-noise values less than this value are not integrated. Peaks
with signal-to-noise values greater than this value are integrated.
Range: 0.0 to 999.0
Enable Valley
Detection
Uses the valley detection approximation method to detect
unresolved peaks. This method drops a vertical line from the apex
of the valley between unresolved peaks to the baseline. The
intersection of the vertical line and the baseline defines the end of
the first peak and the beginning of the second peak.
Expected Width (sec)
The expected peak width parameter (in seconds). This parameter
controls the minimum width that a peak is expected to have if
valley detection is enabled.
With valley detection enabled, any valley points nearer than the
expected width/2 to the top of the peak are ignored. If a valley
point is found outside the expected peak width, the TraceFinder
application terminates the peak at that point. The application
always terminates a peak when the signal reaches the baseline,
independent of the value set for the expected peak width.
Range: 0.0 to 999.0
Thermo Scientific
Constrain Peak Width
Constrains the peak width of a component during peak
integration of a chromatogram. You can then set values that
control when peak integration is turned on and off by specifying a
threshold and a tailing factor. Selecting the Constrain Peak Width
check box activates the Peak Height (%) and Tailing Factor
options.
Peak Height (%)
A signal must be above the baseline percentage of the total peak
height (100%) before integration is turned on or off. This text box
is active only when you select the Constrain Peak Width check
box.
Range: 0.0 to 100.0%
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Table 58. Genesis peak detection parameters (Sheet 3 of 3)
Parameter
Description
Tailing Factor
A factor that controls how the TraceFinder application integrates
the tail of a peak. This factor is the maximum ratio of the trailing
edge to the leading side of a constrained peak. This text box is
active only when you select the Constrain the Peak Width check
box.
Range: 0.5 through 9.0
Peak S/N Cutoff
The peak edge is set to values below this signal-to-noise ratio.
This test assumes it has found an edge of a peak when the baseline
adjusted height of the edge is less than the ratio of the baseline
adjusted apex height and the peak S/N cutoff ratio.
When the S/N at the apex is 500 and the peak S/N cutoff value is
200, the TraceFinder application defines the right and left edges of
the peak when the S/N reaches a value less than 200.
Range: 50.0 to 10000.0
Valley Rise (%)
The peak trace can rise above the baseline by this percentage after
passing through a minimum (before or after the peak). This
criteria is useful for integrating peaks with long tails.
This method drops a vertical line from the apex of the valley
between unresolved peaks to the baseline. The intersection of the
vertical line and the baseline defines the end of the first peak and
the beginning of the second peak.
When the trace exceeds rise percentage, the TraceFinder
application applies valley detection peak integration criteria. This
test is applied to both the left and right edges of the peak.
Range: 0.1 to 500.0
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Valley S/N
Specifies a value to evaluate the valley bottom. Using this
parameter ensures that the surrounding measurements are higher.
Default: 2.0
Range: 1.0 to 100.0
# Background Scans
Number of background scans performed by the TraceFinder
application.
Report Noise As
Determines if the noise used in calculating S/N values is calculated
using an RMS calculation or peak-to-peak resolution threshold.
Options are RMS or Peak To Peak.
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ICIS Detection Method
The ICIS peak detection algorithm is designed for MS data and has superior peak detection
efficiency at low MS signal levels.
Figure 82. ICIS peak detection
Table 59. ICIS peak detection parameters (Sheet 1 of 3)
Parameter
Description
Detection Algorithm
Specifies the ICIS peak detection algorithm.
Detection Method
Highest peak: Uses the highest peak in the chromatogram for
component identification.
Nearest RT: Uses the peak with the nearest retention time in the
chromatogram for component identification.
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Table 59. ICIS peak detection parameters (Sheet 2 of 3)
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Parameter
Description
Smoothing
Determines the degree of data smoothing to be performed on the
active component peak prior to peak detection and integration.
The ICIS peak detection algorithm uses this value.
Range: Any odd integer from 1 through 15 points
Default: 1
Area Noise Factor
The noise level multiplier used to determine the peak edge after
the location of the possible peak. The ICIS peak detection
algorithm uses this value.
Range: 1 through 500
Default: 5
Peak Noise Factor
The noise level multiplier used to determine the potential peak
signal threshold. The ICIS peak detection algorithm uses this
value.
Range: 1 through 1000
Default: 10
Baseline Window
The TraceFinder application looks for a local minima over this
number of scans. The ICIS peak detection algorithm uses this
value.
Range: 1 through 500
Default: 40
Constrain Peak Width
Constrains the peak width of a component during peak
integration of a chromatogram. You can then set values that
control when peak integration is turned on and off by specifying a
peak height threshold and a tailing factor. Selecting the Constrain
Peak Width check box activates the Peak Height (%) and Tailing
Factor options.
Peak Height (%)
A signal must be above the baseline percentage of the total peak
height (100%) before integration is turned on or off. This text box
is active only when you select the Constrain Peak Width check
box.
Range: 0.0 to 100.0%
Tailing Factor
A factor that controls how the TraceFinder application integrates
the tail of a peak. This factor is the maximum ratio of the trailing
edge to the leading side of a constrained peak. This text box is
active only when you select the Constrain the Peak Width check
box.
Range: 0.5 through 9.0
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Table 59. ICIS peak detection parameters (Sheet 3 of 3)
Parameter
Description
Noise Method
The options are INCOS or Repetitive.
INCOS: Uses a single pass algorithm to determine the noise level.
The ICIS peak detection algorithm uses this value.
Repetitive: Uses a multiple pass algorithm to determine the noise
level. The ICIS peak detection algorithm uses this value. In
general, this algorithm is more accurate in analyzing the noise than
the INCOS Noise algorithm, but the analysis takes longer.
Thermo Scientific
Min Peak Width
The minimum number of scans required in a peak. The ICIS peak
detection algorithm uses this value.
Range: 0 to 100 scans
Default: 3
Multiplet Resolution
The minimum separation in scans between the apexes of two
potential peaks. This is a criteria to determine if two peaks are
resolved. The ICIS peak detection algorithm uses this value.
Range: 1 to 500 scans
Default: 10
Area Tail Extension
The number of scans past the peak endpoint to use in averaging
the intensity. The ICIS peak detection algorithm uses this value.
Range: 0 to 100 scans
Default: 5
Area Scan Window
The number of allowable scans on each side of the peak apex. A
zero value defines all scans (peak-start to peak-end) to be included
in the area integration.
Range: 0 to 100 scans
Default: 0
RMS
Specifies that the TraceFinder application calculate noise as RMS.
By default, the application uses Peak To Peak for the noise
calculation. RMS is automatically selected if you manually
determine the noise region.
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Avalon Detection Method
The Avalon peak detection algorithm is designed for UV data. The Avalon peak detection
algorithm also supports negative peaks. You can edit the Event values from the Avalon Event
List.
Figure 83. Avalon peak detection
Table 60. Avalon peak detection parameters
Parameter
Description
Detection Algorithm
Specifies the Avalon peak detection algorithm.
Detection Method
Highest peak: Uses the highest peak in the chromatogram for
component identification.
Nearest RT: Uses the peak with the nearest retention time in the
chromatogram for component identification.
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Smoothing
Determines the degree of data smoothing to be performed on the
active component peak prior to peak detection and integration.
The ICIS peak detection algorithm uses this value.
Default: 1
Range: Any odd integer from 1 through 15 points
Time/Event/Value
Displays the events specified in the Avalon Event List dialog box.
Initially displays only the default events that cannot be edited or
deleted.
Autocalc Initial Events
Automatically calculates the events in the Event list.
Edit
Opens the Avalon Event List dialog box where you can edit the
Time/Event/Value parameters. See “Avalon Event List.”
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Avalon Event List
The event list includes both user-defined and noneditable default events. The application
displays the default events when you choose Avalon sensitivity. You cannot delete these events
or change their time or values. For a detailed list of events and value ranges, see Event types.
Figure 84. Avalon Event List dialog box
Table 61. Avalon Event List dialog box parameters
Thermo Scientific
Parameter
Description
Time (Min)
Specifies the start time of the event.
Event
Specifies the type of event. For a detailed list of events and value
ranges, see “Event types.”
Value
Specifies the value of the event.
Add
Adds a new event to the list with the current Time/Event/Value
parameters.
Delete
Removes the selected Time/Event/Value parameter from the event
list.
Change
Applies the current parameter values.
Cancel
Closes the dialog box without making any changes. Any additions,
deletions, or changes revert to their original state.
Apply
Closes the dialog box.
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Figure 85. Event types
Table 62. Event type descriptions (Sheet 1 of 2)
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Event type
Description
Start Threshold
Specifies the threshold at the start of a peak. The Start Threshold is
directly related to the RMS noise in the chromatogram.
Range: 0 to 999 999 999
End Threshold
Specifies the threshold at the end of a peak. The End Threshold is
directly related to the RMS noise in the chromatogram.
Range: 0 to 999 999 999
Area Threshold
Controls the area cutoff. Any peaks with a final area less than the area
threshold will not be detected. This control is in units of area for the
data.
Range: 0 to 999 999 999
P-P Threshold
The peak-to-peak resolution threshold controls how much peak
overlap must be present before two or more adjacent peaks create a
peak cluster. Peak clusters have a baseline drop instead of
valley-to-valley baselines. Specified as a percent of peak height
overlap.
Range: 0.1 to 99.99
Negative Peaks
Permits detection of a negative going peak. Automatically resets after
finding a negative peak.
Valid values: On or Off
Bunch Factor
Specifies the number of points grouped together during peak
detection. This event controls the bunching of chromatographic
points during integration and does not affect the final area
calculation of the peak. A high bunch factor groups peaks into
clusters.
Range: 0 to 999
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Table 62. Event type descriptions (Sheet 2 of 2)
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Event type
Description
Tension
Controls how closely the baseline should follow the overall shape of
the chromatogram. A lower tension traces the baseline to more
closely follow changes in the chromatogram. A high baseline tension
follows the baseline less closely, over longer time intervals.
Range: 0 to 999.99 minutes
Tangent Skim
Using this event, you can tangent skim any peak clusters. By default,
it chooses the tallest peak in a cluster as the parent. You can also
identify which peak in the cluster is the parent. Tangent skim peaks
are detected on either side (or both sides) of the parent peak. Tangent
skim automatically resets at the end of the peak cluster.
Range: 0 to 1
Shoulders On
Allows peak shoulders to be detected (peaks which are separated by
an inflection rather than a valley) Sets a threshold for the derivative.
Shoulders Off
Disables peak shoulder detection.
Range: 0 to 50
Force Cluster On
Force the following peaks to be treated as a cluster (single peak).
Force Cluster Off
End the forced clustering of peaks.
Disable Cluster On
Prevent any peaks from being clustered.
Disable Cluster Off
Permit clusters to occur again.
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Editing the Reports Page
Use the Reports page to specify the reports and report output formats that you want to create
for the method. See Reports Page.
Follow these procedures:
• To open the Reports page
• To configure the compounds in the reports
• To specify output formats
 To open the Reports page
Click Reports in the Method View navigation pane.
The Reports page for the method opens (see “Reports page” on page 307), displaying
only the reports that are configured in the Configuration Console. To configure the
reports that are available, see “Specifying the Reports” on page 72.
 To configure the compounds in the reports
In the Target Screening Report Settings pane, select one of the following options:
• Include All Compounds: Generates reports that include all compounds from the
screening library, whether or not they are found in the samples.
• Include Only Found Compounds: Generates reports that include only the
compounds from the screening library that are found in the samples.
 To specify output formats
1. To edit the Report Title, double-click the name and type a new title.
The TraceFinder application uses this title for all reports that use this master method. You
cannot edit the Report Title from other report views.
2. To specify the type of report output to create for each report (hard copy, PDF, CSV, or
Excel), select the check box in the appropriate column.
3. To duplicate an output type for all reports, click the cell to select it, and then right-click
and choose Copy Down from the shortcut menu.
All check boxes in the column below the selected cell duplicate the selected or cleared
state of the selected cell.
By default, all report types are cleared.
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Reports Page
Use the features on the Reports page to specify the reports and report output formats that you
want to create with the method.
Figure 86. Reports page
Table 63. Reports page parameters
Parameter
Description
Report list columns
Thermo Scientific
Report
The name of a report.
Print
Sends reports to the default printer.
Create PDF
Saves reports as PDF files.
Create CSV
Saves reports as CSV files.
Create Excel
Saves reports as Excel files.
Found
Indicates that the report template is identified in the
C:\TraceFinderData\32\Templates\ReportTemplates folder.
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Saving a Master Method to a New Name
Saving a Master Method to a New Name
You can save any method to a new name, or you can use the current method data to overwrite
an existing method. The new method contains all the data of the original method.
 To save a method to a new name
1. From the main menu, choose File > Save As.
The Save Master Method As dialog box opens, displaying all quantitative and target
screening methods.
Table 64. Save Master Method As dialog box parameters
Parameter
Description
Method
Name of the methods for the selected type.
Type
Type of method: Quan or Screening.
Date Changed
Date the method was last updated.
Size
Size in megabytes.
Domain
TraceFinder domain for which the method was created.
New Method
Name of the new method to create.
Path
Path to the selected method in the Methods folder.
2. Do one of the following:
• In the New Method box, type a name for the new method.
The application enables the Save button.
• In the Method column, select a method to overwrite.
The application enables the Overwrite button.
3. Click Save or Overwrite.
The application saves all the method data using the specified name and opens the
Acquisition page of the new method.
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Importing Published Master Methods
Importing Published Master Methods
In the TraceFinder application, you can import published methods to use for detecting,
processing, and reporting. The TraceFinder installation provides the following folder of
published methods:
…\Thermo\TraceFinder\3.2\General\Published Master Methods
 To import a published master method
1. Choose Method View > Import Published Method from the main menu.
The Import Published Method dialog box opens.
2. Select a method to import.
3. Click Import.
The application reports that the method successfully imported and saves the method in
the following folder:
…\TraceFinderData\32\Methods\General
You can use any of the Open Method commands to open this method just as you would a
method that you created.
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Using the Acquisition Mode
This chapter describes the tasks associated with the Acquisition mode.
Contents
• Working with Batches
• Real Time Status Pane
• Sample Types
When you plan to work with multiple samples or use similarly designed batches, use the
Acquisition mode to reduce the amount of data you must enter.
Because the nature and types of batches are often similar (in some cases specified by laboratory
standard practices), you can define a batch template that supplies the basic structure of a
batch.
IMPORTANT When user security is activated, you must have Acquisition Wizard –
Template Editing permission to create a batch template.
Using a master method, you can create a batch and run the samples. A batch represents one or
more samples that are to be acquired, processed, reviewed, and reported as a set. After you
create a batch of samples, you can submit the batch and review the results in the Analysis
mode or you can go directly to viewing and printing reports.
You can set up a calibration batch with known concentrations of the target compounds and
compare the calibration values against samples in future batches.
You can also use the Quick Acquisition feature to quickly submit a single sample from any
page in the Acquisition mode. See Appendix A, “Using Quick Acquisition.”
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Working with Batches
This section includes instructions for the following tasks:
• Opening and Navigating the Acquisition Mode
• Creating and Submitting Batches
Opening and Navigating the Acquisition Mode
 To access the Acquisition mode
Click Acquisition in the navigation pane.
The navigation pane for the Acquisition mode opens.
As you progress through the Acquisition mode using any of these methods for creating a
batch, the task pane at the top of the view tracks your progress. As you complete each
stage, you can hold your cursor over the view name in the task pane to display the
parameters that you specified for the batch. See Example task pane when you have
completed the Acquisition mode.
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Figure 87. Example task pane when you have completed the Acquisition mode
Hold your cursor over Batch Selection, Sample Definition,
or Report Selection to view the parameters for your batch.
Categories in the Sample Definition list:
QC Samples: QC Std
Calibration Samples: Cal Std
Blank Samples: Matrix Blank
Unknown Samples: All other samples
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Creating and Submitting Batches
To create and submit a batch, the Acquisition mode uses a wizard-style interface to guide you
through these major steps:
1. Selecting a Batch
2. Defining the Sample List
3. Selecting and Reviewing Reports
4. Submitting the Batch
The Acquisition mode provides multiple techniques for creating either a batch or a batch
template.
• To start a new quantitative batch
• To start a new screening batch
• To start a new batch from a template
• To select a prepared batch
• To reinject samples in a previously acquired batch
• To create a quantitative batch template
• To create a screening batch template
Each batch creation technique has an associated workflow, as shown in the following
flowcharts. Each workflow uses a different combination of Acquisition mode pages.
Workflow for Creating an Original Batch
Batch and
Method
Samples
Reports
Finish
To create an original batch, start with the instructions “To start a new quantitative batch” on
page 316 or “To start a new screening batch” on page 318.
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Workflow for Acquiring a Prepared Batch
Batch
Finish
Samples
To acquire a prepared batch, start with the instructions “To select a prepared batch” on
page 320.
Workflow for Reinjecting a Previously Acquired Batch
Batch
Samples
Finish
To process a previously acquired batch, start with the instructions “To reinject samples in a
previously acquired batch” on page 321.
Workflow for Creating or Editing a Batch Template
Template and
Method
Samples
Finish
IMPORTANT When user security is activated, you must have Acquisition Wizard –
Template Editing permission to create a batch template.
To create a batch template, start with the instructions “To create a quantitative batch
template” on page 321 or “To create a screening batch template” on page 322.
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Selecting a Batch
On a Batch Selection page of the Acquisition mode, you can create a new quantitative or
screening batch in any of your current projects/subprojects. Or, you can submit a batch that
you previously prepared and saved, reinject the samples in a batch that you previously
acquired, or create a batch template to use for future batches.
Follow these procedures:
• To start a new quantitative batch
• To start a new screening batch
• To start a new batch from a template
• To select a prepared batch
• To reinject samples in a previously acquired batch
• To create a quantitative batch template
• To create a screening batch template
 To start a new quantitative batch
1. Click Create a New Batch in the navigation pane.
2. Select the Quantitative Batch option.
3. Select the batch folder where you want to create the new batch.
4. Type a unique name for the new batch in the Batch Name box.
If the name you enter is not unique, a red warning flashes.
5. Select a method from the Method Selection list.
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The Method Compound Data pane displays the compounds in the method. You cannot
edit the compounds list from the Acquisition mode.
6. To continue to the next page, click Next.
The Sample Definition page opens. See “Defining the Sample List” on page 324.
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 To start a new screening batch
1. Click Create a New Batch in the navigation pane.
2. Select the Screening Batch option.
3. Select the batch folder where you want to create the new batch.
4. Type a name for the new batch in the Batch Name box.
If the name you enter is not unique, a red warning flashes.
5. Select a method from the Method Selection list.
The Method Compound Databases pane displays the compound databases in the
method. The application uses these databases to identify the compounds in the samples.
You cannot edit the compound database list from the Acquisition mode.
6. To continue to the next page, click Next.
The Sample Definition page opens. See “Defining the Sample List” on page 324.
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 To start a new batch from a template
1. Click Create a New Batch in the navigation pane.
2. Select either the Screening Batch or the Quantitative Batch option.
The Available Templates pane displays only batch templates for the selected option.
3. In the Available Templates pane, select the template and method combination that you
want to use.
The system creates a batch name with the selected template name and appends the date
and time stamp. You can change the default batch folder or method associated with this
template.
4. (Optional) Click
new batch.
and select a different batch folder where you want to create the
5. (Optional) Select a different method to use for the new batch.
6. To continue to the next page, click Next.
The Sample Definition page of the Acquisition mode opens. See “Defining the Sample
List” on page 324.
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 To select a prepared batch
1. Click Submit a Prepared Batch in the navigation pane.
The application displays all your unacquired, saved batches. The TraceFinder application
stores all unacquired batches in the …\TraceFinderData\32\Projects\… folder.
2. Select the batch that you want to acquire.
3. To continue to the next page, click Next.
The Finish page of the Acquisition mode opens. From the Finish page, you can save the
batch, submit the batch for acquisition, or go to the Sample Definition page to edit the
sample list for this batch.
• If the batch is unreadable, the application reports that the batch file is not valid and
cannot be opened.
• If a sample in the batch is unreadable, the application cannot open the sample. The
application creates a new sample with the same name and flags the sample. You must
complete the missing information such as Sample Type, Level, and so forth, and then
save the batch before you submit it for acquisition. Or, you can browse in a new raw
data file to replace the corrupt file.
4. Do one of the following:
• To edit the sample list, click Previous.
For detailed instructions, see “Defining the Sample List” on page 324.
–or–
• To prepare the batch for acquisition, click Submit,
.
For detailed instructions, see “Submitting the Batch” on page 340.
–or–
• To save the batch to be acquired later, click Save,
.
The TraceFinder application saves your batch in the following folder:
…\TraceFinderData\32\Projects\...
The TraceFinder application closes the Acquisition mode and returns you to the
mode you were last using.
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 To reinject samples in a previously acquired batch
1. Click Reinject Samples in the navigation pane.
2. On the Batch page, select the batch that you want to reacquire.
The Batch page displays all previously acquired batches, both quantitative and screening.
3. To continue to the next page, click Next.
The Sample Definition page of the Acquisition mode opens. See “Defining the Sample
List” on page 324.
• If the batch is unreadable, the application reports that the batch file is not valid and
cannot be opened.
• If a sample in the batch is unreadable, the application creates a new sample with the
same name and flags the sample. You must complete the missing information, such as
Sample Type, Level, and so forth, and then save the batch before you submit it for
acquisition. Or, you can browse in a new raw data file to replace the corrupt file.
 To create a quantitative batch template
1. Click Create or Edit a Template in the navigation pane.
Note When user security is activated, you must have Acquisition Wizard – Template
Editing permission to create a batch template.
2. Select the Quantitative Batch option.
3. Click
and select the folder where you want to create the new batch template.
4. Type a name for the new batch template in the Template Name box.
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5. Select a method from the Method Selection list.
The Method Compound Data pane displays the compounds in the method. You cannot
edit the compounds list from the Acquisition mode.
6. To continue to the next page, click Next.
The Sample Definition page of the Acquisition mode opens. See “Defining the Sample
List” on page 324.
 To create a screening batch template
1. Click Create or Edit a Template in the navigation pane.
Note When user security is activated, you must have Acquisition Wizard – Template
Editing permission to create a batch template.
2. Select the Screening Batch option.
3. Click
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4. Type a name for the new batch template in the Template Name box.
5. Select a method from the Method Selection list.
The Method Compound Databases pane displays the screening databases available for the
selected method.
6. Select the check box for each database that you want to use for screening.
7. To continue to the next page, click Next.
The Sample Definition page of the Acquisition mode opens. See “Defining the Sample
List.”
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Defining the Sample List
Use the Samples page on the Sample Definition page of the Acquisition mode, to create a list
of samples for the batch. See “Samples” on page 334. You can add samples, insert samples,
import a sample list, or remove samples from the list. You can use the Reference Sample page
to select a reference sample to use as a reference peak in the Data Review. See “Reference
Sample” on page 337.
To create the sample list, you can use either of two sets of function buttons (described in the
following graphic) or you can use commands on the shortcut menu (see the Shortcut Menu
section of the “Samples page parameters” on page 334).
Icons in the toolbar
Import samples
Add samples
Remove samples
Insert samples
Buttons at the bottom of the sample definition page
Add samples
Insert samples
Import samples
As you enter sample values, you can use the Copy Down and Fill Down commands to quickly
enter column values. For detailed instructions on using Copy Down and Fill Down to enter
column values, see Appendix C, “Using Copy Down and Fill Down.”
Use any of the following procedures to create a sample list. When you finish defining the list
of samples, click Next.
• When you are creating a batch from scratch, creating a batch from a template, or editing
a batch template and you click Next, the Report Selection page opens. See “Selecting and
Reviewing Reports” on page 338.
• When you are editing a prepared batch or reinjecting samples and you click Next, the
Finish Selection page opens. See “Submitting the Batch” on page 340.
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Follow these procedures:
• To add samples to the list
• To insert samples into the list
• To import samples into the list
• To remove samples from the list
• To reinject a sample from a previously acquired batch
• To select channels for the batch
• To assign a specific channel to a sample
• To select a reference sample
• To add an auto sample type
• To specify different instrument methods for samples
 To add samples to the list
1. Select the number of sample rows to add
and then click the Add icon,
or
.
2. Type a file name in the Filename column for each sample.
Each file name must be unique.
3. Select a sample type from the Sample Type list for each sample.
Available sample types
Matrix Blank
Solvent
QC Std
Unknown
Cal Std
For a detailed description of each sample type, see “Sample Types” on page 365.
4. For each Cal Std or QC Std sample, select a level from the Level list.
The master method defines the sample levels. If there are no levels to select in the Level
list, ask a user with Method Development permission to edit the method and specify the
levels. Then return to the Acquisition mode, and begin the batch again. The application
does not save a batch when you leave the Acquisition mode.
If you have Method Development permission, do the following:
a. Return to the Method Development mode.
b. Open the method.
c. Click the Compounds tab.
d. Click the Calibration Levels tab.
e. Add the levels.
f.
Save the method.
For detailed instructions, see “Calibration Levels” on page 219.
5. For each sample, type a vial position in the Vial Position column.
Tip Use the Fill Down command to make entering vial positions easier.
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6. For each sample, type a volume in the Injection Volume column.
The minimum injection volume value allowed is 0.1 μL; the maximum injection volume
value allowed is 5000 μL.
7. (Optional) Type or edit the values for the remaining columns.
Note When you use the scroll bar at the bottom of the sample list, the Status,
Filename, Sample Type, Groups, Qual Processing, Level, Sample ID, and Sample
Name columns stay fixed while the other columns scroll right and left.
For instructions to automatically copy or fill values in these columns, see Appendix C,
“Using Copy Down and Fill Down.”
 To insert samples into the list
1. Select the sample above which you want to insert new Unknown samples.
You cannot use the Insert command to create the first sample row.
2. Select the number of samples to insert
and then click the Insert icon,
or
.
The application inserts the Unknown samples above the selected sample.
Inserted
samples
3. For each sample, type a file name in the Filename column.
Each file name must be unique.
4. For each sample, select a sample type from the Sample Type list.
Available sample types
Matrix Blank
Solvent
QC Std
Unknown
Cal Std
5. For each Cal Std or QC Std sample, click the Level cell and select a level from the list.
The master method defines the sample levels. If there are no levels to select from the Level
list, ask a user with Method Development permission to edit the method and specify the
levels. Then return to the Acquisition mode, and begin the batch again. The application
does not save a batch when you leave the Acquisition mode.
If you have Method Development permission, follow the instructions in step 4 of the
procedure “To add samples to the list” on page 325.
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6. Type a vial position in the Vial Position column for each sample.
Tip Use the Fill Down command to make entering vial positions easier.
7. For each sample, type a volume in the Injection Volume column.
The minimum injection volume allowed is 0.1 μL; the maximum injection volume
allowed is 5000 μL.
8. (Optional) Type or edit the values for the remaining columns.
Note When you use the scroll bar at the bottom of the sample list, the Status,
Filename, Sample Type, Groups, Qual Processing, Level, Sample ID, and Sample
Name columns stay fixed while the other columns scroll right and left.
 To import samples into the list
1. Click Import,
.
The Sample Import Tool dialog box opens.
Use this dialog box to import a sample list from a CSV, an XML, or an SLD file.
2. Click Browse and select a CSV, an XML, or an SLD file with the sample definitions that
you want to import.
Note The .csv, .xml, or .sld file format must match the TraceFinder file format.
3. From the Imported Samples Will Be list, select either Appended to the End of the List
or Inserted at the Selected Row.
4. Click Import.
The Sample Import Tool dialog box closes, and the application adds the specified samples
to the sample list.
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When you import samples from an Xcalibur sequence file (.sld), the TraceFinder
application makes the following column name substitutions.
Xcalibur column
TraceFinder column
Position
Vial position
Inj Vol
Injection volume
Dil Factor
Conversion Factor
When you import samples from an Xcalibur sequence file (.sld), the TraceFinder
application makes the following sample type substitutions.
Xcalibur sample type
TraceFinder sample type
Blank
Matrix Blank
QC
QC Std
Std Bracket
Cal Std
For each imported sample, the application uses the Instrument Method specified in the
local method.
5. For each Cal Std or QC Std sample, click the Level cell and select a level from the list.
The master method defines the sample levels. If there are no levels to select from the Level
list, ask a user with Method Development permission to edit the method and specify the
levels. Then return to the Acquisition mode, and begin the batch again. The application
does not save a batch when you leave the Acquisition mode.
If you have Method Development permission, follow the instructions in step 4 of the
procedure “To add samples to the list” on page 325.
For detailed instructions about defining calibration levels, see “Calibration Levels” on
page 219.
6. Type a vial position in the Vial Position column for each sample.
Tip Use the Fill Down command to make entering vial positions easier.
7. Type a volume in the Injection Volume column for each sample.
The minimum injection volume value allowed is 0.1 μL; the maximum injection volume
value allowed is 5000 μL.
8. (Optional) Type or edit the values for the remaining columns.
Note When you use the scroll bar at the bottom of the sample list, the Status,
Filename, Sample Type, Groups, Qual Processing, Level, Sample ID, and Sample
Name columns stay fixed while the other columns scroll right and left.
9. (Optional) When using multiplexing, select a channel for each imported sample.
Imported samples default to Auto.
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 To remove samples from the list
1. Select the samples that you want to remove.
Tip Use the CTRL or SHIFT keys to select multiple samples.
2. Right-click and choose Remove Selected Samples from the shortcut menu.
 To reinject a sample from a previously acquired batch
1. In the sample list, select the sample to reinject.
2. Right-click and choose Reinject Selected Samples from the shortcut menu.
The TraceFinder application creates a copy of the selected sample and appends INJ001 to
the file name. Additional reinjections of the same sample are numbered INJ002, INJ003,
and so forth.
The TraceFinder application copies all parameter values from the original sample.
A green status icon indicates previously acquired samples (acquired and processed) and
the sample name is grayed out. A blue status icon indicates samples created for reinjection
(not acquired).
When you submit this batch, the application acquires only the reinjection samples.
 To select channels for the batch
Note These features are available only when you have activated multiplexing in the
Configuration console. See “Multiplexing” on page 61.
To disable a configured channel, clear the check box for the channel in the Multiplexing
Channels area at the bottom of the page.
By default, all configured channels are selected. The configured channels are determined
by the multiplexing settings in the Configuration console. See “Multiplexing” on page 61.
Clearing a channel in the Multiplexing Channels area does not remove this channel
selection from the Channels list for each sample. When you assign a channel to a sample,
be careful not to assign a channel that is not available.
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 To assign a specific channel to a sample
1. Scroll to the Channel column.
Note The Channel column is available only when you have activated multiplexing in
the Configuration console. See “Multiplexing” on page 61.
All samples default to Auto.
2. Select a channel from the Channel list.
When you submit the batch, samples that are set to Auto run on any of the available
channels and samples that are set to a specific channel run only on that channel.
If you select a channel that is not available for this batch, the application flags the sample
sequence on the Finish page of the Acquisition mode. See the previous procedure, To
select channels for the batch.
3. If you see this error, do the following:
a. Click Previous to return to the Sample Definition page.
The incorrect sample is marked with an error flag.
b. Correct the channel selection.
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 To select a reference sample
1. Click the Reference Sample tab.
The Reference Sample page in the Sample Definition page opens. See “Reference Sample”
on page 337.
You can select one reference sample to use as a reference peak in the Data Review.
2. Right-click the Reference Sample page and choose Add Reference Sample from the
shortcut menu.
The Open Chromatograph Reference Sample dialog box opens.
Note If you are using a new method, you will not see any samples here. You must
create and save a batch using the current method to see available samples in this list.
3. Select a batch from the list.
The TraceFinder application displays only batches that were created using the current
master method.
4. Select a sample from the list of processed samples on the right.
The TraceFinder application displays all the processed samples in the selected batch. To
use a sample as a reference sample, the sample must have been processed with the current
master method.
5. Click Open.
6. The application adds the reference sample to the Reference Sample page.
7. (Optional) Enter values for Sample ID, Sample Name, Comment, and Barcode Actual.
8. (Optional) Change the Vial Position for the sample.
The application uses the peak in this sample as a reference peak in the Analysis mode. See
“Reference Peak” on page 478.
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 To add an auto sample type
1. Click the Auto Samples tab.
The Auto Samples page opens. See “Auto Samples” on page 336.
2. Right-click and choose Add Auto Sample from the shortcut menu, or click the Add New
Auto Sample icon,
.
The application adds a Solvent sample to the sample list.
You can add, insert, or remove samples from this list as you would any sample list.
3. To change the sample type to a Matrix Blank, click the Sample Type column and select
Matrix Blank from the list.
4. In the Injection Volume column for the sample, type a volume.
The minimum injection volume value allowed is 0.1 μL; the maximum injection volume
value allowed is 5000 μL.
5. In the Number of Injections column, type the number of injections available in the
designated Solvent or Matrix Blank vial.
After auto sample injections have occurred, you can return to this page to view the
number of Injections Used in each vial.
6. In the Vial Position column, type the vial position for the Solvent or Matrix Blank
sample.
 To specify different instrument methods for samples
Note By default, the Instrument Method column is not displayed on the Sample
Definition page. See Instrument method column.
1. Display the Instrument Method column in the sample list:
a. Right-click the sample list and choose Modify Columns from the shortcut menu.
The Modify Columns dialog box opens.
b. In the Available Columns pane, select Instrument Method.
c. Click
pane.
to move the Instrument Method column to the Displayed Columns
d. Click OK.
The application displays the Instrument Method column, defaulting to the instrument
method specified in the master method.
2. Click the Instrument Method column and select an instrument method from the list.
This list contains all the available instrument methods. The application prefixes
instrument methods from external sources with “Ext:”.
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You can specify a different instrument method for each sample.
Figure 88. Instrument method column
When you submit the batch, the application saves a copy of the selected instrument
methods to the following folders:
External instrument methods:
…\TraceFinderData\32\Projects\…\batch\Methods\method\ExternalMethods
Local instrument methods:
…\TraceFinderData\32\Projects\…\batch\Methods\method
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Samples
Use the features on the Samples page to create a list of samples for the batch.
Figure 89. Samples page on the Sample Definition page
Table 65. Samples page parameters (Sheet 1 of 2)
Parameter
Definition
Previous
Returns you to the previous Acquisition page.
Next
Takes you to the next Acquisition page.
Status color codes
Sample is not acquired.
Sample is acquired but not processed.
Sample is acquired and processed.
Sample is currently acquiring.
Sample Controls
Add
Adds the specified number of empty rows to the sample grid.
Insert
Inserts the specified number of empty rows above the selected row.
Import
Opens the Sample Import Tool to import samples from a CSV, an XML, or an SLD file.
Multiplexing Channels
These features are available only when you have activated multiplexing in the
Configuration console. See “Multiplexing” on page 61.
All Channels
Uses all configured channels to acquire this batch.
Channel 1-n
Uses only the selected channels to acquire this batch.
Shortcut menu commands
Add Sample
Adds a single empty row to the sample grid.
Insert Sample
Inserts a single empty row to the sample grid above the selected row.
Insert Copy Sample
Copies the currently selected row and inserts a copy above the row.
Reinject Selected
Samples
Creates a copy of the selected sample and appends INJ001 to the file name. Additional
reinjections of the same sample are numbered INJ002, INJ003, and so forth.
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Table 65. Samples page parameters (Sheet 2 of 2)
Parameter
Definition
Remove Selected
Samples
Removes selected samples from the sample grid.
Import Samples
Opens the Sample Import Tool. See “To import samples into the list” on page 327.
Copy Down
Copies the value in the selected row to all rows below it. For detailed instructions about
using the Copy Down command, see Appendix C, “Using Copy Down and Fill Down.”
Fill Down
Enters sequential values in the column starting with the value in the selected row and
ending with the last row in the column. For detailed instructions about using the Fill
Down command, see Appendix C, “Using Copy Down and Fill Down.”
Modify Columns
Opens the Modify Columns dialog box. See “Column Display” on page 371.
Enable/Disable Sample
Weight Calculation
Displays or hides the Sample Volume, Dilution Factor, Sample Weight, Calculation Type,
and Final Units columns.
Copy
Copies the data in the selected rows or columns to the Clipboard. Use this command to
copy sample information to a text editor or spreadsheet application. You cannot paste this
data back into the Acquisition mode sample list.
Copy with Headers
Copies the data in the selected rows or columns and the associated column headers to the
Clipboard. Use this command to copy sample information to a text editor or spreadsheet
application. You cannot paste this data back into the Acquisition mode sample list.
Paste
Pastes a single column of copied data from a text editor or spreadsheet application, into the
selected column.
Undo Last Paste
Removes the last pasted item in the Acquisition mode sample list.
Export to CSV File
Opens the Save As dialog box where you can save the current sample list to a CSV file.
Edit Instrument Method Opens the Instrument Setup window where you can edit the parameters of the instrument
method.
• When you edit an external method, the application updates the method in the
…\Xcalibur\methods folder.
• When you edit an internal method, the application updates the method in the
…\TraceFinderData\32\Projects\project\subproject\batch\Methods\method folder.
For detailed information about editing instrument methods, see “Working with
Instrument Methods” on page 113.
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Auto Samples
Use the features on the Auto Samples Sample page to identify the Solvent or Matrix Blank
samples to use for any Auto Sample or Auto Sample and Reinject failure actions as specified
on the Intelligent Sequencing page of the method. See “Editing the Intelligent Sequencing
Page” on page 243.
Each sample type that you specify for a failure action on the Intelligent Sequencing page must
be defined on the samples list on the Auto Samples page.
Figure 90. Auto Samples page on the Sample Definition page
Table 66. Auto Samples page parameters
Column
Description
Sample Type
The sample type for the auto sample injection as specified on the Intelligent Sequencing page of
the method—either Solvent or Matrix Blank.
Default: Solvent
Injection Volume
The injection volume used for the sample acquisition as specified on the Samples page.
Range: 0.1 through 5000 μL
Injections Used
The number of times a vial has been used. The count is cumulative across all batches.
Number of
Injections
The number of injections available in the designated Solvent or Matrix Blank vial.
Vial Position
Vial position for this sample type as specified on the Samples page.
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Reference Sample
Use the features on the Reference Sample page to select a sample to use as a reference peak in
Data Review.
Figure 91. Reference Sample page on the Sample Definition page
Table 67. Reference Sample page parameters
Parameter
Status
Description
Sample is not acquired.
Sample is acquired but not processed.
Sample is acquired and processed.
Sample is currently acquiring.
Filename
Name of the raw data file that contains the sample data.
Sample ID
A user-defined, alphanumeric string that identifies a sample.
Sample Name
A user-defined name that identifies a sample.
Vial Position
The tray vial number used for an autosampler acquisition.
Barcode Actual
A user-entered barcode for the vial.
Shortcut menu commands
Add Reference Sample
Opens the Open Chromatogram Reference Sample dialog box where you can select a
reference sample.
Delete Selected
Deletes the reference sample.
Copy
Copies the data in the selected rows or columns to the Clipboard. Use this command to
copy sample information to a text editor or spreadsheet application. You cannot paste this
data back into the reference sample list.
Copy with Headers
Copies the data in the selected rows or columns and the associated column headers to the
Clipboard. Use this command to copy sample information to a text editor or spreadsheet
application. You cannot paste this data back into the reference sample list.
Paste
Pastes a single column of copied data from a text editor or spreadsheet application, into the
selected column.
Export to CSV File
Opens the Save As dialog box where you can save the current sample list to a CSV file.
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Selecting and Reviewing Reports
On the Report Selection page, you can specify the types of reports that you want to create. See
“Report Selection” on page 339. In addition to the report type, you can specify a report
description for each of your reports.
For each report that you generate, you can create a hard-copy printout, a PDF file, a CSV file,
or an Excel file.
Use any of the following procedures to create a reports list. When you finish specifying your
report options, click Next to go to the Finish page and submit your batch. See “Submitting
the Batch” on page 340.
The application writes the resulting output files for your reports to the
…\TraceFinderData\32\Projects\…\batch\Reports folder.
Follow these procedures:
• To edit a report title
• To specify a report in print format or as a PDF, a CSV, or an Excel file
 To edit a report title
Select the Report Title column and edit the default title.
The default report title is the same as the report name.
 To specify a report in print format or as a PDF, a CSV, or an Excel file
1. For each type of report that you want to create, select the corresponding check box in the
Print, Create PDF, Create CSV, or Create Excel column.
2. To duplicate the output type for all reports, right-click the cell and choose Copy Down
from the shortcut menu.
All check boxes in the column below the selected cell duplicate the selected or cleared
state in the selected cell. This action applies only to report types that make this output
format available.
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Report Selection
Use the features on the Report Selection page to specify the types of reports that you want to
create.
Figure 92. Report Selection page
Table 68. Report Selection page parameters
Parameter
Description
Report Name
The name of a report.
Report Title
User-editable description to be used on a report.
Print
Reports to be sent to the printer.
Create PDF
Reports to be saved as PDF files.
Create CSV
Reports to be exported as CSV files.
Create Excel
Reports to be exported as Excel files.
Shortcut menu:
Copy Down
Copies the selected or cleared state to all subsequent reports in the column.
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Submitting the Batch
In the Finish page of the Acquisition mode, you can specify a startup method, a shutdown
method, or a calibration batch. You can save the batch to be acquired later, or you can acquire
and process data and optionally create reports. See “Finish page” on page 347.
Note If you are working with a batch template, the only available function is Save.
Follow these procedures:
• To specify startup or shutdown methods
• To automatically update the timed SRM information
• To specify a calibration batch
• To specify device states
• To save a batch for later acquisition
• To start an acquisition
• To view the output files
 To specify startup or shutdown methods
1. Select a method from the System Startup Method list.
The TraceFinder application runs this method before running the batch. No autosampler
injection takes place. This feature is not available for all instruments.
2. Select a method from the System Shutdown Method list.
The TraceFinder application runs this method after running the batch. This feature is not
available for all instruments.
 To automatically update the timed SRM information
Select the Auto TSRM Update check box.
When you submit the batch, the application updates the TSQ method with mass
transitions, collision energy, and other appropriate data for TSRM functionality.
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 To specify a calibration batch
1. In the Calibration area, select a calibration (.calx) file from the list.
Note You must acquire at least one batch with the current method to create a
calibration (.calx) file.
2. To add calibration data from the current batch to the selected calibration file, select the
Extend Calibration option.
 To specify device states
In the System Status area, select the name of the device, right-click, and then choose a
device state from the shortcut menu.
Table 69. Instrument states (Sheet 1 of 2)
Instrument state
Description
Turn Device On
Keeps the system in the On state when the current run finishes,
so you can begin another run without waiting. All power and
flows are maintained at operational levels.
Default: On
Turn Device Standby
Keeps the system in the Standby state when the current run
finishes, so you can begin another run with only a short delay
between runs.
Some devices do not have a Standby feature. For devices with
this feature, the device enters a power-saving or
consumable-saving mode, and you can switch the device back
on in approximately 15 minutes. Depending on the
instrument, this state turns liquid flows off but maintains
heaters and other subsystems in an On state so that there is no
warm-up time required when you change from Standby to On.
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Table 69. Instrument states (Sheet 2 of 2)
Instrument state
Description
Turn Device Off
Keeps the system in the Off state when the current run
finishes. The Off state indicates that all power to the
instrument, which the TraceFinder application can control, is
turned off. This includes power to all heaters and
subassemblies, but in some cases not all subassemblies.
Some devices do not have an Off feature. For devices that do
have this feature, the device enters a power-saving or
consumable-saving mode, and you can switch the device back
on. When several runs are queued, the application uses the
system power scheme of the last submitted run.
Instrument status indicators
Green indicates that the device is turned on or is running.
Yellow indicates that the device is in standby mode or is
waiting for contact closure.
Red indicates that the device is turned off or that there is an
error with the device.
 To save a batch for later acquisition
From the Finish page, click Save,
.
The TraceFinder application saves your batch as a prepared file.
 To start an acquisition
1. Click Submit,
.
The Submit Options dialog box opens. For detailed descriptions of the parameters, see
“Submit Options dialog box” on page 344.
2. To acquire (or reacquire) the submitted samples, select the Acquire Data check box.
• When all submitted samples have been previously acquired, this option is (by default)
not selected.
• When any of the submitted samples has not been acquired, this option is (by default)
selected.
3. To process the submitted samples, select the Process Data check box.
You can process the data with or without performing peak detection. You might, for
example, want to turn off peak detection when reprocessing samples.
4. (Optional) Select the Create Reports check box.
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5. (Optional with multiplexing activated) Select the Priority Sequence check box.
The application acquires the priority batch on the next available channel or the assigned
channel.
6. (Optional without multiplexing activated) Select the Priority Sequence check box and
then select one of the following priority options to place the batch in the queue:
• Next Available Batch places the batch immediately after the currently acquiring
batch.
• Next Available Sample places the batch immediately after the currently acquiring
sample.
Note When you select Full Sequence Submission in the Configuration console, these
options are unavailable because the current batch and the current sample are, in effect,
the same thing.
7. Select the Use check box for the device that you want to use for this acquisition.
8. (Optional) Select the Start Device check box to indicate the device that will initiate
communication with the other instruments.
This is usually the autosampler.
9. (Optional) Select the Start When Ready check box, which starts all instruments together
when they are all ready.
When this is cleared, individual instruments can start at different times and then have to
wait for the last instrument to be ready.
10. Do one of the following:
To start the selected processes, click OK.
The selected processes begin, and the TraceFinder application shows the real-time display
at the bottom of the current window. You can begin another batch in the Acquisition
mode while you watch the real-time display of the currently acquiring batch.
–or–
Click Cancel to exit the Acquisition mode without performing any tasks.
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Figure 93. Submit Options dialog box
Acquire Data
selected
Acquire Data
not selected
Table 70. Submit Options dialog box parameters (Sheet 1 of 2)
Parameter
Description
User Name
Name of the current user.
Samples
Number of samples to be submitted for acquisition, processing, or reporting.
Acquire Data
Submits the current batch to acquisition.
• When all submitted samples have been previously acquired, this option is (by default)
not selected.
• When any of the submitted samples has not been acquired, this option is (by default)
selected.
Process Data
(Default) Processes the data for the current batch.
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Table 70. Submit Options dialog box parameters (Sheet 2 of 2)
Parameter
Description
With Peak Detection
(Default) Processes the data with peak detection.
When you clear this option, the application reprocesses samples without performing peak
detection.
Create Reports
Creates reports for the current batch.
Priority Sequence
With multiplexing activated, places the batch immediately after the currently acquiring
batch.
Without multiplexing activated, specifies one of the following priority options to place the
batch in the queue:
Next Available Batch: Places the batch immediately after the currently acquiring batch.
Next Available Sample: Places the batch immediately after the currently acquiring sample.
Note When you select Full Sequence Submission in the Configuration console, these
options are unavailable because the current batch and the current sample are, in effect, the
same thing.
Acquisition pane
Device Name
Lists all configured instruments.
If the instrument that you want to use is not configured, close the TraceFinder application,
configure the instrument, and then reopen the TraceFinder application. You cannot
configure an instrument while the TraceFinder application is running.
Available only when you select the Acquire Data check box.
Use
Specifies the instruments used for this acquisition.
Available only when you select the Acquire Data check box.
Start Device
Specifies the instrument that initiates the communication with the other instruments. This
is usually the autosampler.
Available only when you select the Acquire Data check box.
Start When Ready
Starts the specified device when all the instruments are ready to acquire data. When this is
cleared, individual instruments can start at different times and then must wait for the last
instrument to be ready.
Post-run System
State
Specifies the system state after it acquires the last batch: On (default), Standby, or Off.
Hide/Show Details
Collapses or expands the acquisition details of the Submit Options dialog box.
OK
Begins the selected processes.
Cancel
Closes the Submit Options dialog box without submitting any tasks.
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 To view the output files
Locate the files to view from the following directories:
The TraceFinder application writes saved batches to the project folder:
…\TraceFinderData\32\Projects\…
For each acquired sample, the application writes an RSX file to the batch Data folder:
…\TraceFinderData\32\Projects\…\Data
The application saves method information to the batch Methods folder:
…\TraceFinderData\32\Projects\…\Methods
The application writes the reports to the batch Reports folder:
…\TraceFinderData\32\Projects\…\batch\Reports
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Finish
Use the features on the Finish page to save the batch to be acquired later or acquire and
process data and optionally create reports.
Figure 94. Finish page
Table 71. Finish page parameters
Parameter
Description
System Status
The System Status pane displays the following:
• Devices used for the acquisition
• Project, subproject, and name of the batch
• Number of acquired and unacquired samples in the batch
• Number of reports to be printed and saved as PDF, CSV, or Excel files
• Local method and instrument method used for the batch
• Number of compounds in the method
System Startup Method
The instrument methods that run before and after the batch. No autosampler injection
System Shutdown Method takes place. These features are not available for all instruments.
Auto TSRM Update
Calibration
Updates the TSQ method with mass transitions, collision energy, and other appropriate
data for TSRM functionality.
• Use calibration: Uses the selected calibration file to process the current data.
• Extend calibration: Adds calibration data from the current batch to the selected
calibration file.
Save
Saves the current batch as a prepared batch.
Submit
Opens the Submit Options dialog box where you can choose to generate reports.
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Real Time Status Pane
Real Time Status Pane
You can access the Real Time Status pane from any mode in the TraceFinder application.
 To access the Real Time Status Pane from any mode
Click Real Time Status in the upper right corner of the TraceFinder window.
The Real Time Status pane opens at the bottom of the current view.
Figure 95. Real Time Status pane
The Real Time Status pane has four pages of information and a real-time trace pane:
• Acquisition Page
• Instrument Page
• Devices Page
• Queues Page
• Real-Time Trace Display
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Acquisition Page
Use the Acquisition page to monitor the progress as the application acquires the samples.
Use the Start,
, Stop,
, or Pause,
to control batches in the Acquisition queue.
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 To display the last acquired raw data file in a qualitative browser
On the Acquisition page of the real-time status pane, right-click and choose View Last
File in Qual Explorer from the shortcut menu.
The last acquired file opens in either the FreeStyle or Qual Browser application.
 To open the Instrument Setup window
Right-click anywhere in the Acquisition page and choose Open Instrument Method
Editor from the shortcut menu.
The Thermo Xcalibur Instrument Setup window opens, displaying the currently running
instrument method.
For detailed information about editing instrument methods, see “Working with
Instrument Methods” on page 113.
Note Changes you make and save to the instrument method do not affect the
currently running batch.
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Instrument Page
Use the Instrument page to monitor the currently acquiring sample.
When you run single sample
submission, this displays the
sample name instead of the
batch name.
 To view the last acquired file in a qualitative browser
Right-click anywhere in the top pane of the Instrument page and choose View Last File
in Qual Explorer from the shortcut menu.
The last acquired file opens in either the FreeStyle or Qual Browser application.
 To open the Instrument Setup window
Right-click anywhere in the top pane of the Instrument page and choose Open
Instrument Method Editor from the shortcut menu.
The Thermo Xcalibur Instrument Setup window opens, displaying the currently running
instrument method.
For detailed information about editing instrument methods, see “Working with
Instrument Methods” on page 113.
Note Changes you make and save to the instrument method do not affect the
currently running batch.
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Devices Page
Use the Devices page to monitor the status of the instrument. The feedback you see on the
Devices page depends on the instrument you are using. The following examples show an
Accela autosampler and an Aria™ multiplexing device.
Accela Autosampler Feedback
Aria Multiplexing Feedback
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Follow these procedures:
• To pause the autosampler
• To control the channels
• To view the pressure trace
• To access the Aria multiplexing controls
• To view the last acquired file in a qualitative browser
• To open the Instrument Setup window
 To pause the autosampler
1. Click Hold Autosampler.
The autosampler finishes the current autosampler step and then pauses. The autosampler
and LC pumps continue to run.
2. To restart the autosampler, click Hold Autosampler again.
 To control the channels
Right-click the channel name and choose a command from the shortcut menu.
Table 72. Autosampler shortcut menu commands (Sheet 1 of 2)
Thermo Scientific
Command
Description
On
Turns on a stopped pump and continues acquiring the sample
list assigned to that channel.
Off
After the current sample completes, the application stops
acquiring and the pump shuts down.
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Table 72. Autosampler shortcut menu commands (Sheet 2 of 2)
Command
Description
Standby
After the current sample completes, the application stops
acquiring. The pump continues to run.
Disable / Enable
Disable: Prevents the channel from receiving samples. When
you choose Disable during a run, the application finishes the
current sample on the channel and then stops.
Enable: Allows the channel to receive samples.
When you disable a channel that is set to On, the channel is
highlighted in green and the status is READY. You can turn
the channel to Off or Standby.
 To view the pressure trace
1. Click the Pres tab.
The Pressure page displays a pump pressure graph for each sample in the batch. A
fluctuation or change in the pump pressure could indicate a change in the
chromatography conditions.
2. To view the pressure for a specific pump, select the Pres 1 or Pres 2 option.
By default, the pressure for all pumps are displayed.
3. To view the pressure for a specific channel, select the corresponding channel number.
By default, the pressure for all channels is displayed.
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 To access the Aria multiplexing controls
Click Direct Control.
The Aria MX Direct Control window opens.
For detailed descriptions of the features in this window, refer to the Transcend Systems with
Xcalibur Software User Guide.
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 To view the last acquired file in a qualitative browser
Right-click in the header of the Devices page and choose View Last File in Qual
Explorer from the shortcut menu.
The last acquired file opens in either the FreeStyle or Qual Browser application.
 To open the Instrument Setup window
Right-click in the header of the Devices page and choose Open Instrument Method
Editor from the shortcut menu.
The Thermo Xcalibur Instrument Setup window opens, displaying the currently running
instrument method.
For detailed information about editing instrument methods, see “Working with
Instrument Methods” on page 113.
Note Changes you make and save to the instrument method do not affect the
currently running batch.
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Queues Page
Use the Queues page to monitor and control the Acquisition, Processing, and Reporting
queues.
• Queue-Level Commands: Pause or remove batches in any of the queues.
• Batch-Level Commands: Pause or remove entire batches or samples within batches from
any of the queues.
• Additional Commands: Open the FreeStyle application or the Instrument Setup window.
Queue-Level Commands
Use the queue-level commands to pause or remove batches in any of the queues on the
Queues page. See “Queue-Level Shortcut Menu” on page 359.
Follow these procedures:
• To pause all batches in a queue
• To remove a single batch from a queue
• To remove all batches in a queue
• To remove all pending batches
 To pause all batches in a queue
1. Select a queue (Acquisition, Processing, or Reporting).
Note When multiplexing is activated, you can have as many as four samples acquiring
at once. Pausing the Acquisition queue does not affect any acquiring samples.
2. Right-click and choose Pause Queue from the shortcut menu.
After the current sample completes, the application pauses all batches and samples in the
specified queue. Only the selected queue is affected.
3. To restart a paused queue, select the queue, right-click, and choose Resume Queue from
the shortcut menu.
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 To remove a single batch from a queue
1. Select a queue (Acquisition, Processing, or Reporting).
2. Right-click and choose Stop Active Batch from the shortcut menu.
Note This command is available only when there are active batches in the queue.
Paused batches and batches that contain only pending samples are not “active.”
The application confirms that you want to remove the active batch from the selected
queue. After the current sample completes, the application removes the batch and all
pending samples from the queue. Only the selected queue is affected.
 To remove all batches in a queue
1. Select a queue (Acquisition, Processing, or Reporting).
2. Right-click and choose Stop All Batches from the shortcut menu.
The application removes all batches with pending samples from the selected queue. The
current sample continues to acquire. Only the selected queue is affected.
 To remove all pending batches
1. Select a queue (Acquisition, Processing, or Reporting).
2. Right-click and choose Remove Pending Batches from the shortcut menu.
Note A pending batch is a batch in which all samples are pending. If any sample in
the batch is active, the batch is not affected by this command.
The application removes all batches that contain only pending samples. Only the selected
queue is affected.
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Queue-Level Shortcut Menu
Use the commands on the shortcut menu to pause or remove batches in any of the queues on
the Queues page.
Figure 96. Queue-level shortcut menu
Table 73. Queue-level shortcut menu commands
Thermo Scientific
Command
Description
Pause Queue
After the current sample completes, the application pauses the
specified queue. Only the selected queue is affected.
Resume Queue
Returns the paused queue to active status.
Stop Active Batch
Removes all pending samples from the specified queue. The active
sample is not affected.
Stop All Batches
Removes all pending samples and batches from the specified
queue. The active sample is not affected.
Reactivate All Batches
Returns all paused batches to active status.
Remove Pending
Batches
Removes all pending batches from the specified queue. The active
batch is not affected.
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Batch-Level Commands
Use the batch-level commands to pause or remove entire batches or samples within batches
from any of the queues on the Queues page. See “Batch-level shortcut menu.”
Follow these procedures:
• To remove a single pending sample from a batch
• To remove all pending samples from a batch
• To stop a batch
• To remove a pending batch
 To remove a single pending sample from a batch
1. Select a pending sample.
2. Right-click the sample and choose Remove Sample from the shortcut menu.
The application confirms that you want to remove the selected sample from the batch and
then removes the sample.
 To remove all pending samples from a batch
1. Select a batch in any of the queues (Acquisition, Processing, or Reporting).
The batch must have at least one pending sample.
2. Right-click and choose Remove Pending Samples from the shortcut menu.
The application confirms that you want to remove all pending samples from the batch
and then removes the samples. If the batch includes only pending samples, the
application removes the batch from the queue.
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 To stop a batch
1. Select an active batch in any of the queues (Acquisition, Processing, or Reporting).
Note The batch must have at least one active sample and one pending sample.
2. Right-click and choose Stop Batch from the shortcut menu.
The application confirms that you want to remove the selected batch from the queue.
After the current sample completes, the application removes the batch and all pending
samples from the queue.
 To remove a pending batch
1. Select a pending batch in any of the queues (Acquisition, Processing, or Reporting).
Note A pending batch is a batch in which all samples are pending. If any sample in
the batch is active, this command is not available.
2. Right-click and choose Remove Pending Batch from the shortcut menu.
The application confirms that you want to remove the selected batch from the queue and
then removes the batch from the queue.
Figure 97. Batch-level shortcut menu
Table 74. Batch-level shortcut menu commands
Command
Description
Stop Batch
After the current sample completes, the application removes all
samples in the selected batch.
Remove Pending Batch Removes all samples from the selected pending batch.
Remove Pending
Samples
Thermo Scientific
Removes all pending samples from the selected batch.
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Additional Commands
Use the commands on this shortcut menu to open the FreeStyle application or the Instrument
Setup window.
 To view the last acquired file in a qualitative browser
Right-click below the queues list on the Queues page and choose View Last File In Qual
Explorer from the shortcut menu.
Note You must click in the white space below the list of queues. Clicking on or to the
right of the queues displays queue-, batch-, or sample-level shortcut menus.
The last acquired file opens in either the FreeStyle or Qual Browser application.
 To open the Instrument Setup window
Right-click below the queues list on the Queues page and choose Open Instrument
Method Editor from the shortcut menu.
Note You must click in the white space below the list of queues. Clicking on or to the
right of the queues displays queue-, batch-, or sample-level shortcut menus.
The Thermo Xcalibur Instrument Setup window opens, displaying the currently running
instrument method.
For detailed information about editing instrument methods, see “Working with
Instrument Methods” on page 113.
Note Changes you make and save to the instrument method do not affect the
currently running batch.
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Real-Time Trace Display
As each sample acquires, the real-time chromatogram pane shows the retention time and
intensity of the TIC trace.
By default, the Real Time Status pane shows only the TIC trace as each sample acquires. To
observe specific traces, such as the internal standard, use the RTV Display Traces function to
display multiple traces.
When you create your method, you can specify additional traces to display in the real-time
viewer and in which order the traces are displayed. The application always displays the TIC
trace in the top pane. See “Real Time Status Pane” on page 348.
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 To display multiple traces
Right-click the chromatogram pane and choose the number of traces to display.
The chromatogram pane displays real-time chromatograms for the selected number of
traces.
The TIC is always displayed at the top. When there are more traces than can fit in the
pane, you can scroll through the traces.
For each trace, the application displays the mass or precursor mass.
Figure 98. Real-time trace display with multiple traces
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Sample Types
Sample Types
The TraceFinder application uses the following sample types in all sample definitions and
reports.
Table 75. Sample type definitions
Thermo Scientific
Sample type
Definition
Matrix Blank
Contains no target compounds but might contain an ISTD when you
use the internal standard quantitative analysis technique. By analyzing a
blank sample, you can confirm that there are no residual compounds in
the solvent system that can cause erroneous results.
Cal Std
(Calibration standard) Contains known amounts of all target
compounds. The purpose of a standard is to measure the response of the
instrument to the target compounds so that the processing software can
generate a calibration curve for each compound.
QC Std
(Quality Check standard) Contains a known amount of one or more
specific target compounds. The application places check standard
samples in the sequence so that it can test quantitative analysis results
for quality assurance purposes. After the application analyzes the QC
Std sample, it compares the measured quantity with the expected value
and an acceptability range. The quantitative analysis of a QC Std sample
is classified as passed if the difference between the observed and expected
quantities is within the user-defined tolerance. A QC Std sample is
classified as failed if the difference between the observed and expected
quantities is outside the user-defined tolerance.
Solvent
Contains only solvent.
Unknown
Used for quantitative analysis of samples.
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This chapter includes instructions about using the features of the Analysis mode.
Contents
• Working in the Batch View
• Working in Data Review for Quantitation Methods
• Working in Data Review for Target Screening Methods
• Working in the Local Method View
• Working in the Report View
• Working in the Report Designer
Use the Analysis mode to do the following:
• Submit batches for acquisition, processing, or reports.
• Review batches, batch data, reports, and local methods.
 To access the Analysis mode
Click Analysis in the navigation pane.
The Analysis navigation pane opens.
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Working in the Batch View
Working in the Batch View
In the Batch View, you can manually create and edit a new batch or open and edit a previously
saved batch. When you submit a batch, you can acquire and process data and optionally create
reports for the submitted samples.
The Analysis mode includes a toolbar:
Use the toolbar or the equivalent commands on the Batch View shortcut menu to create the
sample list and submit samples for acquisition. See “Toolbar” on page 377 or “Batch View
Shortcut Menu” on page 381.
This section includes the following topics:
• Samples Page
• Auto Samples Page
• Reference Samples Page
• Threshold Samples Page
 To open the Batch View
1. Click Analysis in the navigation pane of the current mode.
2. In the Analysis navigation pane, click Batch View.
The Batch View navigation pane opens.
Available only for quantitative batches
when you activate Intelligent Sequencing
in the Configuration console.
Available only for quantitative batches.
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Samples Page
To open the Samples page, click Samples in the Batch View navigation pane.
This section contains information about the following topics:
• Samples Page Features
• Creating a New Batch
• Editing a Batch
• Submitting a Batch
Samples Page Features
The Samples page is divided into two panes:
• Samples pane
Use the samples pane to create a batch. See “Samples Pane” on page 370.
• Compound Active Status pane
Use the Compound Active Status pane to make specific compounds active or inactive. See
“Compound Active Status Pane” on page 383.
Samples pane
Compound Active Status pane
Tip To resize the panes, drag the separators that divide the panes.
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Samples Pane
The samples pane includes the following features:
• Column Display
• Status Indicators
• Groups
• Blank Subtraction in Target Screening Batches
• Sample Weight Calculation
• Instrument Methods
• Toolbar
• Batch View Sample List
• Batch View Shortcut Menu
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Column Display
The sample list contains many columns of information. You can scroll to see all the columns
of information, and you can customize which columns to display and their display order.
Follow these procedures:
• To scroll the sample list
• To customize the column display
 To scroll the sample list
Use the horizontal scroll bar at the bottom of the sample list to view all the information.
When you use the scroll bar at the bottom of the sample list, the Status, Filename, Sample
Type, Groups, Qual Processing, Level, Sample ID, and Sample Name columns stay fixed
while the other columns scroll right and left.
 To customize the column display
1. Right-click the sample list and choose Modify Columns from the shortcut menu.
The Modify Columns dialog box opens. See “Modify Columns dialog box.”
2. Use the arrow buttons to move all the columns that you want displayed to the Displayed
Columns pane.
These columns appear after the Status, Filename, Sample Type, Groups, Qual Processing,
Level, Sample ID, and Sample Name columns.
3. To arrange the order of the columns, do the following:
a. In the Displayed Columns pane, select a column name.
b. Use Up or Down to move the selected column up or down in the list.
The first column in the list represents the leftmost column in the Batch View sample
list, and the last column in the list represents the rightmost column in the Batch View
sample list.
Note You cannot move the Status, Filename, Sample Type, Groups, Qual
Processing, Level, Sample ID, or Sample Name columns.
4. To change the width of a column, do the following:
a. In the Displayed Columns pane, select the column width.
b. Type a new value for the width.
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5. Repeat step 4 for all columns whose widths you want to change, and click OK.
The columns in the sample list immediately reflect your changes. The application uses
these settings for all sample lists in the Batch View.
Figure 99. Modify Columns dialog box
Table 76. Button descriptions for the Modify Columns dialog box
Button
Description
Moves all columns to the Displayed Columns pane.
Moves the selected column to the Displayed Columns pane.
The following buttons apply to all columns, except for those that are fixed: Status, Filename,
Sample Type, Groups, Qual Processing, Level, Sample ID, and Sample Name.
Moves the selected column to the Available Columns pane.
Moves all columns except fixed columns.
Moves the selected column name in the Displayed Columns pane one row
up in the column order.
Moves the selected column name in the Displayed Columns pane one row
down in the column order.
Note The application adds a Blank Subtraction column to the fixed columns for target
screening batches only.
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Status Indicators
Status indicators show the current status of each sample during the acquisition and
processing.
Sample is not acquired.
Sample is acquired but not processed.
Sample is acquired and processed.
Sample is currently acquiring.
Status indicators
Groups
Use the Groups feature to assign samples to a group. After you create groups, you can choose
one of the samples as a threshold sample for the group and then view the samples in the group
in the Comparative View in the Analysis mode.
 To create a group
1. For each sample, click the Groups column and type the name of a group.
Note Group names are not case sensitive and are always interpreted as lowercase. For
example, if you assign one sample to “GroupA” and another sample to “groupa”, both
samples are assigned to “groupa” on the Threshold Samples page.
Repeat this for each sample that you want to include in a group.
2. Create as many groups as you want.
Note To assign a sample to multiple groups, separate the groups with a comma.
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For information about specifying a threshold sample for a group of samples, see “Threshold
Samples Page” on page 409.
For information about viewing grouped samples in Data Review, see “Comparative View” on
page 433.
Blank Subtraction in Target Screening Batches
In target screening batches only, use the Blank Subtraction feature to select which matrix
blank samples you want to use for peak subtraction. The application subtracts the areas of the
peaks in the selected matrix blank samples from the matching areas in the unknown samples.
When you process the batch sequence, the application subtracts the peaks in a selected matrix
blank sample from all unknown samples that follow it, until it encounters another matrix
blank sample.
To activate the Blank Subtraction feature, see “Editing the Processing Page” on page 277.
Sample Weight Calculation
Use the sample weight features to calculate the conversion factor for a sample. The application
uses different methods to calculate the conversion factor for liquid or solid calculation types.
Liquid: SampleVolume DilutionFactor
Solid: (SampleVolume × DilutionFactor) SampleWeight
Manual: The application does not calculate the Conversion Factor. Instead, you can enter the
Conversion Factor value.
Follow these procedures:
• To display the features for calculating sample weight
• To calculate the conversion factor for a liquid sample
• To calculate the conversion factor for a solid sample
• To manually specify the conversion factor for a sample
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 To display the features for calculating sample weight
If the Conversion Factor, Sample Volume, Dilution Factor, Sample Weight, Calculation
Type, and Final Units columns are not visible, right-click and choose Enable Sample
Weight Calculation from the shortcut menu.
 To calculate the conversion factor for a liquid sample
Note The application uses the following formula to calculate the Conversion Factor:
SampleVolume DilutionFactor
1. From the Calculation Type list, select Liquid.
For a liquid sample, the Sample Weight value is not editable.
2. In the Sample Volume column, type the volume in ng/mL for your sample.
3. In the Dilution Factor column, type the value for the dilution.
For example, if you have 1000 ng/mL of a substance that is too concentrated for the mass
spectrometer, you can dilute it by 1000. Then your injection volume is 1, your conversion
factor is 1000, and your sample amount is 1000.
4. In the Final Units column, type the units that you want to use for the calculated amount
in the Data Review view or in reports.
 To calculate the conversion factor for a solid sample
Note The application uses the following formula to calculate the Conversion Factor:
(SampleVolume × DilutionFactor) SampleWeight
1. From the Calculation Type list, select Solid.
2. In the Sample Weight column, type the weight in ng for your sample.
3. In the Sample Volume column, type the volume in ng/ml for your sample.
4. In the Dilution Factor column, type the value for the dilution.
For example, if you have 1000 ng/ml of a substance that is too concentrated for the mass
spectrometer, you can dilute it by 1000. Then your injection volume is 1, your conversion
factor is 1000, and your sample amount is 1000.
5. In the Final Units column, type the units that you want to use for the calculated amount
in the Data Review view or in reports.
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 To manually specify the conversion factor for a sample
Note The application uses the specified conversion factor when it calculates the
amount for the sample.
1. From the Calculation Type list, select Manual.
For a manually calculated sample, the only available columns are the Conversion Factor
and the Final Units.
2. In the Conversion Factor column, type the conversion factor to use for your sample.
3. In the Final Units column, type the units that you want to use for the calculated amount
in the Data Review view or in reports.
Instrument Methods
Use the Instrument Methods column to specify instrument methods for the samples.
Note By default, the Instrument Method column is not displayed in the Batch View
sample list.
 To specify instrument methods for samples
1. Display the Instrument Method column in the sample list:
a. Right-click the sample list and choose Modify Columns from the shortcut menu.
The Modify Columns dialog box opens.
b. In the Available Columns pane, select Instrument Method.
c. Click
pane.
to move the Instrument Method column to the Displayed Columns
d. Click OK.
The application displays the Instrument Method column, defaulting to the instrument
method specified in the master method.
2. Click the Instrument Method column and select an instrument method from the list.
This list contains all the available instrument methods. Instrument methods from
external sources are prefixed with “Ext:”.
You can specify a different instrument method for each sample.
When you submit the batch for acquisition, the application saves a copy of the selected
instrument methods to the following folders:
External instrument methods:
…\TraceFinderData\32\Projects\…\batch\Methods\method\ExternalMethods
Local instrument methods:
…\TraceFinderData\32\Projects\…\batch\Methods\method
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Toolbar
The Analysis mode includes this toolbar for creating and submitting a batch.
Table 77. Toolbar icons
Icon
Description
Adds the specified number of new, empty samples to the end of the
sample list. See the instructions “To add samples to the list” on
page 387.
Inserts a new, empty sample or samples above the selected sample. See
the instructions “To insert samples into the list” on page 387.
Removes the selected samples from the sample list. See the
instructions “To remove samples from the list” on page 388.
Adds imported samples from a CSV, an XML, or an SLD file to the
sample list. See the instructions “To import samples into the list” on
page 387.
Submits only the selected samples for acquisition, processing, or
report generation. See the instructions “To submit samples in the
batch” on page 398.
Submits the batch for acquisition, processing, or report generation.
See the instructions “To submit samples in the batch” on page 398.
Opens the Acquisition mode where you can use a batch template to
define a standard sequence composed of various sample types to be
assembled into a batch of samples. See “Working in Data Review for
Quantitation Methods” on page 410.
Opens the Acquisition mode where you can create a batch template
that contains the basic settings and sample types for your batches. See
“Using the Acquisition Mode” on page 311.
Opens the Quick Acquisition window where you can quickly submit a
single sample. See Appendix A, “Using Quick Acquisition.”
Opens the Audit Viewer where you can view audit logs. See
Chapter 9, “Using the Audit Viewer.”
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Batch View Sample List
The sample list displays all the quantitative data for the samples of a batch.
Status indicators for each sample indicate if the sample is currently acquiring, not acquired,
acquired, or processed.
The sample list includes the following columns of information:
Figure 100. Batch View sample list
Note
• In target screening batches only, the sample list includes a Blank Subtraction column
after the Sample Type column.
• Cells in the sample list that are not editable, such as Barcode Actual, are shaded and
empty.
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Table 78. Batch View sample list columns (Sheet 1 of 2)
Column
Status
Description
Sample is not acquired.
Sample is acquired but not processed.
Sample is acquired and processed.
Sample is currently acquiring.
Groups
Threshold group to which a sample belongs. Samples can be viewed by group in the
Comparative View of Data Review.
Filename
Name of the raw data file that contains the sample data.
Sample Type
Defines how the TraceFinder application processes the sample data. Each sample is classified
as one of the following sample types:
Matrix Blank, Solvent, Cal Std, QC Std, or Unknown
Default: Unknown
Qual Processing
Indicates samples to be processed with the qualitative peak processing criteria specified in
the method. The Qualitative View displays processed data for the selected samples.
Blank Subtraction
Specifies a matrix blank sample to use for blank subtraction.
Level
The level defined for a calibration sample or quality control sample.
Sample ID
A user-defined, alphanumeric string that identifies a sample.
Sample Name
A user-defined name that identifies a sample.
Vial Position
The tray vial number used for an autosampler acquisition.
Injection Volume
The injection volume (in microliters) of the injected sample.
When you are using an autosampler, you can set the default injection volume in the
Autosampler dialog box in the Instrument View. The minimum and maximum injection
volumes that you can use depend on the Autosampler you configure. The usable range
depends on the injection mode and might be smaller than the displayed range.
The Injection Volume value set in the master method overwrites the value in the instrument
method.
Range: 0.1 through 5000 μL
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Table 78. Batch View sample list columns (Sheet 2 of 2)
Column
Description
Calculation Type
Liquid: The application calculates the Conversion Factor as
SampleVolume DilutionFactor
Solid: The application calculates the Conversion Factor as
(SampleVolume × DilutionFactor) SampleWeight
Manual: Sample Volume, Dilution Factor, Sample Weight, and Final Units columns are not
available, and the Conversion Factor value is editable.
Conversion Factor
Editable only when Calculation Type is Manual. Default: 1
Sample Volume
Default: 1
Dilution Factor
Default: 1
Sample Weight
Available only when Calculation Type is Solid. Default: 1
Final Units
Specifies the calculated amount in the Data Review view or in reports.
Default: 1
Instrument Method
Specifies the instrument to use for the acquisition. This column is hidden by default. To
display this column, see “To customize the column display” on page 371.
Channel
Specifies the channel on which the sample was run. If the sample is not acquired, the value is
Pending. The Channel column is available only when you have activated multiplexing in the
Configuration console. See “Multiplexing” on page 61.
Barcode Expected
A user-entered barcode for the vial.
Barcode Actual
An actual barcode for the vial. This value is not editable.
Comment
A user-defined comment for the sample.
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Batch View Shortcut Menu
The Batch View includes a shortcut menu for creating a batch.
Table 79. Batch View shortcut menu commands (Sheet 1 of 2)
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Command
Description
Add Sample
Adds a single empty row to the sample grid.
Insert Sample
Inserts a single empty row to the sample grid above the selected
row.
Insert Copy Sample
Copies the currently selected row and inserts a copy above the
row.
Reinject Selected
Samples
Creates a copy of the selected sample and appends INJ001 to the
file name. Additional reinjections of the same sample are
numbered INJ002, INJ003, and so forth.
Remove Selected
Samples
Removes selected samples from the sample grid.
Import Samples
Opens the Sample Import Tool. See “To import samples into the
list” on page 387.
Browse in Raw File
(Move)
Opens a dialog box where you can select a raw data file to use for
the selected sample row. The application removes the raw data
file from the source location.
Browse in Raw File
(Copy)
Opens a dialog box where you can select a raw data file to use for
the selected sample row. The application copies the raw data file
from the source location.
Map Raw Files to
Samples
Opens a dialog box where you can select multiple raw data files
to use for the selected sample rows.
Copy Down
Copies the value in the selected row to all rows below it. This
command is available only when you have selected a value that
can be copied down.
Fill Down
Enters sequential values in the column starting with the value in
the selected row and ending with the last row in the column.
This command is available only when you have selected a value
that can be filled down.
Modify Columns
Opens the Modify Columns dialog box. See “Column Display”
on page 371.
Enable/Disable Sample
Weight Calculation
Displays or hides the Sample Volume, Dilution Factor, Sample
Weight, Calculation Type, and Final Units columns.
Copy
Copies the data in the selected rows or columns to the Clipboard.
Use this command to copy sample information into a text editor
or spreadsheet application. You cannot paste this data back into
the Batch View sample list.
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Table 79. Batch View shortcut menu commands (Sheet 2 of 2)
Command
Description
Copy with Headers
Copies the data in the selected rows or columns and the
associated column headers to the Clipboard. Use this command
to copy sample information into another text editor or
spreadsheet application. You cannot paste this data back into the
sample list.
For example
Copy with Headers
from TraceFinder
Paste into an Excel spreadsheet.
Paste
Pastes a single column of copied data from another text editor or
spreadsheet application into the selected column.
Undo Last Paste
Removes the last pasted item in the Batch View.
Export to CSV File
Opens the Save As dialog box where you can save the current
sample list to a CSV file.
Edit Instrument Method Opens the Instrument Setup window where you can edit the
parameters of the instrument method.
• When you edit an external method, the application updates
the method in the …\Xcalibur\methods folder.
• When you edit an internal method, the application updates
the method in the
…\TraceFinderData\32\Projects\…\batch\Methods\method
folder.
For detailed information about editing instrument methods, see
“Working with Instrument Methods” on page 113.
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Compound Active Status Pane
In the Compound Active Status pane, you can choose specific compounds to be active or
inactive.
 To set a compound as active or inactive
1. In the sample list, select a sample.
All compounds in the selected sample are listed in the Compound Active Status pane.
The default active/inactive status is determined by the identification settings in the local
method. For information about setting the identification parameters, see “Identification”
on page 158.
• To display compounds alphabetically, right-click and choose Sort by Compound
Name from the shortcut menu.
• To display compounds from shorter to longer retention time, right-click and choose
Sort by Retention Time from the shortcut menu.
2. Select or clear the Active check box for the compound.
For instructions about changing the active/inactive status in the Data Review view, see
“Inactive and Excluded Compounds” on page 463.
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Compound Active/Inactive Status
You can specify which compounds are active or inactive in the Local Method View or the
Batch View.
Figure 101. Active and inactive compounds in the Local Method View
For details about setting the status on the Identification page, see “Identification” on
page 158.
Figure 102. Active and inactive compounds in the Batch View
For details about setting the status in the Batch View, see “Compound Active Status Pane” on
page 383.
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Creating a New Batch
In the Batch View, you can create a new batch.
Follow these procedures:
• To create a new batch
• To add samples to the list
• To insert samples into the list
• To import samples into the list
• To remove samples from the list
• To copy a sample
• To reinject a sample
• To edit sample values
• To browse in raw data files
• To customize the column display
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 To create a new batch
1. Choose File > New > Batch from the main menu.
The Create New Batch dialog box opens, displaying all drives that contain projects. See
“Create New Batch” on page 393.
2. Select a drive from the list.
Tip The application displays all configured and enabled repositories.
3. Select the folder where you want to store your batch.
Tip To activate the Create button, you must enter a unique batch name. If the Create
button is not activated, you have entered a batch name that is already used.
To create a new folder for the storage location, see “Editing Folders for Batches” on
page 395.
4. Select either Quan or Screening from the Type list.
The batch list displays all batches in the selected folder. The Method list displays all
methods for the selected type: quantitative or target screening.
5. Select a master method from the Method list.
The list displays all available methods of the selected type, either quantitative or target
screening.
6. Click Create.
A new batch opens with one Unknown sample.
The batch name in the title bar indicates that you are creating either a quantitative or a
target screening batch.
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 To add samples to the list
1. To add a single sample row, right-click the sample list and choose Add Sample from the
shortcut menu.
2. To add multiple sample rows, select the number of rows and then click the Add Sample
icon,
.
The application adds the specified number of new, empty samples to the end of the
sample list.
 To insert samples into the list
Select the sample above which you will insert new, Unknown samples, and then do one of
the following:
• To insert a single sample row, right-click and choose Insert Sample from the shortcut
menu.
• To insert multiple sample rows, select the number of rows and then click the Insert
Sample icon
.
The application inserts the Unknown samples above the selected sample.
Inserted samples
 To import samples into the list
1. Choose Batch > Import Samples from the main menu, or click the Import Samples
icon,
.
The Sample Import Tool dialog box opens.
From this dialog box, you can import samples from a CSV, an XML, or an SLD file.
2. Click Browse and select a CSV, an XML, or an SLD file that contains the samples to
import.
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3. From the Imported Samples Will Be list, select Appended to the End of the List or
Inserted at the Selected Row.
4. Click Import.
The Sample Import Tool dialog box closes, and the application adds the specified samples
to the sample list.
When you import samples from an Xcalibur sequence file (SLD), the TraceFinder
application makes the following column name substitutions:
Xcalibur column
TraceFinder column
Position
Vial Position
Inj Vol
Injection Volume
Dil Factor
Conversion Factor
When you import samples from an Xcalibur sequence file (.sld), the TraceFinder
application makes the following sample type substitutions:
Xcalibur sample type
TraceFinder sample type
Blank
Matrix Blank
QC
QC Std
Std Bracket
Cal Std
5. (Optional) When using multiplexing, select a channel for each imported sample.
Imported samples default to Auto.
Note The Channel column is available only when you have activated multiplexing in
the Configuration console. See “Multiplexing” on page 61.
 To remove samples from the list
1. Select the samples that you want to remove.
Tip Use the CTRL or SHIFT keys to select multiple samples.
2. Right-click and choose Remove Selected Samples from the shortcut menu.
 To copy a sample
1. Select the sample that you want to copy.
2. Right-click and choose Insert Copy Sample from the shortcut menu.
The TraceFinder application inserts the copy above the selected sample.
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 To reinject a sample
1. In the sample list, select the sample that you want to reinject.
2. Right-click and choose Reinject This Sample from the shortcut menu.
The TraceFinder application creates a copy of the selected sample and appends INJ001 to
the file name. Additional reinjections of the sample are numbered INJ002, INJ003, and
so forth. The application copies all parameter values from the original sample.
 To edit sample values
1. For each sample, do one of the following:
Type a new file name over the current filename.
–or–
Double-click the Filename column and locate a raw data file to use for the sample.
–or–
Right-click and choose Browse in Raw File from the shortcut menu, and then locate a
raw data file to use for the sample.
By default, the application sets the Sample Type to Unknown.
2. For each sample, click the Sample Type column and select a sample type from the list.
Available sample types
Matrix Blank
Solvent
QC Std
Unknown
Cal Std
3. For each Cal Std or QC Std sample, select a level from the Level list.
The sample levels are defined in the master method. If there are no levels to select in the
Level list, do the following:
a. Return to the Method Development mode.
b. Open the method.
c. Click the Compounds tab.
d. Click the Calibration Levels tab.
e. Add the levels.
f.
Save the method.
g. Return to the Analysis mode, and then click Update.
The application updates the local method with the new sample levels.
For detailed instructions about specifying calibration levels, see “Calibration Levels” on
page 219.
4. Type a vial position in the Vial Position column for each sample.
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5. Type a volume in the Injection Volume column for each sample.
The minimum injection volume value allowed is 0.1 μL; the maximum injection volume
value allowed is 5000 μL.
6. (Optional) Type or edit the values for the remaining columns.
Note When you use the scroll bar at the bottom of the sample list, the Status,
Filename, Sample Type, Groups, Qual Processing, Level, Sample ID, and Sample
Name columns stay fixed while the other columns scroll right and left.
For instructions to automatically copy or fill values in these columns, see Appendix C,
“Using Copy Down and Fill Down.”
 To browse in raw data files
1. Do one of the following:
Double-click the Filename column.
–or–
Right-click and choose Browse in Raw File from the shortcut menu.
The What Raw File Would You Like to Use dialog box opens.
2. Select a raw data file to use for the sample or use the CTRL key to select multiple files,
and then click Open.
The application overwrites the selected, unacquired sample in the batch with the first
“browsed in” file and adds any additional browsed in files below the selected sample.
For all browsed-in raw data files, the application sets the Status to Acquired,
the Sample Type to Unknown.
, and sets
Note You cannot overwrite an acquired sample. When you select a sample that is
acquired, the application adds all browsed in files below the selected sample.
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 To customize the column display
1. Right-click the Batch View sample list and choose Modify Columns from the shortcut
menu.
The Modify Columns dialog box opens.
Table 80. Button descriptions for the Modify Columns dialog box
Button
Description
Moves all columns to the Displayed Columns pane.
Moves the selected column to the Displayed Columns pane.
The following buttons apply to all columns, except for those that are fixed: Status,
Filename, Sample Type, Groups, Qual Processing, Level, Sample ID, and Sample
Name.
Moves the selected column to the Available Columns pane.
Moves all columns except those that are fixed.
Moves the selected column name in the Displayed Columns pane one
row up in the column order.
Moves the selected column name in the Displayed Columns pane one
row down in the column order.
Note The application adds a Blank Subtraction column to the fixed columns for
target screening batches only.
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2. Use the arrow buttons to move all the columns that you want displayed to the Displayed
Columns pane.
All the columns you select appear after the Status, Filename, Sample Type, Groups, Qual
Processing, Level, Sample ID, and Sample Name columns.
3. To arrange the order of the columns, do the following:
a. In the Displayed Columns pane, select a column name.
b. Use Up or Down to move the selected column up or down in the list.
The first column in the list represents the leftmost column in the Batch View sample
list, and the last column in the list represents the rightmost column in the Batch View
sample list.
Note You cannot move the Status, Filename, Sample Type, Groups, Qual
Processing, Level, Sample ID, or Sample Name columns.
4. To change the width of a column, do the following:
a. In the Displayed Columns pane, select the column width.
b. Type a new value for the width.
5. When you have completed your changes, click OK.
The columns in the sample list immediately reflect your changes. The application uses
these settings for all sample lists in the Batch View.
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Create New Batch
Use the Create New Batch dialog box to select a folder and method for your batch and to
name the new batch.
Table 81. Create New Batch dialog box parameters (Sheet 1 of 2)
Parameter
Description
Create New Folder
Adds one of the following:
• When a drive is selected, adds a new project-level folder to the drive.
• When a project folder is selected, adds a subproject-level folder to the selected project.
• When a subproject folder is selected, adds a lower-level folder to the subproject.
Or, right-click and choose Create Folder from the shortcut menu.
With no confirmation prompt, immediately removes the selected folder.
Delete Folder
You cannot delete a folder that contains lower-level folders; you must delete the lower-level
folders first.
Or, right-click and choose Delete from the shortcut menu.
Renames the selected folder.
Rename Folder
Or, right-click and choose Rename from the shortcut menu.
Batch table
Batch
Name of batches in the selected project.
Type
Type of batch: Quan or Screening.
Date Changed
Date that the batch was last updated.
Samples
Number of samples in the batch.
Method
Name of the method used to create the batch.
Size
Size of the batch in megabytes.
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Table 81. Create New Batch dialog box parameters (Sheet 2 of 2)
Parameter
Description
Domain
TraceFinder domain in which the batch was created.
New batch parameters
New Batch
Name of the new batch to create.
Note If the Create button is not activated, you have entered a name that is already used or
you have not selected a method.
Type
Type of batch to create: Quan or Screening.
Method
Method used to create the new batch.
Path
Path to the project in the TraceFinderData\32\Projects folder where the batch is created.
Buttons
Create
Creates the specified batch and opens the Batch View for the new batch.
Cancel
Closes the Create New Batch dialog box without creating a batch.
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Editing Folders for Batches
From the Create New Batch dialog box, you can create new folders for your batches. You can
also delete or rename folders.
Use these procedures:
• To create new project folders
• To delete project folders
• To rename project folders
 To create new project folders
1. In the Create New Batch dialog box. select the folder for which you will create a new
lower-level folder.
• You can select the main TraceFinderData\32\Projects folder and create a new folder
under it.
• You can select one of the existing folders and create a lower-level folder under it.
2. Click the Create Folder icon,
.
The application adds a new lower-level folder to the selected folder.
3. Select the new folder name and type a name for the folder.
Folder names are limited to 30 characters and can contain spaces and special characters,
except for the following special characters: \ / : + ? ” < >
Note After you add a lower-level folder, you cannot rename the parent folder.
 To delete project folders
1. In the Create New Batch dialog box. select the folder to delete.
2. Click the Delete Folder icon,
.
With no confirmation prompt, the application immediately removes the selected folder.
Note You cannot delete folders that contains lower-level folders; you must delete the
lower-level folders first.
 To rename project folders
1. In the Create New Batch dialog box, select the folder to rename.
2. Click the Rename Folder icon,
.
Note You cannot rename folders that contain lower-level folders.
3. Type a new name for the folder and press ENTER.
The application saves the new folder name.
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Editing a Batch
In the Batch View, you can open a saved batch and edit the sample list. You can add samples,
edit samples, or remove samples. If the batch has already been acquired, you can select specific
samples for reinjection. If the batch has unacquired samples when you complete your edits,
you can save it as a “ready to acquire” batch.
Follow these procedures:
• To open a saved batch
• To open a recent batch
• To edit samples in a batch
• To reinject a sample from a previously acquired batch
 To open a saved batch
1. Choose File > Open > Batch from the main menu.
The Open Batch dialog box opens. See Open Batch dialog box.
2. Select a project and a subproject.
3. Select Quan, Screening, or Any from the Type list.
The batch list displays all batches created with the selected type of method.
4. Select a batch from the list.
5. Click Open.
The selected batch opens in the Batch View.
Figure 103. Open Batch dialog box
Table 82. Open Batch dialog box parameters (Sheet 1 of 2)
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Parameter
Description
Batch
Name of batches in the selected project.
Type
Type of batch: Quan or Screening.
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Table 82. Open Batch dialog box parameters (Sheet 2 of 2)
Parameter
Description
Date Changed
Date the batch was last updated.
Samples
Number of samples in the batch.
Method
Name of the method used to create the batch.
Size
Size of the batch in megabytes.
Domain
TraceFinder domain in which the batch was created.
Path
Path to the project in the TraceFinderData\32\Projects folder
where the batch is stored.
Buttons
Type
Type of batch to display in the Batch list: Quan, Screening, or
Any.
Open
Opens the Batch View for the selected batch.
Cancel
Closes the Open Batch dialog box without opening a batch.
 To open a recent batch
Choose File > Recent Files > batch from the main menu.
The selected batch opens in the Batch View.
 To edit samples in a batch
Use the commands described in “Working in the Batch View” on page 368.
You can add new samples, edit samples, or delete samples.
 To reinject a sample from a previously acquired batch
1. In the sample list, select the sample that you want to reinject.
2. Right-click and choose Reinject This Sample from the shortcut menu.
The TraceFinder application creates a copy of the selected sample and appends INJ001 to
the file name. Additional reinjections of the sample are numbered INJ002, INJ003, and
so forth. The application copies all parameter values from the original sample.
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A green status icon indicates previously acquired samples (acquired and processed), and
the sample name is grayed out. A blue status icon indicates samples created for reinjection
(not acquired).
When you submit all samples in this batch, the application acquires all samples (including
previously acquired samples).
3. To save this batch with the new samples for reinjection, choose File > Save > Batch from
the main menu.
The batch is saved as a prepared batch that is ready to submit. You can open this batch
from the Reinject Samples page in the Acquisition mode and submit the batch. The
application acquires only the samples that have not been previously acquired.
Submitting a Batch
In the Batch View, you can submit an entire batch or only selected samples in the batch.
When you submit a batch for acquisition and processing, you can choose to create reports for
the submitted samples. See “Submit Options dialog box” on page 400.
For a description of commands on the shortcut menu, see “Batch View shortcut menu
commands” on page 381.
 To submit samples in the batch
1. Do one of the following:
• To submit all samples in the batch, click the Submit Batch icon,
.
• To submit specific samples, select the samples and click the
Submit Selected Samples icon,
.
The Submit Options dialog box opens. See “Submit Options dialog box” on page 400.
2. To acquire (or reacquire) the submitted samples, select the Acquire Data check box.
• When all submitted samples have been previously acquired, this option is not selected
by default.
• When any of the submitted samples have not been acquired, this option is selected by
default.
3. To process the submitted samples, select the Process Data check box.
You can process the data with or without performing peak detection. For example, you
might want to turn off peak detection when reprocessing samples.
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4. (Optional) Select the Create Reports check box.
5. (Optional with multiplexing activated) Select the Priority Sequence check box.
The application acquires the priority batch on the next available channel or the assigned
channel.
6. (Optional without multiplexing activated) Select the Priority Sequence check box and
then select one of the following priority options to place the batch in the queue:
• Next Available Batch places the batch immediately after the currently acquiring
batch.
• Next Available Sample places the batch immediately after the currently acquiring
sample.
7. (Optional) Click Show Details to display additional Acquisition parameters.
8. Select the Use check box for the device that you want to use for this acquisition.
9. (Optional) Select the Start Device check box to indicate the device that will initiate the
communication with the other instruments.
This is usually the autosampler.
10. (Optional) Select the Start When Ready check box to have all instruments start together
when they are all ready.
When this is cleared, individual instruments can start at different times and then must
wait for the last instrument to be ready.
11. To start the selected processes, click OK.
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Figure 104. Submit Options dialog box
Acquire Data
selected
Acquire Data
not selected
Table 83. Submit Options dialog box parameters (Sheet 1 of 2)
Parameter
Description
User Name
Name of the current user.
Samples
Range of samples to be submitted for acquisition, processing, or reporting.
Acquire Data
Submits the current batch to acquisition.
• When all submitted samples have been previously acquired, this option is (by default)
not selected.
• When any of the submitted samples has not been acquired, this option is (by default)
selected.
Process Data
(Default) Processes the data for the current batch.
With Peak Detection
(Default) Processes the data with peak detection.
When cleared, this option lets you reprocess samples without performing peak detection.
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Table 83. Submit Options dialog box parameters (Sheet 2 of 2)
Parameter
Description
Create Reports
Creates reports for the current batch.
Priority Sequence
With multiplexing activated, places the batch immediately after the currently acquiring
batch.
Without multiplexing activated, specifies one of the following priority options to place the
batch in the queue:
• Next Available Batch places the batch immediately after the currently acquiring batch.
• Next Available Sample places the batch immediately after the currently acquiring
sample.
Acquisition pane
Device Name
Lists all configured instruments.
If the instrument that you want to use is not configured, close the TraceFinder application,
configure the instrument, and then reopen the TraceFinder application. You cannot
configure an instrument while the TraceFinder application is running.
Available only when the Acquire Data check box is selected.
Use
Specifies the instruments used for this acquisition.
Available only when the Acquire Data check box is selected.
Start Device
Specifies the instrument that initiates the communication with the other instruments. This
is usually the autosampler.
Available only when the Acquire Data check box is selected.
Start When Ready
Starts the specified device when all the instruments are ready to acquire data. When this is
cleared, individual instruments can start at different times and then must wait for the last
instrument to be ready.
Post-run System
State
Specifies the system state after it acquires the last batch.
On (default), Standby, or Off.
Buttons
Hide/Show Details
Collapses or expands the acquisition details of the Submit Options dialog box.
OK
Begins the selected processes.
Cancel
Closes the Submit Options dialog box without submitting any tasks.
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Saving a Batch to a New Location
You can move the current batch to a different project folder, or you can make a copy of the
current batch and save the copy to a different project folder.
Follow these procedures:
• To save a batch to another project folder
• To move a batch to another folder
• To create new project folders
• To delete project folders
• To rename project folders
 To save a batch to another project folder
1. Choose File > Save > Save Batch As from the main menu in the Analysis mode.
The Save Batch As dialog box opens. See “Save Batch As Dialog Box” on page 404.
2. Select a storage location.
The default storage location is C:\TraceFinderData\32\Projects.
3. Select or create a project folder.
4. Type a name for the new batch.
If you are saving the batch to a different folder, you must give it a unique name. You
cannot overwrite an existing batch in a folder.
5. Click Save.
When you save the batch to a different folder, the reports reflect the original project
folders and the application does not save the calibration history.
 To move a batch to another folder
1. Choose File > Save > Move Batch from the main menu in the Analysis mode.
The Save Batch As dialog box opens. See “Save Batch As Dialog Box” on page 404.
2. Select a storage location.
The default storage location is C:\TraceFinderData\32\Projects.
3. Select or create a project folder.
4. Type a name for the new batch.
You must give the batch a unique name in the new subproject folder. You cannot
overwrite an existing batch.
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5. Click Save.
When you move the batch, the reports reflect the original project and subproject folders
and the application does not save the calibration history.
 To create new project folders
1. In the Save Batch As dialog box. select the folder for which you will create a new
lower-level folder.
• You can select the main TraceFinderData\32\Projects folder and create a new folder
under it.
• You can select one of the existing folders and create a lower-level folder under it.
2. Click the Create Folder icon,
.
The application adds a new lower-level folder to the selected folder.
3. Select the new folder name and type a name for the folder.
Folder names can contain spaces and special characters, except for the following special
characters: \ / : + ? ” < >
Note After you add a lower-level folder, you cannot rename the parent folder.
 To delete project folders
1. In the Save Batch As dialog box. select the folder to delete.
2. Click the Delete Folder icon,
.
With no confirmation prompt, the application immediately removes the selected folder.
Note This feature is not available for folders that contain lower-level project or batch
folders; you must first delete the lower-level project or batch folders.
 To rename project folders
1. In the Save Batch As dialog box. select the folder to rename.
2. Click the Rename Folder icon,
.
Note This feature is not available for folders that contain lower-level project or batch
folders; you must first delete the lower-level project or batch folders.
3. Type a new name for the folder and press ENTER.
The application saves the new folder name.
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Save Batch As Dialog Box
Use the features on the Save Batch As dialog box to save a batch to a new name or to move a
batch to a different project folder.
Figure 105. Save Batch As dialog box
Table 84. Save Batch As dialog box parameters (Sheet 1 of 2)
Parameter
Description
Create New Folder
Adds one of the following:
• When a drive is selected, adds a new project-level folder to the drive.
• When a project folder is selected, adds a subproject-level folder to the selected project.
• When a subproject folder is selected, adds a lower-level folder to the subproject.
Or, right-click and choose Create Folder from the shortcut menu.
With no confirmation prompt, immediately removes the selected folder.
Delete Folder
You cannot delete a folder that contains lower-level project or batch folders; you must first
delete the lower-level project or batch folders.
Or, right-click and choose Delete from the shortcut menu.
Renames the selected folder.
Rename Folder
You cannot rename a folder that contains lower-level project or batch folders; you must first
delete the lower-level project or batch folders.
Or, right-click and choose Rename from the shortcut menu.
Batch table
Batch
Name of batches in the selected project.
Type
Type of batch: Quan or Screening.
Date Changed
Date that the batch was last updated.
Samples
Number of samples in the batch.
Method
Name of the method used to create the batch.
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Table 84. Save Batch As dialog box parameters (Sheet 2 of 2)
Parameter
Description
Size
Size of the batch in megabytes.
Domain
TraceFinder domain in which the batch was created.
New batch parameters
New Batch
Name of the new batch to create.
Note If the Create button is not activated, you have entered a name that is already used or
you have not selected a method.
Path
Path to the project in the TraceFinderData\32\Projects folder where the batch is created.
Buttons
Save
Saves the batch to the specified name and folder and opens the Batch View for the new
batch.
Cancel
Closes the Save Batch As dialog box without saving the batch.
Shortcut menu commands
Create Folder
Adds one of the following:
• When a drive is selected, adds a new project-level folder to the drive.
• When a project folder is selected, adds a subproject-level folder to the selected project.
• When a subproject folder is selected, adds a lower-level folder to the subproject.
Delete Folder
Immediately removes the selected folder. There is no prompt to confirm that you want to
delete the selected folder.
You cannot delete a folder that contains lower-level project or batch folders; you must first
delete the lower-level project or batch folders.
Rename Folder
Renames the selected folder.
You cannot rename a folder that contains lower-level project or batch folders; you must first
delete the lower-level project or batch folders.
Expand Child Nodes
Expands all project and subproject folders in the Project tree.
Collapse Child Nodes
Collapses all project and subproject folders in the Project tree.
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Auto Samples Page
The Auto Samples page identifies the Solvent or Matrix Blank samples to use for any Auto
Sample or Auto Sample and Reinject failure actions as specified on the Intelligent Sequencing
page of the method. See “Editing the Intelligent Sequencing Page” on page 243.
Each sample type that you specify for a failure action on the Intelligent Sequencing page must
be defined in the samples list on the Auto Samples page.
 To open the Auto Samples page
Click Auto Samples in the Batch View navigation pane.
The Auto Samples page opens. See Auto Samples page.
 To add an auto sample type
1. Right-click and choose Add Auto Sample from the shortcut menu, or click the Add New
Auto Sample icon,
.
The application adds a Solvent sample to the sample list.
You can add, insert, or remove samples from this list as you would any sample list. See
“Samples Page” on page 369.
2. To change the sample type to a Matrix Blank, click the Sample Type column and select
Matrix Blank from the list.
3. In the Injection Volume column for the sample, type a volume.
The minimum injection volume value allowed is 0.1 μL; the maximum injection volume
value allowed is 5000 μL.
4. In the Number of Injections column, type the number of injections available in the
designated Solvent or Matrix Blank vial.
After auto sample injections have occurred, you can return to this page to view the
number of Injections Used in each vial.
5. In the Vial Position column, type the vial position for the Solvent or Matrix Blank
sample.
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Figure 106. Auto Samples page
Table 85. Auto Samples page parameters
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Column
Description
Sample Type
The sample type for the auto sample injection as specified on the
Intelligent Sequencing page—either Solvent or Matrix Blank.
Default: Solvent
Injection Volume
The injection volume used for the sample acquisition as specified on
the Samples page.
Range: 0.1 through 5000 μL
Injections Used
The number of times a vial has been used. The count is cumulative
across all batches.
Number of
Injections
The number of injections available in the designated Solvent or Matrix
Blank vial.
Vial Position
Vial position for this sample type as specified on the Samples page.
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Reference Samples Page
The Reference Samples page displays the reference samples that you selected for this batch.
 To specify a chromatogram reference sample
1. In the Batch View, click Reference Samples.
An empty reference sample table opens.
2. Click the Add Reference Sample icon,
Reference Sample from the shortcut menu.
, or right-click and choose Add
The Open Chromatogram Reference Sample dialog box opens.
Note If you are using a new method, no reference samples appear here. You must first
process a batch using the current method to see the reference samples in this list.
3. Select a project from the list of projects.
4. Select a subproject from the list of subprojects.
5. Select a batch from the list of batches.
The application displays only batches that were created using the current master method.
6. Select a sample from the list of processed samples.
The application displays all the processed samples in the selected batch. Before using a
sample as a reference sample, you must have processed the sample with the current master
method.
7. Click Open.
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Threshold Samples Page
For each group in a batch, you can specify a sample in the group as the threshold sample to
use in the Comparative View.
 To specify a threshold sample
1. In the Batch View, click Threshold Samples.
2. Click the Sample list for each group and select a sample in the group to be the threshold
sample.
The Comparative View uses the threshold method and amount you specified in the method,
the group you created on the Samples page, and the threshold sample you selected on this
page to define the threshold guide that it displays on the sample peak plots.
For information about specifying the method to use for creating a threshold guide, see
“Threshold” on page 237.
For information about creating groups, see “Groups” on page 373.
For information about using the threshold guide in the Comparative View, see “Comparative
View” on page 433.
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Working in Data Review for Quantitation Methods
In the Data Review view, you can view the data generated by the quantitation master method.
Use Data Review to verify the data for a compound before you generate reports.
 To open the Data Review view
1. Click Analysis in the navigation pane.
The Analysis navigation pane opens.
2. Click Data Review.
The Data Review navigation pane opens.
Choose from a Sample View, Compound View, Comparative View, or Qualitative View to
analyze the data generated by the master method.
This section includes the following topics:
• Sample View
• Compound View
• Comparative View
• Qualitative View
• Features Common to All Data Review Pages
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Sample View
The Sample View displays the following information in three different panes: a list of all
samples in the current batch, the compound results for all compounds in the method, and
peak plots for all compounds found in the currently selected sample.
These are the default panes and their locations:
Sample Peaks pane
Samples pane
Compound Results pane
When you select a sample in the Samples Pane, the associated Compound Results Pane flags
any compound with errors in the selected sample. The associated Sample Peaks Pane displays
the chromatogram, retention time, area, height, and signal-to-noise ratio for all compounds in
the selected sample. The Sample Peaks pane highlights the compound selected in the
Compound Results pane.
The Sample View display includes the following features:
• Samples Pane
• Compound Results Pane
• Sample Peaks Pane
• Caution Flags
• Viewing Sample View Panes
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Samples Pane
Use the Samples pane in the Sample View to select a specific sample. The associated
Compound Results Pane displays all compounds in the method and flags any compound with
errors in the selected sample.
 To hide or display columns in the Samples pane
1. Click the Field Chooser icon,
, in the upper left corner of the pane.
The Field Chooser displays all available columns of data for the Samples pane.
Note The Field Chooser also lists any custom columns that you defined in the
Configuration Console. See “Creating Custom Columns” on page 63.
2. Select the check box for each column that you want to display, or clear the check box for
each column that you want to hide.
The application immediately displays or hides the column in the Samples pane.
3. When you are finished modifying the column display, click
Chooser.
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Figure 107. Samples pane
Compound error in the
selected sample
Selected sample
No compound error in the
selected sample
Table 86. Samples pane columns
Column
Description
Flags
Caution flag displayed when a compound in the sample has an
error. See “Caution Flags” on page 417.
Status
Sample is not acquired.
Sample is acquired but not processed.
Sample is acquired and processed.
Sample is currently acquiring.
Thermo Scientific
Sample Name
A user-defined name that identifies a sample.
Sample Type
Defines how the TraceFinder application processes the sample
data. Each sample is classified as one of the following sample
types: Matrix Blank, Solvent, Cal Std, QC Std, or Unknown.
Comments
User-defined comments for the sample.
Excluded
Turns a compound on or off in the calibration curve in the
Compound Details pane.
Filename
A user-defined name that identifies a sample.
Level
The level defined for a calibration sample or quality control
sample.
Sample ID
A user-defined, alphanumeric string that identifies a sample.
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Compound Results Pane
Use the Compound Results pane in the Sample View to select a specific compound in the
selected sample. The associated Sample Peaks Pane highlights the selected compound.
 To hide or display columns in the Compound Results pane
1. Click the Field Chooser icon,
, in the upper left corner of the pane.
The Field Chooser displays all available columns of data for the Compound Results pane.
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2. Select the check box for each column that you want to display, or clear the check box for
each column that you want to hide.
The application immediately displays or hides the column in the Compound Results
pane.
3. When you are finished modifying the column display, click
Chooser.
to close the Field
Figure 108. Compound Results pane
Table 87. Compound Results pane columns
Column
Description
Flags
Caution flag displayed when the compound has an error. See
“Caution Flags” on page 417.
Compound
Compound names as identified in the library.
Compound Type
Specified compound type: Target Compound or Internal
Standard.
The remainder of the columns in the results list are common to the Compound Results
pane in the Sample View and the Sample Results pane in both the Compound View and the
Comparative View. See “Common Column Parameters” on page 456.
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Sample Peaks Pane
The Sample Peaks pane in the Sample View displays the chromatogram, retention time, area,
height, and signal-to-noise ratio for all compounds in the Compound Results pane. The
application highlights the chromatogram for the compound that is currently selected in the
Compound Results pane.
 To display details for a compound
Double-click the chromatogram in the Sample Peaks pane.
The Compound Details pane opens.
The Compound Details pane displays information about the quantitative peak,
calibration curve, confirming ion, internal standard, reference peak, ion overlay, and
spectra for the compound.
For a detailed description of the available information in the Compound Details pane, see
“Compound Details” on page 465.
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Caution Flags
In the Sample View, the application displays caution flags in both the Samples pane and the
Compound Results pane.
This section includes the following topics:
• Flags in the Samples Pane
• Flags in the Compound Results Pane
• Error Indicators in the Sample Peaks Pane
Flags in the Samples Pane
The Flags column in the Samples pane displays a caution flag if any compound in the sample
is not in compliance with the method criteria.
Click the caution flag icon,
, to display the details. Information in the pop-up box shows
the compound that is in error and describes the exact error condition.
Error condition
Compound name
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Flags in the Compound Results Pane
The Flags column in the Compound Results pane displays a flag if the compound in the
selected sample is not in compliance with the method criteria.
Selected sample
Hold your cursor over the flag icon,
sample.
Error condition of the Sulfisomidine
compound in the selected sample
, to display details for the compound in the selected
Flags in the Compound Results pane indicate the following:
A red flag for compounds that have violated (or are activated by) any of the values
set in the method. See “Editing the QAQC Page” on page 230.
A red flag for compounds that are outside the specified ion ratio range. See Ion ratio
failure flag.
An orange flag for compounds that are below the LOQ, below the LOD, or
between the LOD and LOQ values specified in the method. For descriptions of
these limits, see “Limits” on page 231.
A green flag for “found” compounds that are over the LOR amount specified in the
method. For a description of the LOR limit, see “Limits” on page 231.
A yellow flag for compounds that are equal to or below the LOR amount specified
in the method.
A yellow flag for compounds that are not found in Calibrator or QC sample types.
The Compound Results pane does not flag compounds that are not found in
Specimen sample types.
No flag for compounds that have no errors or where no report options are selected.
Note These criteria for flag states do not apply to Matrix Blank sample types when the
compound is an internal standard.
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Error Indicators in the Sample Peaks Pane
In the Sample Peaks pane, peak plots are outlined with the color of their associated error flag.
In the following example, the FENTHION peak plot is highlighted in blue to indicate that
FENTHION is the selected compound, and the Sulfisomidine peak plot is outlined in red to
indicate that the Sulfisomidine compound in the selected sample is outside the specified ion
ratio range.
Figure 109. Ion ratio failure flag
Red flag indicating ion ratio failure
Selected peak
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Peak with ion ratio failure outlined in red
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Viewing Sample View Panes
The Sample View display uses multiple panes to display data: Sample Results, Compound
Results, Sample Peaks, and Compound Details. You can display, hide, or move any of these
panes.
 To display or hide a Sample View pane
From the View menu, choose from the following:
• Compounds with Data: Displays or hides the Compound Results pane.
• Sample View Peaks: Displays or hides the Sample Peaks pane.
• Compound Details: Displays or hides the Compound Details pane.
Note The Sample Results pane is required for the Sample View display. You cannot
hide the Sample Results pane.
Displayed panes are indicated with a check mark.
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Data Review Pane Display Features
All Data Review displays have the following procedures in common:
• To move a docked pane
• To make a pane floating or dockable
• To change a pane from a docked pane to a tabbed pane
• To restore the default layout
 To move a docked pane
1. Grab the title bar of the pane and begin dragging the pane.
The application displays docking arrows.
2. Drag the pane over one of the arrows.
As you hold the cursor over a docking arrow, the application displays a blue region
indicating where this arrow will place the pane.
3. Drop the pane onto one of the arrows.
This animation shows the various ways that you can use the docking mechanism to move a
pane. To view the animation, click the filmstrip, and then right-click and choose Full Screen
Multimedia. To stop the animation, press ESC.
 To make a pane floating or dockable
Do one of the following:
• To make a dockable pane floating, right-click the title bar of the pane and choose
Floating.
While a pane is set as floating, you cannot use the docking arrows to dock it or make
it a tabbed pane.
• To make a floating pane dockable, right-click the title bar of the pane and choose
Dockable.
This animation shows how to switch a pane from docked to floating and back to docked. To
view the animation, click the filmstrip, and then right-click and choose Full Screen
Multimedia. To stop the animation, press ESC.
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 To change a pane from a docked pane to a tabbed pane
1. Grab the title bar of the pane and begin dragging the pane.
The application displays docking arrows.
Drop the pane on the center location to create a tabbed pane.
2. Hold the cursor over the center of the docking arrows to display a blue region indicating
the location of the tabbed pane.
3. Drop the pane over the center of the docking arrows.
Note To change a floating pane to a tabbed pane, you must first make the pane a dockable
pane, and then you can make it a tabbed pane.
This animation shows how to change a pane from a docked pane to a tabbed pane and back to
a docked pane. To view the animation, click the filmstrip, and then right-click and choose
Full Screen Multimedia. To stop the animation, press ESC.
 To restore the default layout
Choose View > Restore Default Layout.
The Sample View, Compound View, and Qualitative View each have their own defaults
for which panes are displayed and in which location.
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Compound View
The Compound View uses three different panes to display a list of all compounds available in
the method, all samples in the current batch, and the peak plots for all compounds found in
each sample.
These are the default panes and their locations:
Sample Peaks pane
Compounds pane
Sample Results pane
When you select a compound in the Compounds Pane, the Sample Results Pane flags any
sample that contains errors associated with the selected compound. The Sample Peaks Pane
highlights the selected compound, displays the name of the sample in which the compound
was found, and, for the compound, displays the chromatogram, retention time, area, height,
and signal-to-noise ratio.
The Compound View includes the following features:
• Compounds Pane
• Sample Results Pane
• Sample Peaks Pane
• Caution Flags
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Compounds Pane
Use the Compounds pane in the Compound View to select a specific compound. The Sample
Results Pane displays all samples in the batch and flags any sample that contains errors
associated with the selected compound.
 To hide or display columns in the Compounds pane
1. Click the Field Chooser icon,
, in the upper left corner of the pane.
The Field Chooser displays all available columns of data for the Compounds pane.
2. Select the check box for each column that you want to display, or clear the check box for
each column that you want to hide.
The application immediately displays or hides the column in the Compounds pane.
3. When you are finished modifying the column display, click
Chooser.
to close the Field
Figure 110. Compounds pane
Selected compound
No error associated with
Error associated with
the selected compound the selected compound in
these samples
in this sample
Table 88. Compounds pane columns
Column
Description
Flags
Caution flag displayed when a compound has an error in any of the samples.
Compound
Compound names as identified in the library. If there is no library selected in
the method template, the compound name is identified as [email protected]
Compound
Type
Specified compound type: Target Compound or Internal Standard.
Expected RT Expected retention time for the compound.
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Sample Results Pane
Use the Sample Results pane in the Compound View to select a specific compound in a
specific sample. The Sample Peaks pane highlights the selected compound and displays the
name of the sample in which the compound was found and the following information about
the compound: chromatogram, retention time, area, height, and signal-to-noise ratio. See
Sample Results pane.
 To hide or display columns in the Sample Results pane
1. Click the Field Chooser icon,
, in the upper left corner of the pane.
The Field Chooser displays all available columns of data for the Sample Results pane.
Note The Field Chooser also lists any custom columns that you defined in the
Configuration Console. See “Creating Custom Columns” on page 63.
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2. Select the check box for each column that you want to display, or clear the check box for
each column that you want to hide.
The application immediately displays or hides the column in the Sample Results pane.
3. When you are finished modifying the column display, click
Chooser.
to close the Field
Figure 111. Sample Results pane
Table 89. Sample Results pane columns (Sheet 1 of 2)
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Column
Description
Acquisition Order
Sequentially numbers the samples.
Flags
Caution flag displayed when a compound within the sample has
an error.
Flag Details
Indicates the type of error:
• I: Confirming ion coelution failure or Ion ratio failure
• A: Amount error
• B: Matrix blank error
• H: Peak not found
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Table 89. Sample Results pane columns (Sheet 2 of 2)
Column
Status
Description
Sample is not acquired.
Sample is acquired but not processed.
Sample is acquired and processed.
Sample is currently acquiring.
Filename
A user-defined name that identifies a sample.
Sample Type
Defines how the TraceFinder application processes the sample
data. Each sample is classified as one of the following sample types:
Matrix Blank, Solvent, Cal Std, QC Std, or Unknown.
The remainder of the columns in the Sample Results pane are common to both the Sample
View and the Compound View displays. See “Common Column Parameters” on page 456.
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Sample Peaks Pane
The Sample Peaks pane in the Compound View displays the compound chromatogram,
retention time, area, height, and signal-to-noise ratio associated with the selected compound
in each of the samples in the batch. The application highlights the compound chromatogram
for the sample that is currently selected in the Sample Results pane.
 To display details for a compound
1. Double-click the chromatogram in the Sample Peaks pane.
The application adds the Compound Details pane to the window.
The Compound Details pane displays information about the quantitative peak, calibration
curve, confirming ion, internal standard, reference peak, ion overlay, and spectra for the
compound.
For details about the available information in the Compound Details pane, see “Compound
Details” on page 465.
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Caution Flags
In the Compound View, the application displays caution flags in both the Compounds pane
and in the Sample Results pane.
This section includes the following topics:
• Flags in the Compounds Pane
• Flags in the Sample Results Pane
• Error Indicators in the Sample Peaks Pane
Flags in the Compounds Pane
The Flags column in the Compounds pane displays a caution flag if the compound in any of
the samples is not in compliance with the method criteria.
Selected Sulfisomidine compound
Flags for the Sulfisomidine compound
in each sample
Click the caution flag icon,
, to display the details. Information in the pop-up box shows
the sample where the compound is in error and describes the exact error condition.
Error condition
Sample name
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Flags in the Sample Results Pane
The Flags column in the Sample Results pane displays a flag if the selected compound in the
sample is not in compliance with the method criteria.
Hold your cursor over the flag icon,
the sample.
, to display the details for the selected compound in
Flags in the Sample Results pane indicate the following:
Flag
Description
A green flag for compounds that are over the LOR amount specified in the
method.
A red flag for compounds that have violated (or are activated by) any of the values
set in the method. See “Editing the QAQC Page” on page 230.
A red flag for compounds that are outside the specified ion ratio range. See Ion
ratio failure flag.
An orange flag for compounds that are not found in Cal Std or QC Std sample
types.
“Not found” compounds are below the LOQ, below the LOD, or between the
LOD and LOQ values specified in the method. The Sample Results pane does
not flag compounds that are not found in Unknown sample types.
No flag for compounds that have no errors or where no report options are
selected.
Note These criteria for flag states do not apply to Matrix Blank sample types when the
compound is an internal standard.
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Error Indicators in the Sample Peaks Pane
In the Sample Peaks pane, peak plots are outlined with the color of their associated error flag.
In the following example, the peak plot is highlighted in blue to indicate that Benzo_25557 is
the selected sample and outlined in red to indicate that the FENTHION compound in the
selected sample is outside the specified ion ratio range.
Figure 112. Ion ratio failure flag
Red flag indicating ion ratio failure
Selected peak
Thermo Scientific
Peak with ion ratio failure
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Viewing Compound View Panes
The Compound View display uses multiple panes to display data: Compounds, Sample
Results, Sample Peaks, and Compound Details. You can display, hide, or move any of these
panes.
 To display or hide a Compound View pane
From the View menu, choose from the following:
• Samples with Data: Displays or hides the Sample Results pane.
• Compound View Peaks: Displays or hides the Sample Peaks pane.
• Compound Details: Displays or hides the Compound Details pane.
Note The Compounds pane is required for the Compound View display. You cannot
hide the Compounds pane.
Displayed panes are indicated with a check mark.
For procedures about creating docked, floating, or tabbed panes, see “Data Review Pane
Display Features” on page 421.
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Comparative View
The Comparative View uses three panes to display a list of all compounds available in the
method, all samples in the current batch, and the sample peak plots for all compounds found
in the samples with the horizontal threshold guide.
These are the default panes and their locations:
Sample Peaks pane
Compounds pane
Sample Results pane
The panes in the Comparative View are identical to the Compound View with the addition of
the Group column. This column identifies any groups that a sample belongs to, as specified in
the Batch View.
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The following factors define the threshold guide that the Comparative View displays on the
sample peak plots:
• The threshold method and amount that you specified in the method
• The group that you created on the Sample page
• The threshold sample that you selected on the Threshold Samples page
Horizontal guide indicates
the threshold value as
specified in the method.
This section includes the following topics:
• Configuring Sample Peaks Display Settings
• Manually Integrating Peaks
For information about specifying the method to use for creating a threshold guide, see
“Threshold” on page 237.
For information about creating groups, see “Groups” on page 373.
For information about specifying a threshold sample, see “Threshold Samples Page” on
page 409.
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Configuring Sample Peaks Display Settings
The Sample Peaks pane in the Comparative View displays one row per compound and one
column per sample. The Sample Peaks pane displays all samples in a group when you select
any of the samples belonging to that group.
For information about creating groups, see “Groups” on page 373.
 To change the Sample Peaks pane display
1. From the View menu, choose Chromatogram Pane Settings.
The Chromatogram Plot Settings dialog box opens. See “Chromatogram Plot Settings
Dialog Box” on page 438.
2. To change the number of rows or columns to fit in the Sample Peaks pane, type new
values in the Number of Rows or Number of Columns boxes.
These values do not change the number of rows (compounds) and columns (samples) that
are available in the Sample Peaks pane. These values determine how many rows and
columns you want to view at one time in the display. The default is three rows and three
columns.
In the following examples, the Number of Rows and Number of Columns are set to 1
(Number of Rows equals 1 and Number of Columns equals 1) and the Number of Rows
and Number of Columns are set to 4 (Number of Rows equals 4 and Number of
Columns equals 4).
Figure 113. Number of Rows equals 1 and Number of Columns equals 1
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Figure 114. Number of Rows equals 4 and Number of Columns equals 4
Because there are only three
samples, this column is empty.
3. To change the display type for the y-axis scale, select one of the following:
• Relative: Displays the y-axis scale from 0 to 100.
Horizontal bar indicates
the threshold value as
specified in the method.
Vertical bars indicate the
expected retention time
and window, as specified
in the method.
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• Absolute: Displays the y-axis scale from 0 to the actual value of the most intense peak
in the group.
• Label in Scientific Notation: Displays the y-axis scale in scientific notation.
Note The Sample Peaks pane displays a y axis only on the first chromatogram in each
row. The limits of the scale are determined by the most intense peak in the group.
4. Specify which labels you want to display in the sample peak plots.
For an example of all available peak plot labels, see Peak Plot Labels.
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Chromatogram Plot Settings Dialog Box
Use the Chromatogram Plot Settings dialog box to change the Sample Peaks pane display.
Table 90. Chromatogram Plot Settings dialog box parameters (Sheet 1 of 2)
Parameter
Description
Number of Rows
Specifies the number of rows visible in the Sample Peaks pane.
When Number of Rows equals 1, the application scales the height
of all chromatograms to fill the Y dimension of the Sample Peaks
pane.
Default: 3
Number of Columns
Specifies the number of columns visible in the Sample Peaks pane.
When Number of Columns equals 1, the application scales the
width of all chromatograms to fill the X dimension of the Sample
Peaks pane.
Default: 3
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Table 90. Chromatogram Plot Settings dialog box parameters (Sheet 2 of 2)
Parameter
Description
Y-Axis Type
Displays the y-axis scale as Relative (to the most intense peak),
Absolute, or in scientific notation.
Peak Plot Labels
Displays or hides the following peak labels:
• RT
• Area
• Height
• Filter
• Threshold
• Show All Apex Times
• Sample Filename
• Compound Name
• to Noise
Example with all peak labels displayed:
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Manually Integrating Peaks
Use the manual integration feature to manually add a peak. You can manually add a peak in a
chromatogram plot only when the application fails to identify a peak.
 To manually integrate a peak
1. In the Sample Peaks plot, click the Manual Integration icon.
Manual integration
icon
The cursor changes to look like this:
2. To integrate a peak, do the following:
a. Drag the cursor to describe the beginning and ending base points for the new peak.
Note You must drag the cursor inside the x axis and y axis.
b. Click outside the plot to refresh the display.
Click the first base
point, and then drag to
the second base point.
Click outside the plot to
refresh the view.
The application identifies the peak
and indicates the manual
integration in the labels.
3. To zoom in on an area, do the following:
a. Drag the cursor below the x axis or to the left of the y axis.
The plot zooms to fit the described X or Y dimension into the entire pane. The
application zooms all compounds in the row to the same scale.
b. To return to the original view, right-click and choose Reset Scaling from the shortcut
menu.
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Qualitative View
The Qualitative View uses several different panes to display qualitative information for the
selected sample. See Displaying Qualitative View Panes.
If the application finds no detected peaks for the selected sample, you can manually add
peaks.
To see processed data for a sample in the Qualitative View, you must select the Qual
Processing parameter for that sample in the Batch View before you process the batch. See
“Batch View Sample List” on page 378.
These are the default panes and their locations:
Samples pane
Sample
Peak Details pane
chromatogram pane
Thermo Scientific
Peaks pane
Spectrum pane
Library Hits pane
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The Qualitative View displays data in the following panes:
• Samples Pane
• Peaks Pane
• Sample Chromatogram Pane
• Peak Details Pane
• Spectrum Pane (Library and Data)
• Library Hits Pane
Displaying Qualitative View Panes
The Qualitative View display uses multiple panes to display data: Samples, Peaks, Sample
Chromatogram, Peak Details, Spectrum, and Library Hits. You can display, hide, or move any
of these panes.
 To display or hide a Qualitative View pane
From the View menu, choose to display or hide the following:
• Peaks
• Sample Chromatogram
• Peak Chromatogram: Displays or hides the Peak Details pane.
• Spectrum
• Library Hits
Note The Samples pane is required for the Qualitative View display. You cannot hide
the Samples pane.
Displayed panes are indicated with a check mark.
For procedures about creating docked, floating, or tabbed panes, see “Data Review Pane
Display Features” on page 421.
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Samples Pane
Use the Samples pane in the Qualitative View to select a specific sample. The associated Peaks
Pane displays all peaks found in the selected sample.
 To hide or display columns in the Samples pane
1. Click the Field Chooser icon,
, in the upper left corner of the pane.
The Field Chooser displays all available columns of data for the Samples pane.
2. Select the check box for each column that you want to display, or clear the check box for
each column that you want to hide.
The application immediately displays or hides the column in the Samples pane.
3. Click
to close the Field Chooser.
Figure 115. Samples pane
Table 91. Samples pane columns (Sheet 1 of 2)
Column
Description
Acquisition
Order
Sequentially numbers the samples.
Flags
Caution flag displayed when a compound in the sample has an error. See
“Caution Flags” on page 417.
Status
Sample is not acquired.
Sample is acquired but not processed.
Sample is acquired and processed.
Sample is currently acquiring.
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Table 91. Samples pane columns (Sheet 2 of 2)
Column
Description
Filename
A user-defined name that identifies a sample.
Sample
Type
Defines how the TraceFinder application processes the sample data. Each
sample is classified as one of the following sample types: Matrix Blank,
Solvent, Cal Std, QC Std, or Unknown.
Peaks Pane
The Peaks pane in the Qualitative View works with the Samples pane to display graphical
values for a unique sample and peak combination. For detailed descriptions of parameters in
the Peaks pane, see “Peaks Pane” on page 447.
Follow these procedures:
• To display peaks for a specific compound
• To remove a peak
• To hide or display columns in the Peaks pane
 To display peaks for a specific compound
1. From the Samples pane, select a sample.
The Peaks pane displays the retention times for peaks identified in the selected sample,
the values for the best match methods for each peak, and the library match.
The method specifies which technique to use for identifying peaks: peaks within a specific
retention time range, as a minimum percentage of the height or area of the largest peak,
or as a minimum percentage of the nearest internal standard peak. You can change the
method for identifying peaks in the Method Template Editor. See “Creating a Method
Template” on page 255.
2. In the Peaks pane, select a peak in the sample.
The TraceFinder application displays the selected peak in the Peak Details pane, displays
the Qual Data and Qual Library sections in the Spectrum pane, and locates the selected
peak in the Sample Chromatogram pane.
• The Qual Data section shows spectrum data for the peak in the raw data file.
• The Qual Library section shows actual spectrum for the identified library compound.
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Figure 116. Peak Details pane
Note When you select a data-dependent sample, the peak can be from either a full
scan or a QED spectrum of an SRM-filtered chromatogram.
Figure 117. Spectrum pane
Reference
spectrum from
the library
Actual spectrum
data for the
compound
Figure 118. Selected peak in the Sample Chromatogram pane
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 To remove a peak
1. Select a peak in the Sample Chromatogram pane.
2. Right-click the Peak Details pane and choose Remove Qual Peak from the shortcut
menu.
The TraceFinder application removes the selected peak from all Qualitative View panes.
Note There is no undo for this action, but you can manually add a peak to redefine a
removed peak. See “Sample Chromatogram Pane” on page 448.
 To hide or display columns in the Peaks pane
1. Click the Field Chooser icon,
, in the upper left corner of the pane.
The Field Chooser displays all available columns of data for the Peaks pane.
2. Select the check box for each column that you want to display, or clear the check box for
each column that you want to hide.
The application immediately displays or hides the column in the Peaks pane.
3. When you are finished modifying the column display, click
Chooser.
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Peaks Pane
Use the features in the Peaks pane to display graphical values for each sample and peak
combination.
Figure 119. Peaks pane
Table 92. Peaks pane parameters
Parameter
Description
Filter
Filter used to identify the peaks. Specified in the raw data file or
the master method.
When your raw data file is data-dependent, the filter indicates
this with a “d”.
Data-dependent filter
Thermo Scientific
Peak RT
Peak retention time. The time after injection when the
compound elutes. The total time that the compound is retained
on the column.
SI
Search index method used to search the NIST library.
RSI
(Reverse search index) A method used to search the NIST library.
A reverse search compares a library entry to an unknown
compound (a forward search compares the mass spectrum of an
unknown compound to a mass spectral library entry).
MP
Match probability.
Est Amt
Estimated amount of the compound.
Library Hit
Library compound that matches the identified peak.
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Sample Chromatogram Pane
The Sample Chromatogram pane in the Qualitative View displays all peaks in the selected
sample. The peak selected in the Peaks pane displays a red marker. See “Sample
Chromatogram Pane” on page 449.
 To zoom in on a peak
1. In the Sample Chromatogram pane, drag the cursor to delineate a rectangle around the
peak.
The delineated area expands to fill the view.
2. To restore the default view, right-click the Sample Chromatogram pane and choose Reset
Scaling from the shortcut menu.
 To manually add a peak
1. Zoom in to better identify which peak to add to the results set.
2. Right-click the Sample Chromatogram pane, and choose Add Qual Peak from the
shortcut menu.
3. Click to indicate the left and right base points for the peak.
The TraceFinder application marks the peak in the Sample Chromatogram pane.
The TraceFinder application places the peak delimiter tags at the base point locations and
automatically updates the peak values in the Peaks pane and Peak Details pane. See Peak
Details pane with a manually added peak.
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Figure 120. Peak Details pane with a manually added peak
Manually added
base points
Sample Chromatogram Pane
Use the features on the Sample Chromatogram pane to display peaks in the selected sample.
Figure 121. Sample Chromatogram pane
Table 93. Sample chromatogram pane shortcut menu commands
Thermo Scientific
Command
Description
Add Qual Peak
Select the beginning and ending base points for a new
qualitative peak. Available only when no peak is detected.
Reset Scaling
Resets the original scaling after a zoom operation.
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Peak Details Pane
The Peak Details pane in the Qualitative View displays the selected peak. For a description of
commands on the shortcut menu, see “Peak Details Pane” on page 452.
Follow these procedures:
• To zoom in on a peak
• To manually add a peak
• To remove a peak
• To switch between method and manual integration modes
• To change the displayed information for detected peaks
 To zoom in on a peak
1. In the chromatogram plot, drag the cursor to delineate a rectangle around the peak.
The delineated area expands to fill the view.
2. To restore the default view, right-click the chromatogram plot and choose Reset Scaling
from the shortcut menu.
 To manually add a peak
1. Right-click anywhere in the Peak Details pane, and choose Add Qual Peak from the
shortcut menu.
If a peak is already detected, the Add Qual Peak command is not activated.
2. Click to indicate the left and right base points for the peak.
The TraceFinder application places the peak delimiter tags at these locations and
automatically updates the peak values (area, height, and so forth) in the result set.
Manually added base points
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 To remove a peak
Right-click the Peak Details pane, and choose Remove Qual Peak from the shortcut
menu.
The TraceFinder application removes the peak displayed in the Peak Details pane. All data
for this peak are removed from the Qualitative View panes.
 To switch between method and manual integration modes
Right-click the Peak Details pane and choose Method Integration or Manual
Integration from the shortcut menu.
Initially, the method and manual integration settings that are stored for a compound and
file are identical. When you switch modes, the saved result set does not change. However,
when manual data are available, the Peak Details plots and the result set update as you
switch between method and manual modes.
As you switch between modes, each pane reflects the changes. The generated reports for
these data identify the manual modifications.
 To change the displayed information for detected peaks
1. Right-click the Peak Details pane and hold the cursor over Peak Labels.
2. Choose to display labels for the peak retention time (RT), peak height (AH), peak area
(AA), or signal-to-noise (SN).
Label not displayed in chromatogram
Label displayed in chromatogram
3. To remove a label, select the label type again to clear it.
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Peak Details Pane
Use the features in the Peak Details pane to display the selected peak.
Figure 122. Peak Details pane
Table 94. Peak Details pane shortcut menu commands
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Command
Description
Reset Scaling
Resets the original scaling after a zoom operation.
Method Integration
Displays method integration settings.
Manual Integration
Displays manual integration settings.
Peak Labels
Displays or hides the peak labels (Label Area, Label
Retention Time, Label Height, or Label to Noise).
Remove Qual Peak
Available only for manually added peaks. Removes the
peak displayed in the Peak Details pane.
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Spectrum Pane (Library and Data)
The Spectrum pane in the Qualitative View displays the reference spectrum from the library
and the spectrum data for the selected sample. The top pane displays the spectrum for the
identified compound found in the reference library; the bottom pane displays the actual
spectrum data for the selected peak.
Figure 123. Spectrum pane
Reference
spectrum from
the library
Actual spectrum
data for the
compound
 To zoom in on a peak
1. In either spectrum plot, drag the cursor to delineate a rectangle around the peak.
The delineated area expands to fill the view.
2. To restore the default view, right-click the spectrum plot and choose Reset Scaling from
the shortcut menu.
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Library Hits Pane
The Library Hits pane in the Qualitative View displays the best library matches for the
selected peak. Use this pane to select a different library entry for the peak. For detailed
descriptions of the Library Hits pane parameters, see Library Hits pane.
When you select a library entry other than the original entry, the TIC Report and TIC
Summary Report indicate this with a “P” flag:
P flag
 To change the library entry for a selected peak
In the Library Hits pane, select the check box for the library entry that you want to use to
identify the selected peak.
• In the Spectrum pane, the reference spectra change to show the spectra for the
selected library entry.
• In the Peaks pane, the SI, RSI, MP, and Compound values update to reflect the
selected library entry.
Selected library entry
in the Library Hits pane
Reference spectra
for Hexanone
Peak list for
Hexanone
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Figure 124. Library Hits pane
Table 95. Library Hits pane parameters
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Parameter
Description
<Check box column>
Indicates selected library entries for the selected peak.
Rank
Indicates the order of best matches between the selected
peak and library entries.
SI
(Search index) A method used to search the NIST library.
RSI
(Reverse search index) A method used to search the NIST
library. A reverse search compares a library entry to an
unknown compound (a forward search compares the
mass spectrum of an unknown compound to a mass
spectral library entry).
MP
Match probability.
Library Entry
Library compound that matches the identified peak.
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Features Common to All Data Review Pages
The following features are common to all quantitative batch data review pages.
• Common Column Parameters
• Inactive and Excluded Compounds
• Compound Details
• Exporting Compounds
Common Column Parameters
Table 96. Common parameters for Compound Results and Sample Results tables (Sheet 1 of 7)
Column
Description
%CV
Coefficient of Variance. Standard deviation of the multiple samples of one level, multiplied
by 100, and divided by the average of the multiple samples of that level. This calculation is
based on the areas of the peaks.
%Diff
The calculated amount minus the expected amount, divided by the expected amount, and
then multiplied by 100.
%RSD
Standard deviation of the multiple samples of one level, multiplied by 100, and divided by
the average of the multiple samples of that level. This calculation is based on the calculated
amounts.
Note This RSD value is not the same as the RSD value used with the Average RF curve
type in the method. See “Calibration” on page 215.
The application uses this %RSD value in Data Review and in the Compound Calibration
Report when you acquire multiple samples for the same QC Std or Cal Std samples.
Active
Displays or hides a compound for a particular sample.
• When a compound is marked inactive, the application does not remove its data and
calculated values from the result set. Instead, the TraceFinder application masks the
appearance of that compound for that particular sample and grays the compound in the
compounds list.
• When a calibration standard is marked inactive, the application no longer uses the data
file’s calibration point for the calibration and removes it from the graphical view of the
calibration curve displayed in the Compound Details pane. It is no longer part of the
result set.
In a Sample View, the Active parameter is in the Compound Results pane.
In a Compound View, the Active parameter is in the Sample Results pane.
Acquisition Order
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Sequentially numbers the samples.
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Table 96. Common parameters for Compound Results and Sample Results tables (Sheet 2 of 7)
Column
Description
Actual RT
Actual retention time for the compound. Retention time is the time after injection when a
compound elutes and the total time that the compound is retained on the chromatograph
column.
Adduct
The most intense adduct for the retention time for a compound.
Area
The area obtained by integrating peak intensities from the start to the end of the peak.
When the Response Ratio is specified as Area, this column displays an asterisk (*Area).
Calculated Amt
The amount present in the sample, as determined using the calibration curve and the
response ratio.
Channel
Specifies the channel on which the sample was run. If the sample is not acquired, the value is
Pending. The Channel column is available only when you have activated multiplexing in the
Configuration console. See “Multiplexing” on page 61.
Confirm
The number of criteria confirmed out of the total number specified in the method.
Expected RT
Expected retention time for the compound.
FI
Fragment Ions flag. The application displays one of these indicators:
• A green circle (pass) when the measured m/z value of any of the fragments is within the
mass tolerance specified in the method. On the Isotopes page in the Spectrum pane, the
All Isotopes and Multi-Isotopes flags are also green.
• A red square (fail) when the measured m/z value of none of the fragments is within the
mass tolerance specified in the method. On the Isotopes page in the Spectrum pane, the
All Isotopes and Multi-Isotopes flags are also red.
• A blank when there are no fragments detected.
To display a list of fragments and their pass/fail status, hold your cursor over the indicator.
Filename
Name of the raw data file that contains the sample data.
Final Units
Specifies the calculated amount.
Default: 1
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Table 96. Common parameters for Compound Results and Sample Results tables (Sheet 3 of 7)
Column
Description
Flag Details
Indicates all errors found in the compound.
Type of error:
• I: Confirming ion coelution failure
• A: Amount error
• B: Matrix blank error
• PK: Peak not found
• LS: Library matching error
• IP: Isotope error
• FI: Fragment ions error
• IR: Ion ratio error
Flags
Caution flag displayed when a compound within the sample has an error.
Formula
The formula for the peak as specified in the compound database.
Fragment n
Displays the measured m/z for the fragment ion. The application displays a separate column
for each found fragment.
• For each fragment found in the compound database that passes the filter in the method,
the Compounds table displays the m/z value in green text.
• For each fragment found in the compound database that does not pass the filter in the
method, the Compounds table displays the m/z value in red text.
• For each fragment that is not found in the compound database, the Compounds table
displays N/S (none specified).
Fragment not found in the compound database
Fragment found but does not meet method parameters
Fragment found and meets method parameters
Note Compounds can have a maximum of five fragments, and the Compounds table has
a maximum of five Fragment columns. When a compound contains fewer than five
fragments, all remaining Fragment columns display N/S.
Fragment n (Delta
(ppm/mmu))
The difference between the expected fragment ion m/z from the compound database and the
measured fragment ion m/z.
The application displays a separate delta column for each identified fragment.
Group
Threshold group to which a sample belongs. You can view samples by group in the
Comparative View of Data Review.
Height
The distance from the peak maximum to the peak base, measured perpendicular to the
ordinate. When the Response Ratio is specified as Height, this column displays an asterisk
(*Height).
Integration Mode
Integration mode specified in the method. See “Quan Peak” on page 467.
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Table 96. Common parameters for Compound Results and Sample Results tables (Sheet 4 of 7)
Column
Description
IP
Isotopic Pattern flag. The application displays one of these indicators:
• A green circle (pass) when the score percentage is higher than the specified fit threshold
percentage.
• A red square (fail) when the score percentage is lower than the specified fit threshold
percentage.
• A blank when the parameter is not scored.
To display the score of matched isotopes, hold your cursor over the indicator.
IR
Ion Ratio flag. The application displays one of these indicators:
• A green circle when the ion ratio is within the acceptable ion ratio range.
• A red square when the ion ratio is not within the acceptable ion ratio range.
Isotopic Pattern Score
(%)
The percentage of the number of total isotopes to the number of matched isotopes.
ISTD Amt
Amount of internal standard.
ISTD Response
Response of the internal standard.
Lib Match Name
The name of the best matching compound in the library search. When the application finds
a match in the library, this column displays the matching library entry with the highest
score.
• When the application does not perform a library search, this column displays “N/A” in
black text.
• When the application does not perform an MS/MS scan, this column displays “N/A” in
red text.
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Table 96. Common parameters for Compound Results and Sample Results tables (Sheet 5 of 7)
Column
Description
Library Match Rank
Displays the ranking of the library match. When the application finds a match in the library,
this column displays the library entry’s relative rank, in the format “x of y”, where
• x = the rank of the highest scoring library match.
• y = the total number of library matches from the list of matches for a particular adduct
that contains the highest scoring match.
Results are as follows when the application performs both a library search and an MS/MS
scan and both the library entry and the formula match the target compound:
• The criteria passes when the library score is higher than or equal to the score threshold.
The values in this column are in green text.
• The criteria fails when the library score is lower than the score threshold. The values in
this column are in red text.
When the application does not perform a library search, this column displays “N/A” in
black text.
When the application does not perform an MS/MS scan, this column displays “N/A” in red
text.
Library Score (%)
The score from the library fit. When the application finds a match in the library, this
column displays the highest score associated with the Lib Match Name parameter.
Results are as follows when the application performs both a library search and an MS/MS
scan and both the library entry and the formula match the target compound:
• The criteria passes when the library score is higher than or equal to the score threshold.
The values in this column are in green text.
• The criteria fails when the library score is lower than the score threshold. The values in
this column are in red text.
When the application does not perform a library search, this column displays “N/A” in
black text.
When the application does not perform an MS/MS scan, this column displays “N/A” in red
text.
Range: 1 to 100%
LS
Library Search flag. The application displays one of these flags:
• A green circle when the library search is successful.
• A red square when the library search is not successful.
m/z (Apex)
Mass-to-charge ratio found in the spectra for the peak. Assumes that the charge is 1.
When the application successfully integrates the peak, this column displays the charged m/z
value for the compound, which is the highest intensity in the apex scan.
When the application cannot successfully integrate the peak, this column displays N/F.
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Table 96. Common parameters for Compound Results and Sample Results tables (Sheet 6 of 7)
Column
Description
m/z (Delta (mmu))
Difference between the m/z (Expected) and m/z (Apex). Assumes that the charge is 1.
When the m/z (Apex) column displays m/z value for the compound, this column displays
the delta m/z corresponding to the highest intensity in the apex scan.
• When the mass tolerance is specified in ppm in the master method, then
m/z (Delta) = 1 000 000 × ([m/z (Apex) – m/z (Expected)] × m/z (Expected)).
• When the mass tolerance is specified in mmu in the master method, then
m/z (Delta) = 1000 × m/z (Apex) – m/z (Expected)).
m/z (Expected)
Mass-to-charge ratio from the compound database. Assumes that the charge is 1.
• When an adduct is found, the application displays the neutral mass value for the
compound (calculated from the neutral formula) ± the mass of the most intense adduct
ion found for the compound.
• When no adduct is found, the application displays the neutral mass value for the
compound ± the mass of the first adduct entered in the compound database.
For details about defining adducts for the compound database, see “Specifying Adducts” on
page 52.
For details about adding adducts to compounds, see “Editing Compounds in the Database”
on page 89.
Note When the adduct is a gain, the adduct mass is a positive number. When the adduct
is a loss, the adduct mass is a negative number. The resulting mass value after adding or
subtracting the adduct mass is always a positive number.
Num Isotopes Matched The number of isotopes matched in the expected calculated isotope spectra relative to the
total number of isotopes used in the score calculation, in the format “x of y”, where
• x = the number of isotopes matching the elemental composition used for the Isotopic
Pattern Score calculation.
• y = the total number of isotopes considered in the Isotopic Pattern Score calculation.
This is the number of isotope peaks expected to be above the spectral noise.
PK
Peak found
The application displays one of these flags:
• A green circle when the peak is found.
• A red square when the peak is not found.
Response Ratio
The ratio of the Response value to the IS Response value. If the Response is specified as Area
in the processing method, the units of both Response and IS Response are counts-sec. If the
Response is specified as Height in the processing method, the units of both Response and IS
Response are counts.
RT Delta
Difference between the expected retention time and the measured retention time.
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Table 96. Common parameters for Compound Results and Sample Results tables (Sheet 7 of 7)
Column
Description
Sample Amt
The injected volume multiplied by the conversion factor. For example, if you have
1000 ng/mL of a substance that is too concentrated for the mass spectrometer, you can
dilute it by 1000. Then your injection volume is 1, your conversion factor is 1000, and your
sample amount is 1000.
Sample Type
Defines how the TraceFinder application processes the sample data. Each sample is classified
as one of the following sample types: Matrix Blank, Solvent, Cal Std, QC Std, or Unknown.
Status
Status indicators for each sample indicate if the sample is currently acquiring, not acquired,
acquired, or processed.
Sample is not acquired.
Sample is acquired but not processed.
Sample is acquired and processed.
Sample is currently acquiring.
Theoretical Amt
Theoretical amount of the compound expected in the sample.
Excluded
Turns a compound on or off in the calibration curve in the Compound Details pane.
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Inactive and Excluded Compounds
Use the Active and Excluded columns to control which compounds are used for calculating
the calibration curve and for reporting.
Follow these procedures:
• To make a sample active or inactive
• To exclude a calibration point
 To make a sample active or inactive
1. Select the sample in the Sample Results pane.
All compounds in the selected sample appear in the Compounds pane. Inactive
compounds are grayed out.
2. In the Compounds pane, select the compound whose active/inactive status you want to
change.
• When a compound it marked inactive, the application does not remove its data and
calculated values from the result set. Instead, the TraceFinder application masks the
appearance of that compound for that particular sample and grays the compound
name in the compounds list.
• When a calibration standard is marked inactive, the application no longer uses the
data file’s calibration point for the calibration and removes it from the graphical view
of the calibration curve displayed in the Qualification pane. The calibration point is
no longer part of the result set.
3. In the Sample Results pane, select or clear the Active check box.
Use the horizontal scroll bar at the bottom of the table to scroll to the Active column.
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 To exclude a calibration point
In the sample list, select the Excluded check box for the sample.
Note Only calibration samples have the Excluded check box available.
Use the horizontal scroll bar at the bottom of the table to scroll to the Excluded column.
The application displays a value that is no longer used for calibration as an empty box in
the graphical view of the calibration curve.
Excluded
calibration
point
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Compound Details
Use the Compounds Details pane to display any of the following types of data:
• Quan Peak
• Confirming Ions
• Calibration Curve
• Ion Overlay
• ISTD
• Reference Peak
• Spectra
• Library Match
• Isotope
• Fragments
 To open the Compound Details pane
1. Double-click the chromatogram in the Sample Peaks pane.
The Compound Details pane opens.
By default, the first display pane shows the quantitative peak for the selected compound.
2. In the second pane, select the additional type of data that you want to display.
Follow these procedures to change the display of the peak data in either of the panes:
• To change the peak panes
• To zoom in on a peak
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 To change the peak panes
In any of the peak panes, click
to view a list of commands.
Command
Description
Make All Panels the
Same Size
Evenly divides the area to make all panes the same width.
This command does not change the pane height.
Move Panel Left
Moves the current panel one space to the left. This
command is not available when the current pane is the
leftmost pane.
Move Panel Right
Moves the current panel one space to the right. This
command is not available when the current pane is the
rightmost pane.
Add a Panel
Adds an empty peak pane to the display. You can display a
maximum of four peak panes.
 To zoom in on a peak
1. In any of the views, drag your cursor to delineate a rectangle around the peak or spectra.
The delineated area expands to fill the view.
2. To restore the default view, right-click the chromatogram plot and choose Reset Scaling
from the shortcut menu.
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Quan Peak
A compound can have multiple quantitative peaks. You can switch between quantitative
peaks, but you cannot view multiple quantitative peaks at the same time. The indicator in the
upper right corner of the Quan Peak pane displays which of the multiple quantitative peaks
you are viewing. The Quan Peak pane uses a unique shortcut menu. See “Quan Peak pane
shortcut menu commands” on page 471.
Figure 125. Quantitative peak pane with multiple quantitative peaks
Peak 1 of 2
Peak 2 of 2
Follow these procedures to modify the quantitative or confirming ion peak data:
• To manually add a peak
• To remove a manually created peak
• To switch between method and manual integration modes
• To change the displayed information for detected peaks
• To modify the peak detection settings
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 To manually add a peak
1. Right-click anywhere in the quantitative peak pane, and choose Add Quan Peak from
the shortcut menu.
2. Click the left base of the peak you want to identify.
3. Drag to the right base and release the mouse.
The application places the peak delimiter tags at these locations and automatically
updates the peak values (area, height, and so forth) in the result set.
Manually added right
and left base points
 To remove a manually created peak
Right-click the pane, and choose Cancel Add Peak from the shortcut menu.
The application cancels the Add Peak operation. If you have already completed adding
the peak, select the peak and then choose Remove Quan Peak from the shortcut menu.
 To manually integrate a quantitative peak
1. Hold your cursor over one of the two peak delimiter tags in the peak pane.
When the tag can be selected, the cursor changes to a crosshair-style cursor. You can zoom
in on the baseline to make it easier to select the tag.
Crosshair cursor
2. Drag the peak delimiter tag to another location and automatically update the peak values
(area, height, and so forth) into the result set.
The generated reports for these data identify the manual modifications.
You can store two peak value sets (method and manual integration settings) with each
compound in each file. These settings can result in a different set of stored values. The
application originally calculates the method values based on the processing method
parameters. The manual values are a result of what you have edited.
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 To switch between method and manual integration modes
Right-click the chromatogram view and choose Method Integration Settings or Manual
Integration Settings from the shortcut menu.
Initially, the method and manual integration settings that are stored for a compound and
file are identical. When you switch modes, the saved result set does not change. However,
when manual data are available, the chromatogram plots and the result set update as you
switch between method and manual modes.
As you switch between modes, each pane reflects the changes. The generated reports for
these data identify the manual modifications.
 To change the displayed information for detected peaks
1. Right-click the peak pane and hold the cursor over Peak Labels.
2. Choose to display labels for the peak retention time, peak height, peak area, or signal to
noise.
The label types in the list are selected for displayed labels and are cleared for labels that are
not displayed.
3. To remove a label, select the label type again and clear it.
Label settings are globally applied to quantitative peaks, confirming ion peaks, and
internal standard peaks.
Tip The labels do not always update on all peak displays. To update all labels, select a
different compound, and then reselect the compound whose labels you changed.
 To modify the peak detection settings
1. Right-click the chromatogram view and choose one of the following from the shortcut
menu:
• Peak Detection Settings > Edit Local Method Peak Detection Settings: Makes
changes to the selected compound for all samples in this batch.
• Peak Detection Settings > Edit User Defined Peak Detection Settings: Makes
changes to the selected compound for only the selected sample. The TraceFinder
application saves these changes with the batch and stops applying the local method
detection settings to the compound for this sample only.
The Peak Detection Settings dialog box opens where you can adjust detection settings
that were specified in the method. The title bar of the dialog box lists the selected
compound and indicates whether you are making changes to only the selected sample or
to the local method.
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Figure 126. Peak Detection Settings dialog box
Editing all samples in the batch
Editing only the selected sample
2. Edit any of the detection settings.
For detailed descriptions of all detection settings, see “Detection” on page 160.
3. To save your changes to this compound, click Apply.
• When you are editing a single sample, the application makes changes to the selected
compound for this sample. If the sample is a calibration sample type, this update
changes the calibration curve which, in turn, affects all calculated amounts.
• When you are editing the local method, the application makes changes to the selected
compound for all samples in this batch.
Note The Peak Detection Settings commands are also available on the Confirming Ions
pane.
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Table 97. Quan Peak pane shortcut menu commands (Sheet 1 of 2)
Command
Description
Method Integration Settings
Use Local Method Peak Detection Settings: Applies the
local method integration settings to the selected
compound.
To edit these peak detection settings, use the Peak
Detection Settings > Edit Local Method Peak Detection
Settings command.
Use User Peak Detection Settings: Applies the
user-customized method integration settings to the
selected compound.
To edit these user-customized settings, use the Peak
Detection Settings > Edit User Defined Peak Detection
Settings command.
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Manual Integration Settings
Displays manual integration settings.
Add Quan Peak
–or–
Remove Quan Peak
–or–
Cancel Add Peak
Adds a peak, removes a peak, or cancels an add peak
operation in progress.
Confirming Ion List
Select the confirming ions to be viewed. Not available for
analog compounds.
Send RT to Method
Sets the current retention time as the expected retention
time for the compound in the local method.
Peak Labels
Displays or hides the peak labels (Label Area, Label
Retention Time, Label Height, or Label to Noise).
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Table 97. Quan Peak pane shortcut menu commands (Sheet 2 of 2)
Command
Description
Show Peak Info
Displays peak information for the selected compound, as
in this example:
Reset Scaling
Resets the original scaling after a zoom operation.
Peak Detection Settings
Edit User Defined Peak Detection Settings: Opens the
Peak Detection Settings dialog box where you can make
changes to the selected compound for this sample.
Edit Local Method Peak Detection Settings: Opens the
Peak Detection Settings dialog box where you can make
changes to the selected compound for all samples in this
batch.
After you apply either of these updates, the application
does not retain manual integration settings.
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Confirming Ions
The Confirming Ions pane displays a graphical view of all qualifying/confirming ions for the
selected compound and displays calculated ion ratios and ion ratio acceptance windows. A red
border indicates that an ion ratio is outside of its window. The Confirming Ions pane uses a
unique shortcut menu. See Confirming Ions pane shortcut menu commands.
Note For compounds with an analog detection type, the application displays “No
Confirming Ions are Enabled” in the Confirming Ions pane.
Figure 127. Quantitative peak with multiple confirming ions
Figure 128. Confirming ion with coelution failure
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 To manually integrate a confirming ion peak
1. Hold your cursor over one of the two peak delimiter tags in the peak pane.
When the tag can be selected, the cursor changes to a crosshair-style cursor. You can zoom
in on the baseline to make it easier to select the tag.
2. Drag the peak delimiter tag to another location and automatically update the peak values
(area, height, and so forth) into the result set.
The generated reports for these data identify the manual modifications.
You can store two peak value sets (method and manual integration settings) with each
compound in each file. These settings can result in a different set of stored values. The
application originally calculates the method values based on the processing method
parameters. The manual values are a result of what you have edited.
Note Because a Blank Report displays only the quantitation mass, when you manually
integrate a confirming ion, the manual integration flag in the report is displayed on
the quantitation mass.
Table 98. Confirming Ions pane shortcut menu commands
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Command
Description
Method Integration
Settings
Displays the method integration settings.
Manual Integration
Settings
Displays the manual integration settings.
Add/Remove/Cancel
Quan Peak
Adds a quantitation peak, removes a peak, or cancels an add peak
operation in progress.
Range Calc Method:
Manual
Selects the method used to calculate the ion ratio range windows:
Manual, Average, Weighted Average, or Level.
Range Calc Level
Displays the range based on the calibration level.
Target Ratio
Specifies the theoretical ratio of the confirming ion's response to
the quantification ion's response.
Window Type
Specifies the Absolute or Relative calculation approach for
determining the acceptable ion ratio range.
Window
Specifies the acceptable ion ratio range as a percentage.
Peak Labels
Displays or hides the peak labels (Label Area, Label Retention
Time, Label Height, or Label to Noise).
Show Peak Info
Displays peak information for the selected compound.
Reset Scaling
Resets the original scaling after a zoom operation.
Peak Detection
Settings
Opens the Peak Detection Settings dialog box for the selected
compound.
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Calibration Curve
The Calibration Curve pane displays a graphical view of the calibration curve for the selected
compound and key statistical values for evaluating the quality of the calibration. The
Calibration Curve pane uses a unique shortcut menu. See Calibration Curve pane shortcut
menu commands.
Figure 129. Quantitative peak with a calibration curve plot
 To manually exclude a calibration point
In the sample list, select the Excluded check box for the sample.
Use the horizontal scroll bar at the bottom of the table to scroll to the Excluded column.
When a value is no longer used for calibration, it is displayed as an empty box in the
graphical view of the calibration curve.
Excluded
calibration
point
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Table 99. Calibration Curve pane shortcut menu commands
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Command
Description
Standard Type
Sets the standard type to External or Internal.
Calibration Curve Type
Sets the calibration curve type to one of the following:
• Linear: Allows all settings with this exception: When Origin
is set to Include, all Weighting values are grayed out and
Weighting is set to Equal.
• Quadratic: Allows all settings with this exception: When
Origin is set to Include, all Weighting values are grayed out
and Weighting is set to Equal.
• Average RF: Allows no Weighting or Origin selections. All
Weighting and Origin values are grayed out. Weighting is set
to Equal, and Origin is set to Ignore.
Response Via
Sets the response to Area or to Height.
Weighting
Sets the weighting to equal, 1/X, 1/X^2, 1/Y, or 1/Y^2.
Origin
Sets the origin to Ignore, Force, or Include.
Units
Sets the units.
Done with Settings
Saves the calibration curve settings.
Reset Scaling
Resets the original scale in the calibration curve pane.
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Ion Overlay
The Ion Overlay pane represents an overlay of the entire ion set—quantification and
qualifying/confirming—for the selected compound. Use this pane to graphically review the
peak apex alignment and coeluting peak profiles.
Note For compounds with an analog detection type, the application displays “No Data”
in the Ion Overlay pane.
Figure 130. Quantitative peak with confirming ion overlay
ISTD
The ISTD pane displays the internal standard specified for the compound in the method. See
“To specify an internal standard type for a compound” on page 215.
Figure 131. Quantitative peak with an internal standard
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Reference Peak
The Reference Peak pane displays the reference peak as specified in the method.
Figure 132. Quantitative peak with a reference peak
 To specify a chromatogram reference peak
1. In the Batch View task pane, click Reference Sample.
An empty reference sample table opens.
2. Click the Add Reference Sample icon,
Reference Sample from the shortcut menu.
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The Open Chromatograph Reference Sample dialog box opens.
Note If you are creating a new method, you will not see any reference samples here.
You must create and save a batch using the current method to see the reference
samples in this list.
3. Select a project from the list of projects.
4. Select a subproject from the list of subprojects.
5. Select a batch from the list of batches.
The TraceFinder application displays only batches that were created using the current
master method.
6. Select a sample from the list of processed samples.
The TraceFinder application displays all the processed samples in the selected batch. To
use a sample as a reference sample, the sample must have been processed with the current
master method.
7. Click Open.
The selected sample is displayed as the chromatogram reference sample in the Method
View in the Method Development mode.
Tip To clear the reference sample from the master method, select None in the Set
Chromatogram Reference Samples pane.
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Spectra
The Spectra pane displays a comparison of the spectra found in the data and the method
reference.
Note For compounds with an analog detection type, the application displays “Not
Available” in the Spectra pane.
Figure 133. Quantitative peak with data and reference spectra
Library Match
The Library Match pane displays all library matches for the selected compound.
Figure 134. Library Match for selected compound
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If you have no matches for any of your compounds, make sure you have completed all of the
following:
• You installed a library.
• You selected screening libraries in the Configuration console. See “Screening Libraries” on
page 59.
• You enabled Library Matching in the method. See “To activate library matching” on
page 205.
Isotope
The Isotope pane displays all isotopes for the selected compound.
Note When you select different samples, the current compound remains selected (as long
as that compound is found in the sample).
The isotopes pane displays isotopic pattern results for all adducts of a compound according to
the threshold and deviation parameters defined in the method.
To identify or confirm the presence of a compound, the resulting score percentage from
isotopic pattern matching must be higher than the specified fit threshold percentage.
• An isotope peak is not found if its intensity, relative to the monoisotopic ion’s intensity, is
more than the specified intensity deviation percentage away from the theoretical relative
intensity of the isotope ion.
• An isotope peak is found if its measured m/z is less than the specified mass deviation
amount away from its expected m/z.
To specify isotopic criteria in a method, see “Isotopes” on page 207.
Figure 135. Isotopes for the selected compound
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Table 100. Isotopes pane shortcut menu commands
Command
Description
Reset Scaling
Resets the original scaling after a zoom operation.
Copy to Clipboard
Copies the graphic display to the Clipboard.
Display Overlay Spectra
Display Stack Spectra
Overlays the two spectrum displays, or stacks the simulated
spectrum and the peak apex spectrum.
Show/Hide Noise Label
Adds a noise label to each peak. Expected isotope peaks
(displayed in blue) do not display a noise label.
Show/Hide Resolution
Label
Adds a resolution label to each peak. Expected isotope peaks
(displayed in blue) do not display a resolution label.
Fragments
The Fragments pane displays a composite of all fragments found in the compound. The
application displays the measured peak as a solid red line and displays the expected peak as a
dashed blue line.
Figure 136. Fragments for the selected compound
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Exporting Compounds
You can export compound data to an Excel spreadsheet, to a CSV file, to a compound
database, or to a new quantitation method. These export commands are available from the
File menu in the Sample View, Compound View, and Comparative View.
Follow these procedures:
• To export compounds to an Excel spreadsheet
• To export compounds to a CSV file
 To export compounds to an Excel spreadsheet
1. Choose File > Export Data To > CSV or Excel from the main menu.
The Data Review Export dialog box opens.
2. Click Browse and, in the Export Data to Excel dialog box, locate the folder where you
want to save the file.
3. Type a file name for the XLSX file and click Save.
4. In the File Format area, in the Data Review Export dialog box, select the Excel option.
5. In the Sheet Layout area, select one of the following file formats for the spreadsheet.
• Multiple Worksheets: Writes one sample to each Excel worksheet tab.
• Single Worksheet: Writes all samples to a single Excel worksheet tab.
6. In the Data to Export area, select one of the following sets of data to export.
• Export Visible Columns Only: Writes data from only the displayed columns to the
specified worksheet format.
• Export All Batch Data: Writes data from all columns (displayed or hidden) of all
samples to the specified worksheet format.
7. Click Export.
The application saves the specified compound data to an Excel spreadsheet and opens the
folder where you saved the file. The application names the file Batch.xlsx.
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 To export compounds to a CSV file
1. Choose File > Export Data To > CSV or Excel from the main menu.
The Data Review Export dialog box opens.
2. Click Browse and, in the Export Data to Excel dialog box, locate the folder where you
want to save the file.
3. Type a file name for the CSV file and click Save.
4. In the File Format area, in the Data Review Export dialog box, select the CSV option.
5. In the Sheet Layout area, select one of the following file formats for the spreadsheet.
• Multiple Files: Writes one sample to each CSV file.
• Single File: Writes all samples to a single CSV file.
6. In the Data to Export area, select one of the following sets of data to export.
• Export Visible Columns Only: Writes data from only the displayed columns to the
specified worksheet format.
• Export All Batch Data: Writes all data from all samples in the batch to the specified
worksheet format.
7. Click Export.
The application saves the specified compound data to a CSV spreadsheet.
When you selected to create multiple files, the application opens the folder where you
saved the files. The application names each file Batch_Compound.csv.
When you selected to create a single file, the Excel application opens, displaying the
exported data for all samples. The application names the file Batch.csv.
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The Data Review view displays the data generated by the target screening master method. Use
Data Review to verify the data for a compound before you generate reports.
 To open the Data Review view
1. Click Analysis in the navigation pane.
The Analysis navigation pane opens.
2. Click Data Review.
The Data Review navigation pane opens.
In the target screening display, the panes show a list of all samples in the current batch, the
compound results for all compounds in the method, and chromatogram and spectrum plots
for all compounds found in the currently selected sample.
 To display or hide a pane on the Target Screening page
From the View menu, choose to display or hide the following:
• Samples
• Target Screening Results: Displays or hides the Compounds pane.
• Chromatogram
• Spectrum
Displayed panes are indicated with a check mark.
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Figure 137. Target Screening panes
Chromatogram pane
Samples pane
Compounds pane
Spectrum pane
When you select a sample in the Samples pane, the associated Compounds pane flags any
compound with errors in the selected sample. The associated Chromatogram pane displays
the chromatogram, retention time, area, height, and signal-to-noise ratio for all compounds in
the selected sample. The Spectrum pane highlights the compound selected in the Compounds
pane. You can display, hide, or move any of these panes.
For procedures about creating docked, floating, or tabbed panes, see “Data Review Pane
Display Features” on page 421.
The target screening display includes the following features:
• Samples Pane
• Compounds Pane
• Chromatogram Pane
• Spectrum Pane
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Samples Pane
Use the Samples pane to select a specific sample in the batch. The associated Compounds
Pane displays all compounds in the method and flags any compound with errors in the
selected sample.
Flags in the Samples pane indicate one of the following:
A green circle when the sample/compound/peak combination is identified and fully
confirmed.
A yellow triangle when the sample/compound/peak combination is identified but not
fully confirmed.
A red square when the sample/compound/peak combination is not identified.
Figure 138. Samples pane
Table 101. Samples pane shortcut menu commands
Thermo Scientific
Command
Description
Sort by Alphabetical
Sorts the samples alphabetically by sample name.
Sort by Import Order
Sorts the samples in the order they were processed.
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Compounds Pane
The Compounds pane displays all found peaks in the selected sample and flags any
compound with errors. The compounds table reflects the identified compounds found in the
compound database and the results of the method processing criteria. See “Compounds Pane
Columns” on page 495.
Color Coding for Measured or Calculated Values
The Compounds pane uses color-coded text to indicate the following:
• Green—Indicates that the measured value of scoring and confirmations pass the criteria
specified in the method.
• Red—Indicates that the measured or calculated value does not pass the criteria specified
in the method.
Displaying Multiple Adducts
When the TraceFinder application finds multiple adducts at the same retention time in a
sample, the Compounds pane displays the adducts on separate rows in the table.
Exporting Compounds
Use the functions on the File menu to export data to an Excel spreadsheet, a CSV file, a
compound database, or a new quantitation method.
Follow these procedures:
• To export compounds to an Excel spreadsheet
• To export compounds to a CSV file
• To export compounds to a compound database
• To create a new quantitation method with the selected compounds
• To create a new quantitation method and update the compound database
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 To export compounds to an Excel spreadsheet
1. For each compound that you want to export to an Excel spreadsheet, select the check box
in the Selected column.
2. Choose File > Export Data To > CSV or Excel from the main menu
The Data Review Export dialog box opens.
3. Click Browse and, in the Export Data to Excel dialog box, locate the folder where you
want to save the file.
4. Type a file name for the XLSX file and click Save.
5. In the File Format area, select the Excel option.
6. In the Sheet Layout area, select one of the following file formats for the spreadsheet.
• Multiple Worksheets: Writes one sample to each Excel worksheet tab.
• Single Worksheet: Writes all samples to a single Excel worksheet tab.
7. In the Data to Export area, select one of the following sets of data to export.
• Export Filtered and Selected Rows (Visible Columns Only): Writes data from the
displayed columns of selected samples to the specified worksheet format.
• Export All Batch Data: Writes data from all columns (displayed or hidden) of all
samples to the specified worksheet format.
8. Click Export.
The application saves the specified compound data to an Excel spreadsheet and opens the
folder where you saved the file.
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 To export compounds to a CSV file
1. For each compound that you want to export to a CSV file, select the check box in the
Selected column.
2. Choose File > Export Data > To CSV or Excel from the main menu.
The Data Review Export dialog box opens.
3. Click Browse and, in the Export Data to Excel dialog box, locate the folder where you
want to save the file.
4. Type a file name for the CSV file and click Save.
5. In the File Format area, select the CSV option.
6. In the Sheet Layout area, select one of the following file formats for the spreadsheet.
• Multiple Files: Writes one sample to each CSV file.
• Single File: Writes all samples to a single CSV file.
7. In the Data to Export area, select one of the following sets of data to export.
• Export Filtered and Selected Data Only: Writes data from the selected compounds
to the specified worksheet format.
• Export All Batch Data: Writes all data from all samples in the batch to the specified
worksheet format.
8. Click Export.
The application saves the specified compound data to an CSV spreadsheet and opens the
folder where you saved the file.
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 To export compounds to a compound database
1. For each compound that you want to export to a compound database, select the check
box in the Selected column, including any adducts that you want to export.
2. Choose File > Export Data To > Compound Database from the main menu.
The Export Compounds to CDB dialog box opens.
3. Do one of the following:
• Accept the default target database.
• Click Create and type the name for a new compound database.
• Click Browse and select from the list of compound databases.
4. Click Import.
• When you export compounds to a database that already contains these compounds,
the application updates the retention times in the database.
• When you add compounds to a database that does not contain these compounds, the
application adds all the compound data to the database.
When you export only one adduct for a compound, the application uses the selected
adduct as the peak in the updated or new compound database. When you export multiple
adducts for export, the application uses the adducts in the order of intensity.
The application uses the measured retention time value for the compound in the updated
or new compound database.
The application uses the expected m/z value for the compound in the updated or new
compound database.
The application exports all found fragments to the updated or new compound database.
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 To create a new quantitation method with the selected compounds
1. For each compound that you want to export to a new quantitation method, select the
check box in the Selected column including any adducts that you want to export.
2. Choose File > Export Data To > New Quantitation Method from the main menu.
The Acquisition page of a new quantitation method opens.
3. From the Instrument Method list, select a method (.meth) file to use for acquiring the
data.
4. Choose File > Save from the main menu.
5. In the Save Master Method dialog box, type a name for the method and click OK.
6. Click Compounds in the Method View navigation pane. Observe that the application
exported the selected compounds from the screening method to the new quantitation
method.
The application uses data from the selected compounds as follows:
• Exports quantitation peaks in the order of intensity.
• Exports measured retention time value for the compounds in the new method.
• Exports expected m/z value for the compounds in the new method.
• Exports all found fragments to the new method.
• Adds a filter for both quantitative peaks and confirming ions.
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 To create a new quantitation method and update the compound database
1. For each compound that you want to export, select the check box in the Selected column,
including any adducts that you want to export.
2. Choose File > Export Data > Update Compound Database and Create New
Quantitation Method from the main menu.
The Import Compounds to CDB dialog box opens.
The dialog box lists all compounds selected in the screening batch.
3. Do one of the following:
• Accept the default target database.
• Click Create and type the name for a new target database.
• Click Browse and select from the list of compound databases.
The compounds list indicates which compounds already exist in the target compound
database and which do not.
4. When any of the compounds already exist in the target database, choose one of the
following options:
• Update Retention Times: Updates only the retention times for the duplicate
compounds in the target database.
• Overwrite: Overwrites all compound data for the duplicate compounds in the target
database.
• Skip: Does not write any data from the duplicate compounds to the target database.
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5. Click Import.
The Acquisition page of a new quantitation method opens.
6. From the Instrument Method list, select a method (.meth) file to use for acquiring the
data.
7. Choose File > Save from the main menu.
8. In the Save Master Method dialog box, type a name for the method and click OK.
9. Click Compounds in the Method View navigation pane and observe that the new
method uses the specified compound database and that the application exported the
selected compounds (with the specified options) from the screening method to the new
quantitation method.
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Compounds Pane Columns
The columns of data in the Compounds pane display all parameter values associated with
each compound in the selected sample. See Compounds Pane Parameters.
 To hide or display columns in the Compounds pane
1. Click the Field Chooser icon,
, in the upper left corner of the pane.
The Field Chooser displays all available columns of data for the Compounds pane.
2. Select the check box for each column that you want to display, or clear the check box for
each column that you want to hide.
The application immediately displays or hides the column in the Compounds pane.
3. When you are finished modifying the column display, click
Chooser.
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Compounds Pane Parameters
The Compounds pane displays all parameter values associated with each compound in the
selected sample.
Figure 139. Compounds pane
Table 102. Compounds pane parameters (Sheet 1 of 6)
Column
Description
Displays the current compound database. When you have multiple screening databases,
the application lists the results for each database separately.
Expand the list of found compounds in
the screening database.
Selected
Identifies individual compounds for export. To select all compounds for export, select
the check box in the first column.
Selects all compounds in the
Compounds pane.
Selects the compound for
export.
MZ
Mass-to-charge ratio flag. The application displays one of these indicators:
• A green circle (pass) when the measured m/z value is within the specified threshold.
• A red square (fail) when the measured m/z value is not within the specified threshold.
• A blank when the mass-to-charge value is unavailable.
To display the expected, measured, and delta m/z, hold your cursor over the indicator.
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Table 102. Compounds pane parameters (Sheet 2 of 6)
Column
Description
RT
Retention Time flag. The application displays one of these indicators:
• A green circle (pass) when the measured retention time value is within the RT
Window value specified in the compound database.
• A red square (fail) when the measured retention time value is not within the RT
Window value specified in the compound database. In turn, this results in a failure
flag for the m/z value because the application cannot identify an m/z value that meets
the retention time.
• A blank when the retention time value is unavailable. When the retention time is
selected as “confirm” and the m/z is not detected, there is no flag.
Or, you can set a different retention time window in the method. See “Editing the
Processing Page” on page 277.
To display the expected, measured, and delta retention times, hold your cursor over the
indicator.
IP
Isotopic Pattern flag. The application displays one of these indicators:
• A green circle (pass) when the score percentage is higher than the specified fit
threshold percentage.
• A red square (fail) when the score percentage is lower than the specified fit threshold
percentage.
• A blank when the parameter is not scored.
To display the score of matched isotopes, hold your cursor over the indicator.
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Table 102. Compounds pane parameters (Sheet 3 of 6)
Column
Description
FI
Fragment Ions flag. The application displays one of these indicators:
• A green circle (pass) when the measured m/z value of any of the fragments is within
the mass tolerance specified in the method. On the Isotopes page in the Spectrum
pane, the All Isotopes and Multi-Isotopes flags are also green.
• A red square (fail) when the measured m/z value of none of the fragments is within
the mass tolerance specified in the method. On the Isotopes page in the Spectrum
pane, the All Isotopes and Multi-Isotopes flags are also red.
• A blank when there are no fragments detected.
To display a list of fragments and their pass/fail status, hold your cursor over the
indicator.
LS
Library Search flag. The application displays one of these flags:
• A green circle when the library search is successful.
• A red square when the library search is not successful.
Flag
Indicates the status of the identification and confirmation criteria.
• A green circle when the sample/compound/peak combination is identified and fully
confirmed.
• A yellow triangle when the sample/compound/peak combination is identified but
not fully confirmed.
• A red square when the sample/compound/peak combination is not identified.
Compound Name
The compound name match in the compound database.
Match Result Name
The compound name match in the compound database and the retention time.
Formula
The formula for the peak as specified in the compound database.
Adduct
The most intense adduct for the retention time for a compound.
Confirmed
The number of criteria confirmed out of the total number specified in the method.
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Table 102. Compounds pane parameters (Sheet 4 of 6)
Column
Description
m/z (Expected)
Mass-to-charge ratio from the compound database. Assumes the charge is 1.
• When an adduct is found, the application displays the neutral mass value for the
compound (calculated from the neutral formula) ± the mass of the most intense
adduct ion found for the compound.
• When no adduct is found, the application displays the neutral mass value for the
compound ± the mass of the first adduct entered in the compound database.
For details about defining adducts for the compound database, see “Specifying Adducts”
on page 52.
For details about adding adducts to compounds, see “Editing Compounds in the
Database” on page 89.
Note When the adduct is a gain, the adduct mass is a positive number. When the
adduct is a loss, the adduct mass is a negative number. The resulting mass value after
adding or subtracting the adduct mass is always a positive number.
m/z (Apex)
Mass-to-charge ratio found in the spectra for the peak. Assumes the charge is 1.
When the application successfully integrates the peak, this column displays the charged
m/z value for the compound, which is the highest intensity in the apex scan.
When the application cannot successfully integrate the peak, this column displays N/F.
m/z (Delta)
Difference between the m/z (Expected) and m/z (Apex). Assumes the charge is 1.
When the m/z (Apex) column displays m/z value for the compound, this column displays
the delta m/z corresponding to the highest intensity in the apex scan.
• When the mass tolerance is specified in ppm in the master method, then
m/z (Delta) = 1 000 000 × ([m/z (Apex) – m/z (Expected)] × m/z (Expected)).
• When the mass tolerance is specified in mmu in the master method, then
m/z (Delta) = 1000 × m/z (Apex) – m/z (Expected).
RT (Expected)
The retention time for the peak as specified in the compound database.
RT (Measured)
The found retention time for the peak apex.
RT (Delta)
Difference between the expected and measured retention time for the peak.
Measured Area
The AA value from the chromatogram pane.
Isotopic Pattern Score (%) The percentage of the number of total isotopes to the number of matched isotopes.
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Table 102. Compounds pane parameters (Sheet 5 of 6)
Column
Description
Num Isotopes Matched
The number of isotopes matched in the expected calculated isotope spectra relative to the
total number of isotopes used in the score calculation, in the format “x of y”, where
• x = the number of isotopes matching the elemental composition used for the
Isotopic Pattern Score calculation.
• y = the total number of isotopes considered in the Isotopic Pattern Score calculation.
This is the number of isotope peaks expected to be above the spectral noise.
Lib Match Name
The name of the best matching compound in the library search. When the application
finds a match in the library, this column displays the matching library entry with the
highest score.
• When the application does not perform a library search, this column displays “N/A”
in black text.
• When the application does not perform an MS/MS scan, this column displays
“N/A” in red text.
Library Score (%)
The score from the library fit. When the application finds a match in the library, this
column displays the highest score associated with the Lib Match Name parameter.
When the application performs both a library search and an MS/MS scan and both the
library entry and the formula match the target compound:
• The criteria passes when the library score is higher than or equal to the score
threshold. The values in this column are in green text.
• The criteria fails when the library score is lower than the score threshold. The values
in this column are in red text.
When the application does not perform a library search, this column displays “N/A” in
black text.
When the application does not perform an MS/MS scan, this column displays “N/A” in
red text.
Range: 1 to 100%
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Table 102. Compounds pane parameters (Sheet 6 of 6)
Column
Description
Library Match Rank
Displays the ranking of the library match. When the application finds a match in the
library, this column displays the library entry’s relative rank, in the format “x of y”, where
• x = the rank of the highest scoring library match.
• y = the total number of library matches from the list of matches for a particular
adduct that contains the highest scoring match.
When the application performs both a library search and an MS/MS scan and both the
library entry and the formula match the target compound:
• The criteria passes when the library score is higher than or equal to the score
threshold. The values in this column are in green text.
• The criteria fails when the library score is lower than the score threshold. The values
in this column are in red text.
When the application does not perform a library search, this column displays “N/A” in
black text.
When the application does not perform an MS/MS scan, this column displays “N/A” in
red text.
Fragment n
Displays the measured m/z for the fragment ion. The application displays a separate
column for each found fragment.
• For each fragment found in the compound database that passes the filter in the
method, the Compounds table displays the m/z value in green text.
• For each fragment found in the compound database that does not pass the filter in
the method, the Compounds table displays the m/z value in red text.
• For each fragment that is not found in the compound database, the Compounds
table displays N/S (none specified).
Fragment not found in the compound database
Fragment found but does not meet method parameters
Fragment found and meets method parameters
Note Compounds can have a maximum of five fragments, and the Compounds table
has a maximum of five Fragment columns. When a compound contains fewer than five
fragments, all remaining Fragment columns display N/S.
Fragment n (Delta
(ppm/mmu))
The difference between the expected fragment ion m/z from the compound database and
the measured fragment ion m/z.
The application displays a separate delta column for each identified fragment.
S/N
The signal-to-noise ratio calculated for the found peak.
Left RT
The time point of the left leading edge of the integrated peak.
Right RT
The time point of the right trailing edge of the integrated peak.
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Chromatogram Pane
Use the Chromatogram pane to display all extracted chromatograms of all adducts of the
selected compound.
The first tab displays the most intense target adduct for the peak result. Additional (optional)
tabs display extracted ion chromatograms for other adducts for the target compound at the
same retention time in order of intensity. If no signal exists for an adduct, it displays the XIC
of the expected m/z within the specified retention and chromatogram windows. When you do
not specify a retention time or window, the application displays the full time range.
For each adduct, the Spectrum pane displays the spectrum, isotopes, fragments, and library
matches. See Spectrum Pane.
Figure 140. Chromatogram pane
Table 103. Chromatogram pane shortcut menu commands
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Command
Description
Reset Scaling
Resets the original scaling after a zoom operation.
Copy to Clipboard
Copies the graphic display to the Clipboard.
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Spectrum Pane
Use the Spectrum pane to display the spectrum, isotopes, fragments, and library search
information for the selected adduct in the Chromatogram pane. The Spectrum pane displays
only the identification and confirmation criteria specified in the method. The confirmations
are based only on the most intense adduct. See “Editing the Processing Page” on page 277.
The Spectrum pane includes the following pages of information (when available) for each
selected sample/compound/peak combination:
• Spectrum
• Isotopes
• Fragments
• Library
Spectrum
The application displays the neutral loss (NL) and compound/peak name information on the
right side of the Spectrum page. When data is available, the plot width is the full mass range
in the raw data file. Otherwise, the application scales the width to the scan range.
Figure 141. Spectrum page
Table 104. Spectrum page shortcut menu commands
Thermo Scientific
Command
Description
Reset Scaling
Resets the original scaling after a zoom operation.
Copy to Clipboard
Copies the graphic display to the Clipboard.
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Isotopes
The isotopes page displays isotopic pattern results for all adducts of a compound according to
the threshold and deviation parameters defined in the screening method.
To identify or confirm the presence of a compound, the resulting score percentage from
isotopic pattern matching must be higher than the specified fit threshold percentage.
• An isotope peak is not found if its intensity, relative to the monoisotopic ion’s intensity, is
more than the specified intensity deviation percentage away from the theoretical relative
intensity of the isotope ion.
• An isotope peak is found if its measured m/z is less than the specified mass deviation
amount away from its expected m/z.
To specify threshold and deviation parameters, see “Editing the Processing Page” on page 277.
The Isotopes page displays the isotopes in one of three ways:
• All Isotopes
• Multi-Isotopes
• Individual Isotopes
All isotopes pages use a shortcut menu to specify how you want the data displayed. See
“ Isotopes page shortcut menu commands” on page 509.
All Isotopes
The All Isotopes view displays a composite of all isotopes found in the compound. The
application scales the window with respect to the most intense isotope. The most intense
isotope is usually the first isotope unless you are using halogenated compounds. The
application displays the measured peak as a solid red line; the application displays the
expected peak as a dashed blue line.
The application displays these headers for the All Isotopes view:
Processing
filter
File name
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Scan range for
the isotopes
Retention time
range for all
scans
Number of
averaged
scans
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Figure 142. Isotopes page with stacked spectra for all isotopes
Expected m/z of the isotope
Measured
spectrum
Expected
spectrum
Figure 143. Isotopes page with overlaid spectra for all isotopes
Expected spectrum in blue
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Measured spectrum in red
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Multi-Isotopes
The Multi-Isotopes view displays individual plots for each isotope. You can individually stack
or overlay the plots for each isotope.
The application displays these headers for the Multi-Isotopes view:
Scan range for
the isotopes
Retention time
range for all
scans
Number of
averaged
scans
Figure 144. Isotopes page with overlaid spectra for multi-isotopes
Expected spectrum in blue
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Measured spectrum in red
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Figure 145. Isotopes page with stacked spectra for multi-isotopes
Expected spectrum in blue
Measured spectrum in red
Figure 146. Isotopes page with stacked and overlaid spectra for multi-isotopes
Expected spectrum in blue
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Individual Isotopes
The individual isotopes view displays the expected and measured peaks for a single isotope.
The application displays these headers for the individual isotopes view:
Scan range for
the isotopes
Retention time range
for all scans
Number of averaged
scans
Expected m/z
for isotope 5
Measured m/z
for isotope 5
Delta between
expected and
measured m/z
Figure 147. Isotopes page with overlaid spectra for a single isotope
Expected spectrum in blue
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Measured spectrum in red
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Figure 148. Isotopes page with stacked spectra for a single isotope
Expected spectrum in blue
Measured spectrum in red
Table 105. Isotopes page shortcut menu commands
Thermo Scientific
Command
Description
Reset Scaling
Resets the original scaling after a zoom operation.
Copy to Clipboard
Copies the graphic display to the Clipboard.
Display Overlay Spectra
Display Stack Spectra
Overlays the two spectrum displays, or stacks the simulated
spectrum and the peak apex spectrum.
Show/Hide Noise Label
Adds a noise label to each peak. Expected isotope peaks
(displayed in blue) do not display a noise label.
Show/Hide Resolution
Label
Adds a resolution label to each peak. Expected isotope peaks
(displayed in blue) do not display a resolution label.
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Fragments
The Fragments page displays the maximum number of fragments as specified in the screening
method. See “Editing the Processing Page” on page 277.
If there are no fragments defined in the screening library for the compound, you can add
fragments to the screening library. See “To add a fragment to a target peak” on page 96.
The Fragments page displays the fragments in one of two ways:
• All Fragments
• Individual Fragments
All Fragments
The All Fragments view displays a composite of all fragments found in the compound. The
application displays the measured peak as a solid red line; the application displays the
expected peak as a dashed blue line.
The application displays these headers for the All Fragments view:
Minimum number
of fragments
specified in the
method
Processing
filter
File name
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Figure 149. Fragments page with overlaid spectra for all fragments
Figure 150. Fragments page with stacked spectra for all fragments
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Individual Fragments
The individual fragments view displays the expected and measured peaks for a single
fragment.
The application displays these headers for the individual fragments view:
Minimum number of fragments
specified in the method
Expected m/z
for fragment 1
Measured m/z
for fragment 1
Delta between
expected and
measured m/z
Figure 151. Fragments page with overlaid spectra for a single fragment
Intensity threshold specified in
the method
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Figure 152. Fragments page with stacked spectra for a single fragment
Table 106. Fragments page shortcut menu commands
Thermo Scientific
Command
Description
Reset Scaling
Resets the original scaling after a zoom operation.
Copy to Clipboard
Copies the graphic display to the Clipboard.
Display Overlay Spectra
Display Stack Spectra
Overlays the two spectrum displays, or stacks the simulated
spectrum and the peak apex spectrum.
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Library
The Library page displays the matching library spectrum (in blue) and the experimental
spectrum (in black). The resulting score percentage from a library search match must be
higher than your specified threshold value to identify or confirm the presence of a compound.
See “Editing the Processing Page” on page 277.
The application scales both the matched library spectrum and the highest peak in the
experimental spectra at 100 percent intensity and displays the resulting neutral loss (NL)
value for the matched library entry name on the right of the plot.
The application displays these headers for the individual adducts:
Library match name
Adduct
Library score percentage
Formula
Library match rank
Figure 153. Library page with stacked spectra
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Figure 154. Library page with overlaid spectra
Table 107. Library page shortcut menu commands
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Command
Description
Reset Scaling
Resets the original scaling after a zoom operation.
Copy to Clipboard
Copies the graphic display to the Clipboard.
Display Overlay Spectra
Display Stack Spectra
Overlays the two spectrum displays, or stacks the simulated
spectrum and the peak apex spectrum.
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Working in the Local Method View
Working in the Local Method View
A local method is a copy of a master method associated with a batch. You can edit only the
local copy of the method, or you can edit the master method and overwrite the local copy
with the edited master method.
In the Local Method view, you can edit the local method parameters. A local method is a copy
of a master method associated with a batch. Local methods are named Batch_MasterMethod.
 To open the Local Method View
1. Click Analysis in the navigation pane.
2. In the Analysis navigation pane, click Local Method.
The Local Method view for the currently selected batch opens.
You can edit many of the method parameters in a local method. Editing the local method
does not affect parameters in the master method.
For detailed descriptions of quantitation method parameters, see “Editing a Master
Method” on page 144 (Chapter 5).
For detailed descriptions of target screening method parameters, see “Editing a Master
Method” on page 273 (Chapter 6).
3. Enter any local changes to the method.
4. When you have finished editing the local method, choose File > Save.
5. To process the batch or create new reports with the edited local method, return to the
Batch View and submit the batch.
 To overwrite the local method with the master method in the Batch View
In the Batch View, click Update.
The application overwrites the local method with the master method of the same name.
You can use this feature to overwrite an edited local method with the original master
method or to overwrite the local method with an updated master method.
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Figure 155. Local Method view of a quantitation method
Figure 156. Local Method View of a screening method
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Working in the Report View
Working in the Report View
The Report View displays example reports for the current batch. You must have an open
batch to use the features in the Report View.
Follow these procedures:
• To open the Report View
• To preview a report
• To generate a report as a PDF, an Excel, or a CSV file
• To print a report
• To display a generated report
• To edit a report template
• To create a new report template
 To open the Report View
Click Report View in the navigation pane.
The application opens the Reporting view. For detailed descriptions of all parameters, see
“Report View” on page 522.
 To preview a report
1. In the Template pane, select a report template.
The template list shows all the report templates that you configured in the Configuration
console. See “Specifying the Reports” on page 72.
Figure 157. Example template list
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2. Click Preview,
Using the Analysis Mode
Working in the Report View
.
The application opens the Report Designer, showing the report information for the
current batch in the selected report template format.
For details about using the Report Designer, see “Working in the Report Designer” on
page 524.
 To generate a report as a PDF, an Excel, or a CSV file
1. In the Template pane, select a report template.
2. Select the check box for each of the file types that you want to create: PDF, Excel, or
CSV.
3. Click Generate,
.
The application does the following:
• Displays a green progress bar as it generates the reports.
• Creates a report for the current batch as a PDF, an Excel, or a CSV file, using the
selected report template format.
• Adds information about the generated report to the Generated Reports pane.
For details about the Generated Reports pane, see “Report View” on page 522.
• Saves the report files to the …\TraceFinderData\32\Projects\batch\ReportOutput
folder.
 To print a report
1. In the Template pane, select a report template.
2. Select the check box for the Print file format.
3. Click Generate,
.
The application does the following:
• Creates a report for the current batch using the selected report template format.
• Prints the report to your default printer.
• Adds information about the generated report to the Generated Reports pane.
For details about the Generated Reports pane, see “Report View” on page 522.
• Saves the report files to the …\TraceFinderData\32\Projects\batch\ReportOutput
folder.
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 To display a generated report
In the Generated Reports pane, click View for the report you want to see.
Figure 158. Generated Reports pane showing a PDF report
Opens the generated file.
The application opens the output file.
 To edit a report template
1. In the Template pane, select a report template.
2. Click Design,
.
The application opens the Report Designer showing the template in an Excel spreadsheet.
Figure 159. Report Designer showing the template for the selected report
3. Use the features in the Report Designer to edit the template.
See “Working in the Report Designer” on page 524.
4. When you finish your changes, choose File > Save from the Report Designer menu bar.
 To create a new report template
1. Click New,
.
The application opens the Report Designer showing an empty template in an Excel
spreadsheet.
The Report Type is None.
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In the left pane, the spreadsheet lists all samples in the current batch and all compounds
in the method used for the batch.
Figure 160. Report Designer showing a new, empty template
2. Use the features in the Report Designer to create the report template.
See “Working in the Report Designer” on page 524.
3. When you finish your changes, choose File > Save from the Report Designer menu bar.
The Save Template dialog box opens.
Figure 161. Save Template dialog box
4. Type a name for the new report template and click OK.
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Report View
Use the features in the Report View to display example reports for the current batch.
Figure 162. Report View
Table 108. Report View parameters (Sheet 1 of 2)
Parameter
Description
Template
Displays all report templates.
Rules
Sheet Name
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Specifies each sheet in the report.
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Table 108. Report View parameters (Sheet 2 of 2)
Parameter
Rules
Description
Specifies the type of data used in each sheet in the selected report.
• Batch
• EachSample
• SampleType: SampleType
• CompoundType: CompoundType
• SampleCustomFormula:
Buttons
View Report
Templates
Displays the C:\TraceFinderData\32\Templates\ReportTemplates folder that contains
all report templates.
Opens the selected report template in the Report Designer.
Opens a blank report template in the Report Designer.
Opens the Report Designer showing the report information for the current batch in the
selected report template format.
PDF
Writes the generated report to a PDF file in the
…\TraceFinderData\32\Projects\batch\ReportOutput folder.
Excel
Writes the generated report to a PDF file in the
…\TraceFinderData\32\Projects\batch\ReportOutput folder.
CSV
Saves the generated report as a PDF file in the
…\TraceFinderData\32\Projects\batch\ReportOutput folder.
When the report contains multiple sheets, the application writes each sheet as a separate
CSV file.
Print
Prints the generated report to your default printer.
Generates the selected type of reports for the current batch using the selected report
template.
Generated Reports
Template
Report template used for the report. See “Example template list” on page 518.
Rule
Type of data used in each sheet of the report. See Rules.
Sample
For sample-level reports, the name of each sample in the report.
Output
Type of output specified for the report: PDF, Excel, CSV, or Print.
Generated Report File
Lists the output file name for each report in the …\TraceFinderData\32\Projects folder.
View
Displays the generated output file.
View Generated Reports Displays the C:\TraceFinderData\32\Projects folder that contains all report outputs.
Clear
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Removes all reports from the Generated Reports display. This does not delete the reports
from the C:\TraceFinderData\32\Projects folder.
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Working in the Report Designer
Use the features in the Report Designer to create or edit report templates.
The Report Designer supports reports from previous versions of the TraceFinder application.
Use one of the Excel template files (in C:\TraceFinderData\32\Templates\ReportTemplates).
Each template has an XLS file and a metadata file to support report generation. These
templates can support file sizes up to 70 MB that provide the following:
• A live preview of data
• Excel-like features:
–
Formulas
–
Text formatting
–
Rich content, including images, shapes, and charts
–
User interface layout with worksheet tabs and a ribbon
To create a report, combine the output from the Report Data Manager with the template file
using the Report Generator. After you have combined the data with the template, you can
print, preview your print job, or create a PDF or an Excel file.
With the Report Designer, you can do any of the following to create or edit a report template:
• Make changes to the template as you would in the Excel application.
• Add or remove graphics.
• Add repeated frames of many types.
• Format fonts, colors, and so forth.
• Add or edit formulas.
• Edit template text, headers, and so forth.
In addition to the procedures in this section, you can view video instructions at
http://mytracefinder.com/plugins/reporting/.
This section includes the following topics:
• Editing a Template
• Toolbar Reference
• Quick Tips
Note To edit or create a template, you must have an open batch.
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Editing a Template
Choose what type of report you want and which samples to include in the report, and then
use the Report View to combine the samples and templates into a report.
Use the following procedures:
• To insert graphics into a report template
• To insert a table
• To make changes to a table
• To format header text in the spreadsheet
• To format data in the report grid
• To format cells in the report grid
• To add repeated frames
 To insert graphics into a report template
1. Select cells where you want to place the item.
2. Click the Insert tab.
The Insert page displays the available objects for insertion.
3. Select an item from the toolbar to insert into the cells on the template.
• When you select a series of cells across rows and columns, the application inserts the
item into the selected area.
• When you select a single row of cells, the application inserts the graphic at a default
size.
Figure 163. Example of inserted graphic
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 To insert a table
1. Select a row in the report grid where you want to insert the table.
2. Click the Insert tab and then click the Table icon,
.
The Insert Table dialog box opens.
The left pane lists choices for the type of data that you want to include in the table. You
can select only one item from this list.
The right pane lists the specific parameters that you want to include for that type of data.
You can select as many parameters as you want. The table displays each selected parameter
as a table column.
For example, when you select to display data for a Sample, you can then select sample
parameters to include in the table, such as the raw data file name or sample type.
3. Select a data item in the left pane and then select the parameters for that data type that
you want to include in the table.
4. To edit the header for a table column, select the parameter in the parameters list on the
right, and then type new header text in the Header box in the Field Details area.
The default header name is the same as the parameter name.
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5. To move a column left or right in the table, select the parameter name and click the Up or
Down arrow.
The Up arrow moves the column one position to the left.
The Down arrow moves the column one position to the right.
6. To find the formula for a parameter, select the parameter.
The application displays the formula in the Formula box.
Parameter not selected
Parameter selected (blue background)
Details for selected parameter
7. To switch rows to columns for easier access to large amounts of data, create a pivot table
as follows:
a. Select the Pivot Table check box.
The Pivot Table area expands to display the pivot table options.
b. Select the Use Key check box for the row label.
c. Select the Use Key check box for the column label.
d. Select the operation that you want to use to calculate the aggregate value.
8. When you have made all your table selections, click OK.
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 To make changes to a table
1. Select the table in the report template.
2. Click the Insert tab, and then click the Table icon,
.
The Edit Table dialog box opens, displaying all of the available fields for the selected
template. The Edit Table dialog box is virtually identical to the Insert Table dialog box.
3. Edit the parameters for the table and click OK.
Follow the instructions in “To insert a table” on page 526.
 To format header text in the spreadsheet
1. Select the header in the spreadsheet table.
To change all headers, select an entire header row.
To change a single header, select only a single header cell.
Tip You can also use the SHIFT key to select sequential cells or the CTRL key to
select nonsequential cells anywhere in the grid.
2. Click the Home tab.
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3. Use the Font icons to change the font format.
 To format data in the report grid
1. Select the data you want to format.
To format all rows in a column, select only the first cell of data. Do not select the header
row.
To format a single cell of data, select only that cell.
Tip You can also use the SHIFT key to select sequential cells or the CTRL key to
select nonsequential cells anywhere in the grid.
2. Click the Home tab and use the toolbar icons to edit the font or cells as appropriate:
• Change the font or font size.
• Make the selected text bold.
• Make the selected text italics.
• Underline the selected text.
• Apply borders to the currently selected cells.
• Increase or decrease font size.
• Apply color to the background for selected cells.
• Change the font color.
 To format cells in the report grid
1. Select the cells you want to modify:
To change all cells in a row, select the entire row.
To change a single cell, select only that cell.
Tip You can also use the SHIFT key to select sequential cells or the CTRL key to
select nonsequential cells.
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2. Click the Home tab and use the Alignment or Cells toolbar icons to edit the cells.
3. To align the cell text to the top, center, or bottom of the cell, click
4. To align the cell text to the left, center, or right of the cell, click
.
.
5. To make all contents visible within a cell, click Wrap Text.
6. To join selected cells into one cell, click Merge Cells.
7. To insert cells, rows, or columns into the template, click Insert.
8. To delete rows or columns from the template, click Delete.
9. To change the row height or column width, organize sheets, or protect or hide cells, click
Format.
10. To highlight or emphasize useful cells based on specific criteria, click Conditional
Formatting to use data bars, color scales, or icon sets.
11. To show formulas for selected cells instead of the resulting value, click Show Formulas.
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 To add repeated frames
1. To define a repeat area, select the cells that you want to repeat.
You can repeat only one area per worksheet, but you can repeat it many times. You cannot
insert data tables beneath a repeated area. See “Example of repeated frames” on page 532.
2. Click the Insert tab and then click Repeat.
The Repeat Area Definition dialog box opens.
3. To filter the repeat area according to the filter criteria, type the string syntax in the Filter
String box.
4. Select to repeat for each compound, for each sample, or for both.
5. Define whether the repeat area repeats first for samples or first for compounds:
• To have the repeat area repeat first for samples and then for compounds, clear the
Compound Centric check box.
• To have the repeat area repeat first for compounds and then for samples, select the
Compound Centric check box.
6. To define the number of times to repeat horizontally before wrapping to the next row,
type a number in the Max Horizontal Repeats box.
7. To define the number of times to repeat vertically before inserting an auto-page break,
type a number in the Max Vertical Repeats Per Page box.
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8. To define the maximum suggested number of repeats, type a number in the Repeats in
Design Mode box.
This maximum number of repeats is intended to increase performance. When generating
an actual report, the application does not enforce this limit.
Figure 164. Example of repeated frames
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Toolbar Reference
The Report Designer includes three tabs that display toolbars.
• Home Toolbar
• Insert Toolbar
• Page Layout Toolbar
Home Toolbar
Use the options on the Home toolbar to modify fonts, align cell data, and format cells.
Table 109. Home toolbar options (Sheet 1 of 2)
Parameter
Description
Clipboard
Paste
Paste the contents of the Clipboard. You can also paste only formating or only a
formula.
Copy
Copy text or graphics to use in another place.
Font
Font and size
Change the font or font size.
Bold
Make the selected text bold.
Italic
Make the selected text italics.
Underline
Underline the selected text.
Border
Apply borders to the currently selected cells.
Font size
Increase or decrease font size.
Fill color
Apply color to the background for selected cells.
Font color
Change the font color.
Alignment
Align the cell text to the top, center, or the bottom of the cell.
Align the cell text to the left, center, or the right of the cell.
Wrap text
Make all contents visible within a cell.
Merge cells
Join selected cells into one cell.
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Working in the Report Designer
Table 109. Home toolbar options (Sheet 2 of 2)
Parameter
Description
Cells
Insert
Insert cells, rows, or columns into a template.
Delete
Delete rows or columns from a template.
Format
Change the row height or column width, organize sheets, or protect or hide cells.
Conditional Formatting
Based on specific criteria, highlight or emphasize useful cells using data bars, color
scales, and icon sets.
Show Formulas
Show formulas for selected cells instead of the resulting value.
Insert Toolbar
Use the options on the Insert toolbar to add graphics, plots, and other objects to a template or
report. You can also set up repeating objects and define functions.
Table 110. Insert toolbar options (Sheet 1 of 2)
Parameter
Description
Table
Table
Create a table to manage and analyze data.
Field
Edit the formula for a field by choosing functions and editing arguments.
Repeat
Repeat
Repeat text, cell, or graphic elements.
Refresh
Update the view to reflect recent changes.
Plots
Add a sample TIC.
Add a peak chromatogram.
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Table 110. Insert toolbar options (Sheet 2 of 2)
Parameter
Description
Add an ion overlay.
Add a spectral plot.
Add a comparative spectral plot.
Add a calibration curve.
An isotope plot displays the number of isotopes found, the score, a pass/fail flag, and a plot of
the isotopes.
Add a fragment plot.
Illustrations
Pictures
Insert a picture from a file.
Page Layout Toolbar
Use the options on the Page Layout toolbar to adjust margins, orientation, paper size, and
page breaks. To see your changes, click Print Preview.
Table 111. Page Layout toolbar options (Sheet 1 of 2)
Thermo Scientific
Command
Description
Print Preview
View your report as the application will print it.
Page Setup
Define page details.
Margins
Select page margins for the current view or the entire document.
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Table 111. Page Layout toolbar options (Sheet 2 of 2)
Command
Description
Orientation
Switch the pages from portrait to landscape view.
Size
Choose a page size for the current view or the entire document.
Breaks
Specify where a new page begins in the printed copy.
Template Properties
Opens the SpreadsheetGear Workbook Explorer where you can
specify template options.
Quick Tips
 To insert items in Report Designer
• Insert a data table when the selected cell is above or below any other table, but not in the
same row as a field. You cannot insert tables in repeat areas.
• Insert a data field when the selected cell is not on the same row as a table.
The Insert toolbar provides these options:
• Table – insert or edit data table
• Field – insert or edit data field
• Use these shortcut keys:
CTRL+T
Insert a table.
CTRL+T
Edit a table when the selected cell is inside a table.
CTRL+SHIFT+T
Insert or edit a field.
CTRL+R
Insert or edit a repeating area.
 To format cells and group headers
Because the first row of a data table retains formatting information, edit the formatting of
the first row.
The application copies the formatting to all other rows.
For group header items, the application copies the formatting of the first group header to
the remaining group headers.
 To sort fields
Select a field, then click A-Z to sort on that field.
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Using the Audit Viewer
This chapter includes instructions about using the features of the Audit Viewer. For detailed
descriptions of parameters in the Audit Viewer, see “Audit Viewer” on page 546.
The TraceFinder application records all user access, including logging in, logging out, data
creation and editing (batches, methods, and templates), and manual integration. You can use
the Audit Viewer to view the resulting log files to track modifications to the data. When an
event requires confirmation (as specified in the Administrator Console), the Audit Viewer
records who confirmed each change to a batch, method, or template. When no confirmation
is required, then the Audit Viewer records the user who was logged in when the change
occurred.
In the Administration Console, a user with Auditing permissions can configure the auditing
service by specifying which events are logged, which events require confirmation, a list of
default reasons for a specific event, and whether a user can submit a custom reason. To use the
auditing administration tools, refer to the instructions in the TraceFinder Administrator
Console User Guide.
The application creates the following audit trail log files:
• Application: Records all user access, such as starting and stopping the application, logging
in, logging out, or accessing or saving data in batches and methods. The application saves
the data in the following log file: C:\Thermo\TraceFinder\3.2\Logs\AuditLog.adb.
• Master Method: Records all user interactions with master methods, such as creating,
opening, or editing a master method. The application saves the data in the following log
file: C:\TraceFinderData\32\Methods\MasterMethodName\AuditLog.adb.
• Batch Template: Records all user interactions with batch templates, such as creating,
opening, or editing a batch template. The application saves the data in the following log
file: C:\TraceFinderData\32\Templates\Batches\BatchTemplateName\AuditLog.adb.
• Batch: Records all user interactions with batches, such as creating, opening, editing,
acquiring, processing, or generating reports for a batch. The application saves the data in
the following log file:
C:\TraceFinderData\32\Projects\SubFolder\BatchName\AuditLog.adb.
The Audit Viewer displays all saved audit log files, and you can filter and sort the audit data.
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Use the following procedures:
• To access the Audit Viewer
• To select an audit log
• To view only application, method, batch, or batch template events
• To create a filter for audit log events
• To view audit event details
• To create a filter for an audit log history
• To display the history for an event
 To access the Audit Viewer
Choose Tools > Audit Trail from the TraceFinder main menu or click the Audit Viewer
icon,
.
The Audit Viewer opens. For detailed descriptions of parameters in the Audit Viewer, see
“Audit Viewer” on page 546.
Note The Tools > Audit Trail menu command always opens to application log files,
whereas the Audit Viewer icon is context sensitive and opens to the appropriate type
of log files (application, method, batch, or batch template).
 To select an audit log
1. Click the Open Audit Log icon,
.
The application opens the Audit Log Selection dialog box.
2. Expand a log folder to select an application, batch, method, or batch template audit log
file, and click OK.
The Audit Viewer displays the contents of the selected audit log file, as in this example for
a method.
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 To view only application, method, batch, or batch template events
1. In the Active Log list, select an Active Log file.
• Application logs include application and security events.
• Method logs include application and method events.
• Batch logs include application, method, and batch events.
• Batch template logs include application and batch template events.
The Audit Viewer displays icons for each of the event types included in the log file.
2. Click an icon to turn the display on or off.
In this example, the Events pane displays Batch and Method events and hides Application
events.
Note There is no icon for security events in an application log file. You cannot hide
the display of security events.
 To create a filter for audit log events
1. In the Events pane, click the Create New Filter icon,
.
The Filter Editor dialog box opens.
2. In the View box, type a name for the new filter.
You can also leave the View box empty when you enter your filter criteria. When you
finish adding conditions and click OK (step 8), the application filters the current events
list based on the filter criteria you specify, but the filter is not saved. The Filter list in the
viewer identifies this filter as (Custom).
3. Click the Add icon,
.
The application adds a new, undefined condition to the Condition list.
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4. In the Field list, select one of the following field types.
5. In the Operator list, select one of the available operators.
The available operators depend on the field type that you selected.
6. In the Value box, type a value or select a value from the list.
• For the Date/Time field, type a numerical value in the Value box.
• For the User, Reason, Context, or Details field, type the appropriate text in the Value
box. This value is case sensitive.
• For the Type of Event field, select one of the following values.
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Note You can also click the Tokens icon,
, and select a token for the Value.
Tokens are predefined values, such as dates and sample or compound identifiers.
The Filter at the bottom of the dialog box displays the complete definition for the filter.
7. Repeat steps 3 through 6 for each condition that you want to include in your filter.
8. When you have added all your conditions, click OK.
The application creates the new filter with the specified conditions.
 To view audit event details
In the Events pane, select an event.
The Details pane displays key values based on the type of log you select.
Details for batch log files include the name of the batch.
Details for method log files include the name of the method and
the method type.
Details for batch template log files include the name of the batch
template, the location of the data repository, and the subproject
folder where the template was created.
Details for Application log files include whether the events are for a
batch or method, the location of the data repository, and, for a
batch, the subproject folder where the batch was created.
Details for Security log files include the authentication method
used (Windows Active Directory or local machine) and the
location of the administrator repository.
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 To create a filter for an audit log history
1. In the History pane, click the Create New Filter icon,
.
The Filter Editor dialog box opens.
2. In the View box, type a name for the new filter.
You can also leave the View box empty when you enter your filter criteria. When you
finish adding conditions and click OK (step 8), the application filters the current history
list based on the criteria you specify, but the filter is not saved. The Filter list in the viewer
identifies this filter as (Custom).
3. Click the Add icon,
.
The application adds a new, undefined condition to the Conditions list.
4. In the Field list, select one of the following field types.
5. In the Operator list, select from equals, less than/greater than, or contains.
The available operators depend on the field type that you selected.
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6. In the Value list, type or select a value from the list.
• For the Name, Context, or Details field, type the appropriate text in the Value box.
This value is case sensitive.
• For the OldValue or NewValue field, type a numerical value in the Value box.
• For the ChangeType field, select one of the following values.
• When the selected Field is ItemType, select one of the following values.
Note You can also click the Tokens icon,
, and select a token for the Value.
Tokens are predefined values, such as dates and sample or compound identifiers.
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The Filter at the bottom of the dialog box displays the complete definition for the filter.
7. Repeat steps 3 through 6 for each condition that you want to include in your filter.
8. When you have added all your conditions, click OK.
The applications created the new filter with the specified conditions.
 To display the history for an event
1. In the Events pane, select an event that has a selected check box in the History column.
Select an event that has the
History check box selected.
The History pane displays all unsaved (queued) actions for the selected event.
2. To limit the actions in the history list, select a filter from the Filter list.
See “To create a filter for an audit log history” on page 542.
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Figure 165. Example History filter
When you select this filter,
the History pane displays only these actions for the selected event:
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Audit Viewer
Use the Audit Viewer to view the audit log files to track user access and modifications to the
data.
Figure 166. Application log in the Audit Viewer
Figure 167. Batch log in the Audit Viewer
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Table 112. Audit Viewer parameters (Sheet 1 of 2)
Parameter
Description
Active Log
Name of the current audit log file.
Opens the Audit Log Selection dialog box where you can open a different audit log file.
You can select from these audit log files: application, batch, method, or batch template.
Refreshes the current audit log file in the viewer.
Show
Select to display only specific types of events in the Events list. The selected log file can
contain batch, method, and application events.
Events
Filter
Select a filter view to use for displaying the event log entries.
Opens the Filter Editor dialog box where you can create a filter view.
Opens the Filter Editor dialog box where you can edit the current filter view.
Deletes the current event filter view.
Log
Indicates an event that occurred at the main TraceFinder application level, such as
logging in or opening a batch.
Indicates an event that occurred in the Administration Console.
Indicates an event that occurred in a method template.
Indicates an event that occurred in a method.
Indicates an event that occurred in a batch.
Date/Time
Time stamp of the event.
User
When an event requires confirmation (as specified in the Administrator Console), User is
the user who confirmed each change to a batch, method, or template.
When no confirmation is required, User is the user who was logged in when the change
occurred.
Computer Name
Name of the computer on which the application recorded the event.
Event Type
Specific event that triggered the log file entry. For a complete list of event types, refer to
the TraceFinder Administration Console User Guide.
Context
Name of the sample, batch, method, or application version where the event occurred.
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Table 112. Audit Viewer parameters (Sheet 2 of 2)
Parameter
Description
History
Indicates that there is a history log of queued actions for the event.
Reason
Default or custom reason that the user entered for the event.
Details
Key/Value
Identifying parameters and their values for the selected auditing event. These key
parameters are different for each type of auditing event.
History
Filter
Select a filter view to use for displaying the change history.
Opens the Filter Editor dialog box where you can create a filter view.
Opens the Filter Editor dialog box where you can edit the current filter view.
Deletes the current history filter view.
Order
The sequence of actions that occurred.
Change Type
One of the predefined ChangeType values. See ChangeType.
Context
Name of the specific value on which the action occurred.
Item Type
One of the predefined ItemType values. See ItemType.
Item Name
A user-defined name for the filter.
Old Value/New Value Original parameter value and the changed value.
Details
Key/Value
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Identifying parameters and values for the selected history event.
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A
Using Quick Acquisition
Use the quick acquisition feature to quickly submit samples from any mode in the
application.
Note The Quick Acquisition feature is available only when you activate it in the
Configuration console. See “Quick Acquisition” on page 56.
 To run a quick acquisition
1. Choose Tools > Quick Acquire Sample from the main menu or click the Quick Acquire
Sample icon,
.
The TraceFinder Quick Acquisition window opens.
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2. To create the sequence of samples that you want to acquire, do any of the following:
• Use the Sequence buttons on the toolbar to open and save Xcalibur sequence (.sld) files.
Icon
Description
Replaces the current sequence with a new sequence that contains
one Unknown sample.
Opens the Open dialog box where you can open a saved SLD file.
Saves the current sequence as an SLD file in the
C:\TraceFinderData\Sequences folder.
Opens the Save As dialog box where you can save the current
sequence to a new file name or location.
• Use the Samples buttons on the toolbar to create a sequence of samples.
Icon
Description
Adds the specified number of new, empty samples to the end of
the sample list.
Inserts a new, empty sample or samples above the selected sample.
Removes the selected samples from the sample list.
• (Optional) Use the Tools buttons on the toolbar to open a qualitative browser or the
NIST library browser.
Icon
Description
Opens the qualitative explorer that you configured as your default
qualitative explorer in the Configuration console. See “Launching
a Qualitative Explorer” on page 16.
Opens the NIST library browser. See “Launching the NIST
Library Browser” on page 15.
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3. When you have completed your sequence of samples, click either of the Acquire buttons.
Icon
Description
Submits only the selected samples for acquisition, processing, or
report generation.
Submits the sequence for acquisition, processing, or report
generation.
The application submits the samples for acquisition, processing, and report generation.
See “Acquisition Page” on page 349.
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Isotopic Pattern Details
The TraceFinder application calculates an isotopic pattern score based on the settings in the
method. The application displays this score in the Data Review view. This appendix describes
the isotopic distribution concepts and provides calculation details with examples for the
isotopic pattern score.
Contents
• Isotopic Distribution in Exact Mass Spectra
• Isotopic Pattern Score Calculations
Isotopic Distribution in Exact Mass Spectra
To determine the elemental compositions, the TraceFinder application uses an isotopic
pattern matching algorithm that considers the isotope accurate mass and intensity ratios.
Using a single exact mass, usually the monoisotopic mass of a measured isotope pattern, the
application calculates all possible elemental compositions that lie within a mass tolerance
window. You can filter this list of possible elemental compositions and narrow the results by
using the natural isotopic distribution of elements.
Natural Isotopic Distribution
The following table lists the natural isotopic distribution of the most common elements.
Table 113. Natural isotopic distribution (Sheet 1 of 2)
Element
Isotope
Isotope
order
Exact mass
Hydrogen
1
Carbon
Nitrogen
Thermo Scientific
H
A0
1.0078
2H
A1
2.014102
12
C
A0
12.0
13
C
A1
13.003355
14N
A0
14.003074
15N
A1
15.00109
Mass difference
Abundance (%)
99.9985
+1.006302
0.015
98.890
+1.003355
1.110
99.634
+0.998016
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Isotopic Distribution in Exact Mass Spectra
Table 113. Natural isotopic distribution (Sheet 2 of 2)
Element
Isotope
Isotope
order
Exact mass
Oxygen
16O
A0
15.994915
17
O
A1
16.999132
+1.004217
0.038
18O
A2
17.999161
+2.004246
0.200
Fluorine
19F
A0
18.99840
100
Phosphorus
31
P
A0
30.971459
100
Sulfur
32S
A0
31.972071
95.020
33S
A1
32.971459
+0.999388
0.750
34
S
A2
33.967867
+1.995796
4.210
36S
A4
35.967081
+3.995010
0.020
Mass difference
Abundance (%)
99.762
where:
• A0 represents the monoisotopic peak, which is the most abundant and usually the isotope
with the lowest mass.
For example: 1H, 12C, 14N, 16O, 19F, 31P, and 32S
• A1 represents the isotope where one atom in the molecule is statistically replaced by
another atom approximately 1 amu heavier.
For example: 2H, 13C, 15N, 17O, and 33S
• A2 represents the isotope where:
Two atoms in the molecule are statistically replaced by two other atoms, each
approximately 1 amu heavier.
–or–
One atom is replaced by another atom approximately 2 amu heavier.
For example: 18O and 34S
• A3 represents the isotope where:
Three atoms in the molecule are statistically replaced by three other atoms, each
approximately 1 amu heavier.
–or–
One atom is replaced by another atom approximately 1 amu heavier and one atom is
replaced by another atom approximately 2 amu heavier.
–or–
One atom is replaced by another atom approximately 3 amu heavier.
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• A4 represents the isotope where:
Four atoms in the molecule are statistically replaced by four other atoms, each
approximately 1 amu heavier.
–or–
Two atoms are replaced by two other atoms, each approximately 1 amu heavier, and one
atom is replaced by another atom approximately 2 amu heavier.
–or–
Each atom of the two atoms is replaced by another atom approximately 2 amu heavier.
–or–
One atom is replaced by another atom approximately 1 amu heavier, and one atom is
replaced by another atom approximately 3 amu heavier.
–or–
One atom is replaced by another atom approximately 4 amu heavier.
For example: 36S
• Mass difference is the difference in mass between the A0 isotope and another isotope (A1,
A2, A3, A4, and so on) of the same element.
• Abundance is the percentage of occurrence of each isotope normally in nature.
In the following figure, the x axis shows the mass difference of A1 relative to the monoisotopic
peak (A0) of the 13C, 15N, and 33S isotopes. The y axis shows relative abundance in intensity.
Figure 168. Mass difference and abundance of A1 relative to A0
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Isotopic Pattern Details
Isotopic Distribution in Exact Mass Spectra
In the following figure, the x axis shows the mass difference of A2 relative to the monoisotopic
peak (A0) of the 18O, 34S, and 13C2 isotopes. The y axis shows relative abundance in
intensity.
Figure 169. Mass difference and abundance of A2 relative to A0
Note For a particular isotopic spectrum, the mass difference is always the same between
the A0 isotope and the other isotopes (A1, A2, and so on) of each specific element, but the
intensity varies according to the composition of the molecule—that is, the number of each
element in the molecule.
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Isotopic Pattern Score Calculations
Isotopic Pattern Score Calculations
The TraceFinder application follows the same isotopic distribution logic as described in
“Isotopic Distribution in Exact Mass Spectra” on page 553, but in a different order and with
numerical limits and scores to optimize automatic processing. After the TraceFinder
application determines the possible elemental compositions for a particular compound of
interest, it calculates a expected isotope pattern for each elemental composition candidate and
an isotopic pattern score to represent the fit between the expected and measured isotope
patterns.
The following example describes the isotopic pattern score data and provides the score
calculation details for one specific data set.
Data Set Example
This example uses the Metribuzin target compound in an Apple_PosHCD__40_5_01
sample.
For this compound, note that the Isotopic Pattern Score column shows 90% and the Num
Isotopes Matched column shows “2 of 3” in the Compounds pane in the Data Review. The
compound’s formula is C8H14N4OS and its adduct is H, so the modeled isotopic pattern is
C8H15N4OS.
Figure 170. Isotopic data for Metribuzin
In the Spectrum pane, click the Isotopes tab and zoom in to view the expected isotopic
pattern spectrum compared to the acquired, measured spectrum. The resulting isotopic
pattern score should correlate to a visual inspection of the difference between the expected
isotope display and the measured display for the target compound.
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Figure 171. Isotopic pattern spectra (stacked)
Expected
spectrum
Measured
spectrum
For this example, the processing method used to process the data contains the following
isotopic pattern settings for target screening:
• Fit threshold = 90%
• Allowed Mass Deviation = 5 ppm
• Allowed Intensity Deviation = 10%
• Use Internal Mass Calibration = Cleared
The data for the Metribuzin compound is as follows:
Measured
Expected
A0 m/z = 215.09602
A0 m/z = 215.09611
A0 Noise = 1482
–
A0 intensity = 4.75E4
A0 intensity = 8.55E5
Because the measured and the expected spectra have different intensities, the spectral noise
threshold must proportionally apply to the expected spectrum to decide which peaks are
expected in the measured data.
Noise threshold (expected) = Noise of A0 (measured)  Intensity of A0 (expected) 
Intensity of A0 (measured)
Following the previous formula, the expected noise threshold is 1482 8.55E5  4.75E4 =
2.6676E4.
The expected ions in the measured spectrum are those whose intensities are above the
expected noise threshold. The following tables lists the ions in the expected spectrum. A “”
in the Above Threshold column indicates the expected ions.
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Table 114. Ions in expected spectrum
Thermo Scientific
Isotope
order
m/z
(expected)
Intensity
(expected)
Above threshold
Present in measured
spectrum
A0
215.09611
8.55E5

Yes
A1
216.09945
7.50E4

Yes
A2
217.09191
3.86E4

Yes
A3
218.09521
3.39E3
No
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Calculating Mass and Intensity Deviations
The expected number of ions is 3, as shown by those ions with a “” in the Above Threshold
column of the Ions in expected spectrum table. These are the ions you focus on for the
scoring calculations. This number “3” shows as the value of y in the Num Isotopes Matched
column of the Compounds pane in the Data Review. It indicates the number of expected
isotopic pattern peaks based on the Fourier transform (FT) noise in the spectrum.
In this case, you expect to see the three most intense expected peaks in the measured
spectrum. The masses of those peaks are (in order of intensity from high to low): 215.09611,
216.09945, and 217.09191. When the measured spectrum is more intense or the noise level is
lower, you find more peaks passing the noise threshold and expected in the measured
spectrum, eventually including other isotopic peaks.
The following table shows the mass deviation (delta m/z) data for each of the expected ions.
Table 115. Mass deviation data for the expected ions
Isotope order
m/z (expected)
m/z (measured)
Delta m/z (ppm)
A0
215.09611
215.09602
–0.42
A1
216.09945
216.09879
–3.05
A2
217.09191
217.09712
24
where:
Delta m/z (ppm) = 1 000 000  ([m/z (measured) – m/z (expected)]  m/z (expected))
For example:
1 000 000  ([216.09879 – 216.09945]  216.09945)] = –3.05 ppm
Tip You can see the expected, measured, and delta m/z values on the Isotopes page of the
Spectrum pane. The MS page (see “Isotopic pattern spectra (stacked)” on page 558)
displays the profile measured m/z values, whereas the Isotopes page displays the centroid
measured m/z values, which might be different.
If you want more precision, you can see extra decimal digits for the A0 m/z values in an
exported data file.
If the absolute value of the Delta m/z is less than 5 ppm (the Allowed Mass Deviation value set
in the processing method), the TraceFinder application determines that this ion is
found—that is, the ion is present in the measured spectrum. For this data set example, the
application finds only the A0 and A1 ions, so “2” shows as the value of x in the Num Isotopes
Matched column of the Compounds pane in the Data Review. The application does not find
the A2 expected ion because the absolute value of its Delta m/z of 24 ppm is much higher
than 5 ppm.
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Note You can see from zooming in on the isotopic pattern spectra (see “Isotopic pattern
spectra (stacked)” on page 558) that there are measured peaks in the measured spectrum
closely corresponding to the first two expected ions, but there is not a measured peak
closely corresponding to the 217.09191 expected ion.
The following table lists the intensity deviation (delta intensity) data for each of the expected
ions, relative to the A0 ion’s expected intensity of 8.55E5 and measured intensity of 4.75E4.
Table 116. Intensity deviation data for the expected ions
Isotope
order
m/z (expected)
Intensity
(expected)
Relative intensity
(expected, %)
Intensity
(measured)
Relative intensity
(measured, %)
Delta
intensity
A0
215.09611
8.55E5
100
4.75E4
100
0
A1
216.09945
7.50E4
8.77
8.75E3
18.42
9.65
A2
217.09191
3.86E4
4.51
3.47E4
73.05
68.54
where:
• Relative intensity (expected and measured) values are derived from the isotopic pattern
spectra (see “Isotopic pattern spectra (stacked)” on page 558). Each value is a percentage
of the isotope’s intensity relative to the A0 ion’s intensity.
For example: 7.50E4 8.55E5 = 8.77%
• Delta intensity = Relative intensity (measured) – Relative intensity (expected)
For example: 18.42 – 8.77 = 9.65
In this example, the absolute values of the Delta m/z for the A0 and A1 ions (see “ Mass
deviation data for the expected ions” on page 560) are both less than the Allowed Mass
Deviation of 5 ppm; therefore, the application considers that these two ions are present in the
measured spectrum. The delta intensity of the A1 isotope ion is close to the Allowed Intensity
Deviation of 10% and the delta intensity of the A2 isotope ion is much higher (see “ Intensity
deviation data for the expected ions” on page 561).
The TraceFinder application determines the isotopic pattern score value from a combination
of the mass and intensity deviations between the expected and the measured spectra. In this
case, the application reduces the isotopic pattern score value down to 90 from 100 to reflect
the marginal quality of the intensities of the A1 and A2 isotopes and to penalize for not
finding the A2 isotope.
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Isotopic Pattern Details
Isotopic Pattern Score Calculations
Calculating Isotopic Pattern Score
To score the fit for an isotopic pattern, the TraceFinder application calculates each expected
ion’s fit and then combines the individual fit scores, weighted by their expected intensities.
For each expected ion peak, the application measures the m/z and intensity differences
between the expected and the measured patterns. It then normalizes those differences
(normalized deviation values) to the maximum allowed mass and intensity deviation values set
in the processing method. The application then sums the normalized differences by vector
addition (see Vector sum of intensity (I) and mass (M) deviations).
Figure 172. Measured and expected patterns
Figure 173. Vector sum of intensity (I) and mass (M) deviations
Vector sum
This example starts first with the intensity deviations. The Allowed Intensity Deviation value
set in the processing method is 10, so this is the normalization value. As shown in “ Intensity
deviation data for the expected ions” on page 561, the delta intensity value for the A1 isotope
is close to 10%, resulting in a normalized intensity deviation close to 1.0.
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B Isotopic Pattern Details
Isotopic Pattern Score Calculations
Normalized Intensity Deviation
The following table lists the normalized intensity deviation data for each of the expected ions.
Table 117. Normalized intensity deviation data for the expected ions
Isotope
order
m/z (expected)
Delta
intensity
Allowed
intensity
deviation (%)
Normalized intensity
deviation
A0
215.09611
0
10
0  10 = 0.0
A1
216.09945
9.65
10
9.65  10 = 0.965
A2
217.09191
68.54
10
68.54  10 = 6.854
Next are the mass deviations. For mass deviations, you can control two settings in the
processing method:
• The first setting is the Allowed Mass Deviation that functions as an outer limit in the
same way as the Allowed Intensity Deviation functions as a limit for the intensity.
• The second setting is the Use Internal Mass Calibration check box. If you do not select
this check box in the method, then the application considers any mass value within
2 ppm of the expected m/z as a perfect match (no deviation). If you select this check box,
then the application considers only a mass value within 1 ppm of the expected m/z as a
perfect match.
In this example, the Allowed Mass Deviation value set in the processing method is 5 ppm and
the Use Internal Mass Calibration check box is cleared. The mass normalization is a bit more
complex than the intensity normalization because mass values < 2 ppm (Use Internal Mass
Calibration setting) from the expected m/z are considered to have no deviation from theory;
however, for values between 2 and 5 ppm (Allowed Mass Deviation value) from the expected
m/z, the normalized deviation varies from 0 to 1.
The calculated normalized mass deviation value is as follows:
• 0 if absolute value (Delta m/z) < 2 ppm
where 2 ppm is the value from the Use Internal Mass Calibration setting.
• [absolute value (Delta m/z) – 2 ppm] (5 ppm – 2 ppm) if
absolute value (Delta m/z) 2 ppm
where 2 ppm is the value from the Use Internal Mass Calibration setting and 5 ppm is the
Allowed Mass Deviation value.
In this case, the absolute value of the mass deviation for the A0 ion is less than 2 ppm;
therefore, its normalized mass deviation value is 0.
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Isotopic Pattern Details
Isotopic Pattern Score Calculations
Normalized Mass Deviation
The following table lists the normalized mass deviation data for each of the expected ions.
Table 118. Normalized mass deviation for each of the expected ions
Isotope
order
m/z
(expected)
m/z
(measured)
Delta m/z (ppm)
Internal
calibration (ppm)
Allowed mass
deviation (ppm)
Normalized mass
deviation
A0
215.09611
306.10356
–0.42
2
5
0
A1
216.09945
307.10691
–3.05
2
5
0.35
A2
217.09191
308.11324
24
2
5
7.33
For example: [(24 – 2)] (5 – 2) = 7.33
To calculate the combined deviations, the application uses the Pythagorean theorem to
calculate the vector sum of the normalized deviations. The calculation for the vector sum is as
follows:
Vector sum = Square root [(Normalized intensity deviation)2 + (Normalized mass deviation)2].
However, if the vector sum > 1, then set it to 1.
Calculated Vector Sum
The following table lists the vector sum data for each of the expected ions.
Table 119. Calculated vector sum
Isotope
order
m/z (expected)
Normalized intensity
deviation
Normalized mass
deviation
Vector sum
A0
215.09611
0
0
0
A1
216.09945
0.965
0.35
1
A2
217.09191
6.854
7.33
1
To calculate the final score, you must weigh the vector sum values and then express the result
as a percentage value. Each ion’s weighting contribution to the final isotopic pattern score is
proportional to its intensity.
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B Isotopic Pattern Details
Isotopic Pattern Score Calculations
Weighting Factor Calculations
The following table lists the weighting factor of each of the three expected ions.
Table 120. Weighting factor calculations
Isotope order
m/z (expected)
Intensity (expected)
Weighting factor for final score
A0
215.09611
8.55E5
0.8827
A1
216.09945
7.50E4
0.0774
A2
217.09191
3.86E4
0.0399
Sum = 9.686E5
Sum = 1.000
The weighting factor of each individual ion = Intensity of each ion  Sum of intensities of all
expected ions
For example: 8.55E5 9.686E5 = 0.8827
When not all of the expected ions are present in the measured spectrum, the application
applies a penalty value (1, 2, or 4) to the weighted deviation of each missing ion, lowering the
final isotopic pattern score even further. The penalty value depends on how strong the ion
signal is expected to be in the measured spectrum. For the A2 ion that is not found, the
application sets its penalty to a value of 1, causing its vector sum value of 1 (in Table 119 on
page 564)to be replaced with the penalty value of 1 (in Table 121). In this case, it is the same
number, but for other cases, the penalty value might be different from the vector sum value.
Calculated Isotopic Pattern Score
The following table lists the calculated isotopic pattern score using the weighting factors.
Table 121. Calculated isotopic pattern score
Isotope
order
m/z
(expected)
Deviation (vector
sum or penalty)
Weighting factor
Weighted deviation
A0
215.09611
0 (vector sum)
0.8827
0
A1
216.09945
1 (vector sum)
0.0774
0.0774
A2
217.09191
1 (penalty)
0.0399
0.0399
Sum = 0.12
where:
• Weighted deviation of each individual ion = Deviation  Weighting factor
For example: 1  0.0774 = 0.0774
• Isotopic pattern score = 100% (1.0 – Sum of all weighted deviation values)
For this example, the calculated isotopic pattern score of 100% (1.0 – 0.12) is 88,
which is close to the 90 score displayed in the application.
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Isotopic Pattern Details
Isotopic Pattern Score Calculations
Note Use these calculations to approximate the score displayed in the application.
The calculated score might not match exactly the score in the application because some
internal calculation details are not listed here or there is a discrepancy due to decimal digit
rounding.
In certain cases, closely matching isotopes exist because heavier isotopes contribute to the
isotopic pattern observed in the mass spectra. For example, the isotopes 206.0941 and
206.1006 result from the contribution of one heavier isotope of carbon and one heavier
isotope of nitrogen, respectively, together making up the split A1 isotopic peak. When the
application performs isotopic pattern scoring, this situation appears as a main isotopic
peak with a smaller peak to the side whose m/z is included in the calculations.
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B Isotopic Pattern Details
Isotopic Pattern Score Calculations
Finding the Noise Value
 To find the noise value associated with a mass spectral peak
1. On the Isotopes page of the Spectrum pane, to view the expected spectrum stacked above
the measured spectrum, right-click the spectrum plot area and choose Display Stack
Spectra from the shortcut menu.
2. Zoom in to the peak of interest.
As an example, see “Isotopic pattern spectra (stacked)” on page 558 for the compound
Metribuzin.
3. To view the averaged noise value (N) for a peak in the measured spectrum, right-click the
spectrum plot area and choose Show Noise Label from the shortcut menu.
Noise
In this example, the averaged noise value for the peak is 1579.
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C
Using Copy Down and Fill Down
This appendix describes the Copy Down and Fill Down commands that you can use to make
entering column values easier.
• Use the Fill Down command for the Filename, Sample Name, Sample ID, and Vial
Position columns.
• Use the Copy Down command for the Sample Type, Vial Position, Injection Volume,
Conv Factor, Level, Comment, and other columns.
Follow these procedures:
• To automatically copy column values
• To automatically enter sequential column values
• To use Copy Down or Fill Down for a range of samples
 To automatically copy column values
1. Select the cell whose value you want to copy to all cells below it.
Observe the difference between a selected and nonselected cell.
Selected
Not selected
2. Right-click and choose Copy Down from the shortcut menu.
The value is copied to all rows below the selected row.
 To automatically enter sequential column values
1. Enter a value for the first row of the fill down sequence.
This does not have to be the first sample row. You can begin the fill down procedure from
any row in the sequence.
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Using Copy Down and Fill Down
2. Select the cell whose value is the first in the fill down sequence.
Observe the difference between a selected and nonselected cell.
Selected
Not selected
3. Right-click and choose Fill Down from the shortcut menu.
The application enters sequential column values starting with the value in the selected
row and ending with the last row in the column.
You can repeatedly use the Fill Down command to create multiple sequences.
When you use the Fill Down command for the Vial Position column with an autosampler
configured, the TraceFinder application knows the number of vial positions configured in
your autosampler and numbers the positions accordingly.
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C
Using Copy Down and Fill Down
 To use Copy Down or Fill Down for a range of samples
1. To select a range of sample values, do one of the following:
Drag your cursor to select a contiguous group of sample values.
–or–
Hold down the SHIFT key to select a contiguous group of sample values.
2. Right-click and choose the appropriate command from the shortcut menu.
The column values are copied or entered sequentially starting with the value in the first
selected row and ending with the last selected row.
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I
Index
Symbols
.cdb, defined 2
.csv, defined 2
.db, defined 2
.meth, defined 2
.pmd, defined 2
.raw, defined 2
.xml, defined 2
# Background Scans parameter
Detect page 188
Genesis peak detection 44, 298
% Test parameter 222
%CV parameter 456
%Diff parameter 456
%RSD parameter 456
A
Acquire a New Raw Data File parameter 134
Acquisition command 29
Acquisition page
editing 146
Injection Volume parameter
Batch View 379
method development 149, 275
Instrument Method parameter 150, 276
Ion Range Calc Method parameter 150
Mass Precision parameter 150, 275
Method View 146
Active parameter
Data Review sample list 456
Identification page 159
Actual RT parameter 457
Add Compound command 90
Add Compound from Compound Database command 156
Add Group command 241
Add Sample command
Acquisition mode 334
Batch View sample list 381
Add This Mass as New Confirming Ion command 204
Add This Mass to Existing Quan Mass Ranges command 204
Thermo Scientific
Adduct parameter 457
Adduct parameter, Compound Database, target peak 103
Allowed Intensity Deviation parameter 208, 287
Allowed Mass Deviation parameter 208, 286
Amount parameter 217
Amplifier parameter 283
Analysis command 29
Application Configuration command 32
Area Noise Factor parameter
Detect page 191
ICIS peak detection 46, 300
Area parameter 457
Area Scan Window parameter
Detect page 192
ICIS peak detection 47, 301
Area Tail Extension parameter
Detect page 192
ICIS peak detection 47, 301
Area Threshold, event type 50, 304
Assay Type parameter
Method View
quantitation method 149
screening method 275
Associate a Raw Data File dialog box 137
Auto TSRM Update parameter 347
Autocalc Initial Events parameter, Avalon 194
automated background subtraction options 152
Automatically Create the Master Method parameter 133
Avalon detection algorithm 37
Avalon Event List dialog box 49, 303
B
background subtraction options 152
Background Subtraction Range Option parameter 154
Barcode Actual parameter 337, 380
Barcode Expected parameter 380
Baseline Window parameter
Detect page 191
ICIS peak detection 46, 300
Batch Selection view 316
TraceFinder User Guide
573
Index: C
Batch view 368
batches
Acquisition mode 312
Analysis mode 368
calibration 341
Best Match Method parameter 262
Browse in Raw File command 381
Bunch Factor, event type 50, 304
C
cal1-caln parameter 220
Calculated Amt parameter 457
Calculation Type parameter 380
Calibration Curve Type command 476
Calibration Levels page, Method View 219
Calibration Method parameter 262
Calibration page
Compounds page 215
QAQC page 232
Calibration parameter 347
calibration standard (Cal Std) sample type, defined 365
Carryover Limit parameter 231
CAS No parameter, Identification page 159
CAS parameter, Compound Database 101
Category parameter, Compound Database 101
caution flags 417, 429
Channel parameter
Batch View 380
Data Review 457
Charge State parameter, Compound Database 103
Chk Std page, Method View 233
Chromatogram View Width parameter 283
Collision Energy parameter, Compound Database 104
color codes, Sample Definition view 334
commands
Acquisition 29
Add Compound 90
Add Compound from Compound Database 156
Add Group 241
Add Sample
Acquisition mode 334
Batch View sample list 381
Add This Mass as New Confirming Ion 204
Add This Mass to Existing Quan Mass Ranges 204
Analysis 29
Application Configuration 32
Apply to All Peaks in Compound
Avalon 194
Genesis 189
ICIS 192
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Apply to All Peaks in Method
Avalon 194
Genesis 188
ICIS 192
Apply to All Peaks with Like Sensitivity Settings
Avalon 194
Genesis 189
ICIS 192
Browse in Raw File 381
Calibration Curve Type 476
Confirming Ion List 471
Copy Down 569
Copy with Headers
Acquisition mode 335
Batch View sample list 337, 382
Export Mass List 266
Export to CSV File
Acquisition mode 335
Batch View sample list 337, 382
Fill Down 569
Import Compounds 78
Import Published Method 265, 309
Import Samples 335, 381
Insert Copy Sample
Acquisition mode 334
Batch View sample list 381
Insert Sample
Acquisition mode 334
Batch View sample list 381
Log Off 32
Manual Integration Settings 471
Map Raw Files to Samples 381
Method Integration Settings 471
Methods 29
Modify Columns, Batch View sample list 332, 371, 376
Pause Queue 359
Peak Detection Settings 472
Peak Labels 471
Reactivate All 359
Real Time Status 32
Reinject Selected Samples
Acquisition mode 334
Batch view sample list 381
Remove Pending Batch 361
Remove Pending Batches 359
Remove Pending Samples 361
Remove Selected Samples
Acquisition mode 335
Batch view sample list 381
Send RT to Method 471
Set This Mass as a New Quan Peak 204
Set This Mass as Quan Mass 204
Show Peak Info 472
Thermo Scientific
Index: D
Stop Active Batch 359
Stop All Batches 359
Stop Batch 361
Turn Device Off 342
Turn Device On 341
Turn Device Standby 341
Update Confirming Ion Ratios with This Spectrum
Curve Type parameter
Calibration page 217
Method Template Editor 262
CV Test (%) parameter
Calibration page 232
Chk Std page 233
ISTD page 235
204
comma-separated values, defined 2
Comment parameter
Batch View 380
Data Review 413
Compound parameter
Calibration page 232
Compound Database 101–105
QC levels page 222
Compound Type parameter
Calibration 217
Identification page 159
compound types
internal standards
Detection page 161
Identification page 158
quan
Detection page 161
Identification page 158
target
Detection page 161
Identification page 158
Compounds page, Method View 155
compounds, importing to compound database 78
Confirming Ion List command 471
Constrain Peak Width parameter
Genesis
Detect page 187
peak detection 43, 297
ICIS
Detect page 191
ICIS peak detection 46, 300
contacting us xii
Conversion Factor parameter 380
Copy Down command 569
Copy with Headers command
Acquisition mode 335
Batch View sample list 337, 382
Create Blank Quantitation Method parameter 137
Create PDF parameter
Method view 249, 307
Create XML parameter
Method View
quantitation method 249
screening method 307
Thermo Scientific
D
Data Review view 410, 485
Decimal Places to be Reported parameter 252
Detection Algorithm parameter
Avalon 48, 302
Genesis 42, 296
ICIS 45, 299
Detection Method parameter
Avalon
Detect page 193
peak detection 48, 302
Genesis
Detect page 187
peak detection 42, 296
ICIS
Detect page 191
peak detection 45, 299
Detection page, Method View 160
Detection Type parameter, Times page 174
Detector parameter, Signal page 183
Device Name parameter
Acquisition mode 345
Batch View 401
dialog boxes
Add Library 13
Associate a Raw Data File 137
Audit Log Selection 538
Avalon Event List 49, 303
Filter Editor 539
Import an Xcalibur Method 135
Open Chromatograph Reference Sample 331, 408, 479
Select Compounds from Database 156
Select Compounds to Add 142
Thermo Library Manager 13
Thermo Xcalibur Instrument Setup 147, 274
Thermo Xcalibur Roadmap 12
Dilution Factor parameter 380
Disable Cluster Off, event type 51, 305
Disable Cluster On, event type 51, 305
Display Compounds Above Set Limit parameter 252
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575
Index: E
E
Enable parameter, Ratios page 214
Enable Peak Threshold parameter 262
Enable Valley Detection parameter
Genesis peak detection 43, 297
method development 187
End RT parameter, Times page 175
End Threshold, event type 50, 304
Energy Ramp parameter, Compound Database 104
Estimation Method parameter 218
Event parameter 49, 303
Event types 50, 304
Exclude Matching Quan Peaks parameter 263
Excluded parameter 462
Exclusion Window parameter 263
Expected RT parameter 457
Expected RT parameter, Times page 174
Expected Width parameter
Genesis peak detection 43, 297
method development 187
Experiment parameter, Compound Database 101
Export Mass List command 266
Export to CSV File command
Acquisition mode 335
Batch View sample list 337, 382
Extracted Ion Chromatogram 108
Extracted Mass parameter, Compound Database
confirming peak 105
fragments 105
F
feature summary 4
file types, supported 2
Filename parameter, Batch View 337, 379, 457
Fill Down command 569
Filter parameter
Detection 183
Signal page 182
Final Units parameter
Batch View 380
Data Review 457
Finish view 340
Fit Threshold parameter 208, 286
Flag Values Above Carryover parameter 253
Flag Values Above LOR parameter 253
Flag Values Above ULOL parameter 253
Flag Values Below LOD parameter 253
Flag Values Below LOQ parameter 253
Flag Values Between LOD and LOQ parameter 253
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Flags parameter
Compound Results pane 415
Compounds pane 424
Sample Results pane 426, 458
Samples pane 413, 443
Force Cluster Off, event type 51, 305
Force Cluster On, event type 51, 305
Fragment Ions parameter 285
G
Genesis detection algorithm 37
Groups page, Method View 240
H
Height parameter 458
I
ICIS detection algorithm 37
Identification page, Method View 158
Ignore if Not Defined parameter 285
Import an Xcalibur Method dialog box 135
Import Compounds command 78
Import Published Method command 265, 309
Import Samples command 335, 381
Include Compound Peak Spectrum as Reference Spectrum
parameter 262
Include Confirming Ions parameter 262
Include Data Dependent Filters parameter 154
Injection Amount parameter 134
Injection Volume parameter
Batch View 379
method development 149, 275
Insert Copy Sample command
Acquisition mode 334
Batch View sample list 381
Insert Sample command
Acquisition mode 334
Batch View sample list 381
installing NIST and QED libraries 12
Instrument Method parameter
Acquisition page 150, 276
Batch View 380
Method Forge 134
instrument status indicators 342
Instrument view 113
Integration Mode parameter 458
intensity ratios 553
Intensity Threshold parameter 211, 286
Thermo Scientific
Index: L
Ion Coelution parameter
common peak detection 41
Ratios page 214
Ion Range Calc Method parameter 150
Ionization parameter, Compound Database 101
isotope accurate mass 553
isotopic distribution 553
Isotopic Pattern parameter 286
isotopic pattern, score calculations 557
ISTD Amt parameter 459
ISTD Matching parameter 263
ISTD page, Method View 235
ISTD parameter 217
ISTD Resp parameter 459
L
Lab Name parameter 149, 275
Lens parameter, Compound Database, target peak 104
Level parameter
Batch View 379
QC Levels page 222
Library Search parameter 287
licenses, types of ix
Limit Library Hits parameter 262
Limit the Retention Time Range parameter 262
Limits page, Method View 231
Linked Compound parameter 218
Local Method view 516
LOD (Detection Limit) parameter 231
Log Off command 32
Login parameter 11
LOQ (Quantitation Limit) parameter 231
LOR (Reporting limit) parameter 231
M
m/z (Apex) parameter 460, 499
m/z (Delta) parameter 461, 499
m/z (Expected) parameter 461, 499
Manual Injection parameter 134
Manual Integration Settings command 471
Map Raw Files to Samples command 381
Mass parameter, Compound Database 102
Mass Precision parameter 150, 275
Mass Tolerance parameter 154
Matrix Blank page, Method View 234
Matrix Blank sample type, defined 365
Max Amt Diff (%) parameter 232
Max Conc parameter 234
Max Recovery (%) parameter, ISTD page 235
Max RF Diff (%) parameter 233
Thermo Scientific
Max RSD (%) parameter, Calibration page 232
Max RT (+min) parameter, ISTD page 235
Method Integration Settings command 471
Method parameter
Matrix Blank page 234
Solvent Blank page 236
Method Template Editor 261
Method View
Acquisition page 146
Calibration Levels page 219
Calibration page
Compounds page 215
QAQC page 232
Chk Std page 233
Compounds page 155
Detection page 160
Groups page 240
Identification page 158
ISTD page 235
Limits page 231
Matrix Blank page 234
Processing page 151
QAQC page 230
QC Check page 233
QC Levels page 221
Ratios page 213
Real Time Viewer page 223
Reports page 248
Solvent Blank page 236
Spectrum page 199
Suitability page 195
methods
importing Xcalibur 135
instrument 113
local 516
Method Template Editor 261
update TSQ method 340
Methods command 29
Min Peak Height (S/N) parameter
Genesis 188
ICIS 191
Min Peak Width parameter
Detect page 192
ICIS peak detection 47, 301
Min recovery (%) parameter, ISTD page 235
Min RF parameter 233
Min RT (–min) parameter 235
Min. # of Fragments parameter 211, 285
modes, choosing 29
Modify Columns command, Batch View sample list 332,
371, 376
TraceFinder User Guide
577
Index: N
MS Order parameter, Compound Database
confirming peak 105
target peak 103
Multiplet Resolution parameter
Detect page 192
ICIS peak detection 47, 301
Multiplexing Channels parameter 334
N
Name the Master Method parameter 133
Negative Peaks, event type 50, 304
Neutral Mass parameter, Compound Database 101
NIST library, installing 12
Noise Method parameter
Detect page 192
ICIS peak detection 47, 301
noise value 567
Number of Confirming Ions parameter 262
Number of Scans to Subtract parameter 154
O
Only Select Top Peaks parameter 262
Open Chromatograph Reference Sample dialog box 331, 408,
479
Origin parameter
Calibration 217
Method Template Editor 263
P
parameters
# Background Scans
Detect page 188
Genesis peak detection 44, 298
% Test 222
%CV 456
%Diff 456
%RSD 456
Acquire a New Raw Data File 134
Active
Data Review sample list 456
Identification page 159
Actual RT 457
Adduct 457
Adduct, Compound Database, target peak 103
Allowed Intensity Deviation 208, 287
Allowed Mass Deviation 208, 286
Amount 217
Amplifier 283
Area 457
578
TraceFinder User Guide
Area Noise Factor
Detect page 191
ICIS peak detection 46, 300
Area Scan Window
Detect page 192
ICIS peak detection 47, 301
Area Tail Extension
Detect page 192
ICIS peak detection 47, 301
Assay Type
Method View
quantitation method 149
screening method 275
Auto TSRM Update 347
Autocalc Initial Events, Avalon 194
Automatically Create the Master Method 133
Background Subtraction Range Option 154
Barcode Actual 337, 380
Barcode Expected 380
Baseline Window
Detect page 191
ICIS peak detection 46, 300
Best Match Method 262
cal1-caln 220
Calculated Amt 457
Calculation Type 380
Calibration 347
Calibration Method 262
Carryover Limit 231
CAS No, Identification page 159
CAS, Compound Database 101
Category, Compound Database 101
Channel
Batch View 380
Data Review 457
Charge State, Compound Database 103
Chromatogram View Width 283
Collision Energy, Compound Database 104
Comment
Batch View 380
Data Review 413
Compound
Calibration page 232
Compound Database 101–105
QC levels page 222
Compound Type
Calibration 217
Identification page 159
Constrain Peak Width
Genesis
Detect page 187
peak detection 43, 297
Thermo Scientific
Index: P
ICIS
Detect page 191
ICIS peak detection 46, 300
Conversion Factor 380
Create Blank Quantitation Method 137
Create PDF
Method view 249, 307
Create XML
Method View
quantitation method 249
screening method 307
Curve Type
Calibration page 217
Method Template Editor 262
CV Test (%)
Calibration page 232
Chk Std page 233
ISTD page 235
Decimal Places to be Reported 252
Detection Algorithm
Avalon 48, 302
Genesis 42, 296
ICIS 45, 299
Detection Method
Avalon
Detect page 193
peak detection 48, 302
Genesis
Detect page 187
peak detection 42, 296
ICIS
Detect page 191
peak detection 45, 299
Detection Type, Times page 174
Detector 183
Device Name
Acquisition mode 345
Batch View 401
Dilution Factor 380
Display Compounds Above Set Limit 252
Enable Peak Threshold 262
Enable Valley Detection
Genesis peak detection 43, 297
method development 187
Enable, Ratios page 214
End RT, Times page 175
Energy Ramp, Compound Database 104
Estimation Method 218
Event 49, 303
Exclude Matching Quan Peaks 263
Excluded 462
Exclusion Window 263
Expected RT 457
Expected RT, Times page 174
Thermo Scientific
Expected Width
Genesis peak detection 43, 297
method development 187
Experiment, Compound Database 101
Extracted Mass, Compound Database
confirming peak 105
fragments 105
Filename, Batch View 337, 379, 457
Filter 182
Filter, Detection 183
Final Units
Batch View 380
Data Review 457
Fit Threshold 208, 286
Flag Values Above Carryover 253
Flag Values Above LOR 253
Flag Values Above ULOL 253
Flag Values Below LOD 253
Flag Values Below LOQ 253
Flag Values Between LOD and LOQ 253
Flags
Compound Results pane 415
Compounds pane 424
Sample Results pane 426, 458
Samples pane 413, 443
Fragment Ions 285
Height 458
Ignore if Not Defined 285
Include Compound Peak Spectrum as Reference
Spectrum 262
Include Confirming Ions 262
Include Data Dependent Filters 154
Injection Amount 134
Injection Volume
Batch View 379
method development 149, 275
Instrument Method
Acquisition page 150, 276
Batch View 380
Method Forge 134
Integration Mode 458
Intensity Threshold 211, 286
Ion Coelution
common peak detection 41
Ratios page 214
Ion Range Calc Method 150
Ionization, Compound Database 101
Isotopic Pattern 286
ISTD 217
ISTD Amt 459
ISTD Matching 263
ISTD Resp 459
Lab Name 149, 275
Lens, Compound Database, target peak 104
TraceFinder User Guide
579
Index: P
Level
Batch View 379
QC levels page 222
Library Search 287
Limit Library Hits 262
Limit the Retention Time Range 262
Linked Compound 218
LOD (Detection Limit) 231
Login 11
LOQ (Quantitation Limit) 231
LOR (Reporting limit) 231
m/z (Apex) 460, 499
m/z (Delta) 461, 499
m/z (Expected) 461, 499
Manual Injection 134
Mass Precision 150, 275
Mass Tolerance 154
Mass, Compound Database 102
Max Amt Diff (%) 232
Max Conc 234
Max Recovery (%), ISTD page 235
Max RF Diff (%) 233
Max RSD (%), Calibration page 232
Max RT (+min), ISTD page 235
Method
Matrix Blank page 234
Solvent Blank page 236
Min Peak Height (S/N)
Genesis 188
ICIS 191
Min Peak Width
Detect page 192
ICIS peak detection 47, 301
Min recovery (%), ISTD page 235
Min RF 233
Min RT (–min) 235
Min. # of Fragments 211, 285
MS Order, Compound Database
confirming peak 105
target peak 103
Multiplet Resolution
Detect page 192
ICIS peak detection 47, 301
Multiplexing Channels 334
Name the Master Method 133
Neutral Mass, Compound Database 101
Noise Method
Detect page 192
ICIS peak detection 47, 301
Number of Confirming Ions 262
Number of Scans to Subtract 154
Only Select Top Peaks 262
580
TraceFinder User Guide
Origin
Calibration 217
Method Template Editor 263
Password, login screen 11
Path 134
Peak Height (%)
Genesis
Detect page 187
peak detection 43, 297
ICIS
method development 191
peak detection 46, 300
Peak Noise Factor
ICIS peak detection 46, 300
method development 191
Peak S/N Cutoff
Detect page 188
Genesis peak detection 44, 298
Percentage 234
Polarity, Compound Database 103
Post-run System State 345, 401
Precursor Mass, Compound Database 102
Priority Sequence 345, 401
Product Mass, Compound Database
confirming peak 105
target peak 102
Product Mass, confirming peak 105
QC1-QCn 222
Qualitative Peak Processing Template 154
R^2 Threshold 232
Ranges, compound detection 184
Raw Filename 134
Reference Compound, Identification page 159
Report Concentration 252
Report Name 249, 307
Report Noise As
Detect page 188
Genesis peak detection 44, 298
Response Ratio 461
Response Threshold, Compound Database 101
Response Via
Calibration 217
Method Template Editor 263
RMS
Detect page 192
ICIS peak detection 47, 301
RT
Calibration 217
Calibration levels 220
Calibration page 232
Chk Std page 233
Compound Database 104
Identification page 158
ISTD page 235
Thermo Scientific
Index: P
Limits page 231
Matrix Blank page 234
QC levels page 222
Solvent Blank page 236
S/N Ratio Threshold 285
S/N Threshold
Genesis peak detection 43, 297
method development 187
Sample Amt 462
Sample Comment 134
Sample ID, Batch View 337, 379
Sample Name
Batch View 337, 379
Data Review 427
Sample Type
Batch View 379
Data Review 413, 427, 444, 462
Sample Volume 380
Sample Weight 380
Score Threshold 287
Sensitivity
Avalon 193
Genesis 187
ICIS 191
Method Template Editor 262
Separate Ion Overlay Display 253
Set Ion Ratio to All Confirming Peaks in Compound
214
Set Ion Ratio to All Confirming Peaks in Method 214
Set Peak Windows Settings to All Peaks in Compound
175
Set Peak Windows Settings to All Peaks in Method
175
Shade Row when Sample is Outside of Evaluation
Criteria 252
Show Chromatogram on Quantitation Report 252
Show Quan Peaks Only 223
Smoothing
Avalon
Detect page 194
peak detection 48, 302
Genesis
Detect page 187
peak detection 43, 297
ICIS
Detect page 191
peak detection 46, 300
Specify Default Ion Ratio Ranges 262
Standard type 217
Start Device 345, 401
Start RT, Times page 175
Start When Ready 345, 401
Thermo Scientific
Status, Batch View
Reference Sample 337
sample list 379
Stepoff Value 154
System Shutdown Method 347
System Startup Method 347
System Status 347
Tailing Factor
Genesis
method development 187
peak detection 44, 298
ICIS
method development 191
peak detection 46, 300
Target Ratio 214
Theoretical Amt 462
Threshold Override 285
Time 49, 303
Time Range Peak, Compound Database 104
Time/Event/Value, Avalon peak detection 48, 302
Trace, Detection 183
ULOL (Linearity Limit) 231
Units 217
Upper Limit
Solvent Blank page 236
Use Alternate Calibration Report Format 253
Use an Existing Raw Data File 134
Use as RT Reference, Identification page 159
Use Autosampler 134
Use Data Dependent Scans 264
Use Genesis Algorithm for Qual Processing 263
Use Internal Mass Calibration 208, 287
Use Matrix Blank 283
Use Method Forge 125, 129, 135
Use Reverse Library Searching Only 287
Use RT Limits 283
Use Source CID Scans 283
Use These Libraries 262
Valley Rise (%)
Detect page 188
Genesis peak detection 44, 298
Valley S/N
Genesis peak detection 44, 298
method development 188
Value 49, 303
Vial Position
Batch View 337, 379
Method Forge 134
View Width
peak detection 40
Times page 175
Weighting
Calibration 217
Method Template Editor 263
TraceFinder User Guide
581
Index: P
Window
Compound Database, target peak 104
ion ratio 41
Ratios page 214
retention time 40
Times page 174
Window Override 285
Window Type
peak detection 41
Ratios page 214
XIC 182
Password parameter, login screen 11
password, administrator 9
Path parameter 134
Pause Queue command 359
Peak Detection Settings command 472
Peak Height (%) parameter
Genesis
Detect page 187
peak detection 43, 297
ICIS
method development 191
peak detection 46, 300
Peak Labels command 471
Peak Noise Factor parameter
ICIS peak detection 46, 300
method development 191
Peak S/N Cutoff parameter
Detect page 188
Genesis peak detection 44, 298
Percentage parameter 234
Polarity parameter, Compound Database 103
Post-run System State parameter 345, 401
P-P Threshold, event type 50, 304
Precursor Mass parameter, Compound Database 102
Priority Sequence parameter 345, 401
procedures
Access the Audit Viewer 538
acquisition mode
access real-time display 348
add samples to the sample list 325
assign a specific channel to a sample 330
create a batch template 321–322
import samples into the sample list 327
insert samples into the sample list 326
pause all batches in a queue 357
re-inject a sample from 329
remove a batch from a queue 361
remove a pending batch from a queue 361
remove a pending sample from a queued batch 360
remove a single batch from a queue 358
remove all batches in a queue 358
582
TraceFinder User Guide
remove all pending batches in a queue 358
remove pending samples from a queued batch 360
remove samples from the sample list 329
save a to-be-run batch 342
select a previously acquired batch 321
select a ready-to-acquire batch 320
select a reference sample 331
specify a calibration batch 341
specify device states 341
specify startup or shutdown methods 340
start a new batch 316, 318
start an acquisition 342
update TSRM data 340
view output files 346
analysis mode
access the Analysis mode 367
add samples to the samples list 387
change the displayed information for detected peaks
qualitative peak 451
quantitative peak
Data Review 469
method development 161
change the library entry for a selected peak 454
change the peak panes display 466
copy a sample in the samples list 388
create a new batch 386
customize the column display, Batch View 391
display peaks for a specific compound, qualitative
view 444
edit samples in a batch 397
exclude a calibration point 464
insert samples in the samples list 387
make a compound active or inactive 463
manually add a peak
chromatogram pane 448
qualitative peak pane 450
quantitation peak 468
manually exclude a calibration point 475
manually integrate a confirming ion peak 474
manually integrate a quantitative peak 468
modify the peak detection settings 469
open a recent batch 397
open a saved batch 396
open the Batch View 368
open the Data Review view 410, 485
open the Local Method View 516, 518
reinject a sample 389
reinject a sample from a previously acquired batch
397
remove a manually created peak 468
remove a peak from the peak list 446
remove a peak from the qualitative peak pane 451
remove samples from the samples list 388
Thermo Scientific
Index: P
scroll the samples list 371
submit all samples in the batch 398
switch between method and manual integration
qual mode 451
quan mode 469
zoom in on a peak
chromatogram navigation 448
qual peak 450
quantitation peak 466
spectra pane 453
audit viewer
access the Audit Viewer 538
create an audit log events filter 539
create an audit log history filter 542
select an audit log 538
view audit event details 541
view only application, method, batch, or batch
template events 539
Configuration console
add a quantitation peak to a compound 92
import compounds 78
open the Defaults view 35
remove a compound 91
specify common detection parameters 37
specify default laboratory and instrument names 35
specify default mass precision and intensity scale 36
getting started
choose a node 29
display a log of instrument errors 30
install the NIST library 12
install the QED library 12
log in to the TraceFinder application 9
monitor the instrument status 30
start the TraceFinder application 9
method development mode 219
access the Method Development mode 75, 122, 268
add a compound to the database 90
add a mass as a new compound 168
add a mass as a new confirming ion peak 171
add a mass to the existing quan mass ranges 166
add a quan peak 167
add a quan peak to an existing compound 202
add compounds to the method 162
add confirming ions to an existing compound 203
add ions to get an accumulated signal 201
automatically select compounds to create a new
method 125
calibrate the compounds 258
change the compound reference spectrum 165
change the quantitation mass used for a quan peak
200
create a blank method 137
create a group 240
create a new instrument method 114
create a new multiplexing instrument method 116
Thermo Scientific
create a target screening method 271
export mass list data to an XML file 266
filter the displayed compounds 158, 161
identify the peaks 257
import a master method 265, 309
import an instrument method 118
import an Xcalibur method 135
manually select compounds to create a new method
129
open an instrument method 117
open the Instrument View 113
replace a confirming ion peak 171
replace a quantitation mass 166
replace a quantitative peak with a confirming ion
peak 169
save the method template 260
save the new method 171
select compounds from the compound database 142
set a confirming ion peak as an additional
quantitative peak 169
set automated background subtraction options 152
specify a chromatogram reference sample 408–409
specify an internal standard for a compound 215–
216
specify general information for a master method 146
specify ion ratio criteria 207, 213
specify mass tolerance 153
specify peak criteria 256
specify QC levels and concentrations 221
specify qualitative peak processing 259
specify quantitation flag options 251
specify quantitation limits 250
specify ranges of ions for detection and integration
176
specify report types and output formats 248, 306
specify the maximum concentration as a percentage
234
specify user interface options 251
update confirming ion ratios 199
zoom in the chromatogram or spectrum displays 203
Select an audit log 538
Processing page
Background Subtraction Range Option 154
editing 151
Include Data Dependent Filters parameter 154
Mass Tolerance parameter 154
Method View 151
Number of Scans to Subtract parameter 154
Qualitative Peak Processing Template parameter 154
Stepoff Value parameter 154
Product Mass parameter, Compound Database
confirming peak 105
target peak 102
Product Mass parameter, confirming peak 105
TraceFinder User Guide
583
Index: Q
Q
QAQC page, Method View 230
QC Check page, Method View 233
QC Levels page, Method View 221
QC1-QCn parameter 222
QED library, installing 12
Qualitative Peak Processing Template parameter 154
quality check standard (QC Std) sample type, defined 365
quan report settings, specifying 250
R
R^2 Threshold parameter 232
Ranges parameter, compound detection 184
Ratios page, Method View 213
Raw Filename parameter 134
Reactivate All command 359
Real Time Status command 32
Real Time Viewer page, Method View 223
Reference Compound parameter, Identification page 159
reference spectra 453
Reinject Selected Samples command
Acquisition mode 334
Batch view sample list 381
Remove Pending Batch command 361
Remove Pending Batches command 359
Remove Pending Samples command 361
Remove Selected Samples command
Acquisition mode 335
Batch view sample list 381
Report Concentration parameter 252
report formats, specifying 248
Report Name parameter 249, 307
Report Noise As parameter
Detect page 188
Genesis peak detection 44, 298
Report selection view 338
reports
Acquisition mode 338
listed 6
Reports page, Method View 248
Response Ratio parameter 461
Response Threshold parameter, Compound Database 101
Response Via parameter
Calibration 217
Method Template Editor 263
RMS parameter
Detect page 192
ICIS peak detection 47, 301
RT parameter
Calibration 217
Calibration levels 220
Calibration page 232
Chk Std page 233
Compound Database, target peak 104
Identification page 158
ISTD page 235
Limits page 231
Matrix Blank page 234
QC levels page 222
Solvent Blank page 236
S
S/N Ratio Threshold parameter 285
S/N Threshold parameter
Genesis peak detection 43, 297
method development 187
Sample Amt parameter 462
Sample Comment parameter 134
Sample definition view 324
Sample ID parameter, Batch View 337, 379
Sample Name parameter
Batch View 337, 379
Data Review 427
Sample Type parameter
Batch View 379
Data Review 413, 427, 444, 462
sample types, defined 365
Sample Volume parameter 380
Sample Weight parameter 380
Score Threshold parameter 287
score, isotopic pattern 553
Select Compounds from Database dialog box 156
Select Compounds to Add dialog box 142
Selected Reaction Monitoring 106
Send RT to Method command 471
Sensitivity parameter
Avalon 193
Genesis 187
ICIS 191
Method Template Editor 262
Separate Ion Overlay Display parameter 253
Set Ion Ratio to All Confirming Peaks in Compound
parameter 214
Set Ion Ratio to All Confirming Peaks in Method parameter
214
Set Peak Windows Settings to All Peaks in Compound
parameter 175
Set Peak Windows Settings to All Peaks in Method parameter
175
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TraceFinder User Guide
Thermo Scientific
Index: T
Set This Mass as a New Quan Peak command 204
Set This Mass as Quan Mass command 204
Shade Row when Sample is Outside of Evaluation Criteria
parameter 252
Shoulders On, event type 51, 305
Show Chromatogram on Quantitation Report parameter
252
Show Peak Info command 472
Show Quan Peaks Only parameter 223
Single Ion Monitoring 107
Smoothing parameter
Avalon
Detect page 194
peak detection 48, 302
Genesis
Detect page 187
peak detection 43, 297
ICIS
Detect page 191
peak detection 46, 300
Solvent Blank page, Method View 236
Solvent sample type, defined 365
Specify Default Ion Ratio Ranges parameter 262
spectral noise threshold 558
Spectrum page, Method View 199
SRM experiment type 106
Standard type parameter 217
Start Device parameter 345, 401
Start RT parameter, Times page 175
Start Threshold, event type 50–51, 304–305
Start When Ready parameter 345, 401
status color codes, Sample Definition view 334
Status parameter, Batch View
Reference Sample 337
sample list 379
Stepoff Value parameter 154
Stop Active Batch command 359
Stop All Batches command 359
Stop Batch command 361
Suitability page, Method View 195
supported file types, defined 2
System Shutdown Method parameter 347
System Startup Method parameter 347
System Status parameter 347
ICIS
method development 191
peak detection 46, 300
Tangent Skim, event type 51, 305
Target Ratio parameter 214
templates
batch 321–322
method 255
Tension, event type 51, 305
Theoretical Amt parameter 462
Thermo Xcalibur Instrument Setup dialog box 147, 274
Threshold Override parameter 285
Time parameter 49, 303
Time Range Peak parameter, Compound Database 104
Time/Event/Value parameter, Avalon peak detection 48, 302
Trace parameter, Detection 183
Turn Device Off command 342
Turn Device On command 341
Turn Device Standby command 341
U
ULOL (Linearity Limit) parameter 231
Units parameter 217
Unknown sample type, defined 365
Update Confirming Ion Ratios with This Spectrum
command 204
Upper Limit parameter
Solvent Blank page 236
Use Alternate Calibration Report Format parameter 253
Use an Existing Raw Data File parameter 134
Use as RT Reference parameter, Identification page 159
Use Autosampler parameter 134
Use Data Dependent Scans parameter 264
Use Genesis Algorithm for Qual Processing parameter 263
Use Internal Mass Calibration parameter 208, 287
Use Matrix Blank parameter 283
Use Method Forge parameter 125, 129, 135
Use Reverse Library Searching Only parameter 287
Use RT Limits parameter 283
Use Source CID Scans parameter 283
Use These Libraries parameter 262
user security, activating 56
V
T
Tailing Factor parameter
Genesis
method development 187
peak detection 44, 298
Thermo Scientific
Valley Rise (%) parameter
Detect page 188
Genesis peak detection 44, 298
Valley S/N parameter
Genesis peak detection 44, 298
method development 188
Value parameter 49, 303
TraceFinder User Guide
585
Index: W
vector addition 562, 564
Vial Position parameter
Batch View 337, 379
Method Forge 134
View Width parameter
peak detection 40
Times page 175
views
Batch 368
Batch Selection 316
Data Review 410, 485
Finish 340
Instrument 113
Local Method 516
Report selection 338
Sample definition 324
W
weighting factor 565
Weighting parameter
Calibration 217
Method Template Editor 263
Window Override parameter 285
Window parameter
Compound Database, target peak 104
ion ratio 41
Ratios page 214
retention time 40
Times page 174
Window Type parameter
peak detection 41
Ratios page 214
workflow
acquisition mode 314
general 5
X
XIC parameter, Signal page 182
586
TraceFinder User Guide
Thermo Scientific
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