Thermo Fisher Scientific TraceFinder 2.0 User Guide

Thermo
TraceFinder
Version 2.0
User Guide
Optimized for Quantitation
XCALI-97386 Revision A
October 2011
© 2011 Thermo Fisher Scientific Inc. All rights reserved.
LCquan and TSQ Vantage are trademarks, and Xcalibur and TSQ Quantum 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.
Windows, Excel, and Windows Vista are registered trademarks of Microsoft Corporation in the United States
and other countries. Adobe, Acrobat, Flash, and Reader are registered trademarks of Adobe Systems Inc. in the
United States and other countries.
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.
Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or errorfree and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might
result from any use of this document, even if the information in the document is followed properly.
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, October 2011
Minimum software requirements: Thermo Foundation™ 2.0 SP1; Thermo Xcalibur 2.2 SP1; Microsoft
Windows XP Professional SP3 or Window 7 Professional; (optional) Thermo LC Devices 2.5
For Research Use Only. Not for use in diagnostic procedures.
C
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .viii
System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix
System Activation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
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
Standard Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Custom Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Target Screening Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Chapter 2
Getting Started. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Installing the TraceFinder Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Installing the Power Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Installing the NIST and QED Libraries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Launching the NIST Library Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Launching the Qual Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Converting Legacy Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Choosing a Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Chapter 3
Using the Configuration Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .35
User Administration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Choosing User Roles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Project Administration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Working with Drives. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Working with Projects. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Compound Datastore . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Opening and Saving a Datastore . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Adding Compounds, Quantitation Peaks, and Confirming Ions to a
Datastore . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Choosing Experiment Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
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Contents
Application Configuration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Specifying the Reports Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Specifying Configuration Defaults. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Specifying Detection Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Enabling Optional Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
iv
Chapter 4
Using the Method Development Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .91
Working with Master Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Creating a New Master Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Editing a Master Method. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
Creating a Method Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
Importing Published Master Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
Exporting SRM Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
Working with Instrument Methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
Working with Development Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
Creating a Development Batch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
Editing Samples in a Development Batch . . . . . . . . . . . . . . . . . . . . . . . . . . 207
Acquiring Samples in a Development Batch . . . . . . . . . . . . . . . . . . . . . . . . 209
Viewing Raw Data Files in the Qual Browser . . . . . . . . . . . . . . . . . . . . . . . 210
Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212
Chapter 5
Using the Acquisition Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .215
Working with Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
Opening and Navigating the Acquisition Mode . . . . . . . . . . . . . . . . . . . . . 216
Creating Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218
Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247
Real-Time Display. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249
Acquisition Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 250
Instrument Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251
Devices Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252
Queues Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 256
Real-Time Trace Display. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260
Sample Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 262
Chapter 6
Using the Analysis Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .263
Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265
Working in the Batch View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267
Batch View Panes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 268
Creating a New Batch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271
Editing a Batch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279
Editing Report Output Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 282
Setting Compound Active Status. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 284
Submitting a Batch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 286
Creating a Batch Using the Batch Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . 290
TraceFinder User Guide
Thermo Scientific
Contents
Working in Data Review View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 303
Samples List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 304
Quan Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 314
Qual Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 332
Working in the Report View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 344
Viewing Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 345
Generating Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 349
Working with Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 353
Working with the Active View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 356
Working in the Local Method View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 368
Working in the Batch Template Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 370
Appendix A Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .379
Specifying Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 379
Standard Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 380
Custom Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381
Target Screening Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381
Report Flags . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 382
Sample Standard Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 383
Batch Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 384
Batch Report Rev 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 385
Blank Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 387
Calibration Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 388
Calibration Density Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 391
Check Standard Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 392
Chromatogram Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 393
Compound Calibration Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 394
Compound Calibration Report - Alternate . . . . . . . . . . . . . . . . . . . . . . . . . 396
Confirmation Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 398
Confirmation Report 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 399
High Density Calibration Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 400
High Density Internal Standard Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . 401
High Density Internal Standard Report Long . . . . . . . . . . . . . . . . . . . . . . . 402
High Density Sample Report 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 403
High Density Sample Report 1 Long. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 404
High Density Sample Report 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 405
High Density Sample Report 2 Long. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 406
High Density Sample Report 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 407
High Density Sample Report 3 Long. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 408
Internal Standard Summary Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 409
Ion Ratio Failure Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 410
LCSLCSD Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 411
Manual Integration Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 412
Method Detection Limit Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 413
Method Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 416
Thermo Scientific
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Contents
Method Validation Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 419
MSMSD Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 422
QC Standard Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 423
Quantitation Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 424
Quantitation Report - 2. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 425
Solvent Blank Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 427
Surrogate Recovery Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 428
TIC Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 429
TIC Summary Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 430
Appendix B Using Copy Down and Fill Down . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .433
Appendix C Using Filter Criteria. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .437
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .439
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P
Preface
The TraceFinder 2.0 application is the newest application in the series of Thermo Scientific
GC/MS and LC/MS analytical software.
Contents
• Related Documentation
• Special Notices
• System Requirements
• System Activation
• Contacting Us
 To suggest changes to documentation or to Help
Complete a brief survey about this document by clicking the link below.
Thank you in advance for your help.
Related Documentation
TraceFinder documentation includes the TraceFinder User Guide and four quick reference
guides as PDF files that you can access from the Windows™ Start menu or from within the
TraceFinder application.
 To view TraceFinder documents using the Start menu
Go to Start > All Programs > Thermo TraceFinder > Manuals and choose one of the
following documents:
• TraceFinder User Guide
• TraceFinder Administrator Quick Reference Guide
• TraceFinder Acquisition Quick Reference Guide
• TraceFinder Analysis Quick Reference Guide
• TraceFinder Shortcut Menus Quick Reference Guide
• TraceFinder Custom Reports Tutorial
Thermo Scientific
TraceFinder User Guide
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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 Help Contents, Index, or Search panes.
2. To view the user guide or quick reference guides, choose Help > Manuals> User or
Quick Reference Guide.
The PDF opens in a new window.
Special Notices
This guide includes 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.
viii
TraceFinder User Guide
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Preface
System Requirements
Your system must meet these minimum requirements.
System
Computer
Instruments
(supported or
required)
Requirements
•
•
•
•
•
2.33 GHz processor dual core with 2 GB RAM
CD/R-ROM drive
Video card and monitor capable of 1280 × 1024 resolution (XGA)
75 GB available on the C: drive
NTFS format
Autosamplers:
• Triplus™
• AS3000
GC Devices:
• FOCUS™ GC
• Trace GC Ultra™
GC/MS mass spectrometers
Software
Thermo Scientific
• Microsoft™ Windows XP Professional SP3
or Window 7 Professional
• Microsoft Office 2007 SP2 or Excel™ 2007 SP2
• Microsoft .NET Framework 3.5 SP 1
• Thermo Foundation™ 2.0 SP1
• Thermo Xcalibur™ 2.2 SP1
• Adobe™ Reader™ 9.0
• NIST™ 2008
TraceFinder User Guide
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Preface
System Activation
When you first start the TraceFinder application, a dialog box displays the number of days
remaining in your 60-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:
• 60-Day Evaluation Version (free of charge)
• Full Version Single License
The evaluation version is full-featured and automatically expires 60 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.
For questions regarding activation, contact Thermo Fisher Scientific Technical Support in
San Jose, CA:
• E-mail: [email protected]
• Fax: 408-965-6120
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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.
3. When you finish entering all your information, click Copy.
The application copies this XML text to the Clipboard.
If you have not completed all the information, a pop-up box opens, identifying the
missing information.
4. Paste this XML text in the body of an e-mail and send the e-mail to
[email protected].
Thermo Scientific
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Preface
 To use your activation key
Note You must run the TraceFinder application with ITAdmin or LabDirector rights
when entering the activation key.
1. When you receive your activation key, copy it from the e-mail.
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.
Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need.
 To contact Technical Support
Phone
800-532-4752
Fax
561-688-8736
E-mail
[email protected]
Knowledge base
www.thermokb.com
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xii
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Preface
 To suggest changes to documentation or to Help
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• Send an e-mail message to the Technical Publications Editor at
[email protected].
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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, creating the workflows
that laboratories use. It supports a focused workflow for specific non-bioanalytical laboratory
use, instrument control, and method development functionality in a single software package.
TraceFinder is the primary application for the TSQ Quantum™ XLS triple quadrupole mass
spectrometers.
The TraceFinder application can export SRM data in .xml format so that other applications
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 225.
• Processing (.pmd) and instrument (.meth) method files from the Xcalibur data system
See “Working with Master Methods” on page 94 or “Working with Instrument Methods”
on page 197.
• Compounds from files that use the datastore (.xml) format
See “Adding Compounds, Quantitation Peaks, and Confirming Ions to a Datastore” on
page 59.
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Introduction
About the TraceFinder Application
• Batches, methods, or templates from the following applications:
–
TraceFinder 1.0
–
TraceFinder 1.1
–
EnviroLab Forms/QuanLab Forms/ToxLab Forms 2.5
–
EnviroLab Forms/QuanLab Forms/ToxLab Forms 3.0
See “Converting Legacy Data” on page 19.
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.
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1 Introduction
About the TraceFinder Application
TraceFinder Directory Structure
The TraceFinder application creates folders for projects/subprojects/batches and templates in
the C:\Thermo\TraceFinder\2.0\General directory. Within each batch folder, the application
creates folders for data, methods, and reports.
IMPORTANT You cannot rename or move the folders created by the TraceFinder
application.
Figure 1.
Thermo Scientific
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. The system uses a batch-centric approach and tools to 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 review 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 LabDirector, ITAdmin, Supervisor, Technician, and QAQC
(quality assurance) roles
• Configuration mode for user administration, project administration, datastore
administration, and application administration
• Method Development mode for editing instrument methods, setting processing and error
flag parameters, and setting report options
• Acquisition mode that acts as a wizard to guide you in creating batches and running
samples
• Analysis mode with batch views, data review, local method views, and report views
• Database-capable method development
• Quantification workflows, supporting capabilities present in the LCquan and EnviroLab
Forms, QuanLab Forms, and ToxLab Forms applications
• Standard and customized report formats
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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1 Introduction
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
how the raw data is acquired and processed, how the error checking information evaluates
the results, and how the results appear in reports.
2. Create and submit a batch using one of the batch wizards.
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 the dashboard and 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 lower
right corner of the TraceFinder window. This area displays a green, yellow, or red
status light and a description of the number of samples in the queue (if any).
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 currently selected batch.
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Introduction
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. The reports divide into three groups: Standard, Custom, and Target Screening.
For additional information about standard, custom, or target screening reports and examples
of each standard report type, see “Reports” on page 379. Examples of standard reports (as
PDF files) are also located in the C:\Thermo\TraceFinder\2.0\General\ExampleReports
folder.
Standard Report Types
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Batch Report
BatchReportRevision1
Blank Report
Calibration Report
Chromatogram Report
Compound Calibration Report
Compound Calibration Report - Alternate
Confirmation Report
High Density Calibration Report
High Density Internal Standard Report Long
Internal Standard Summary Report
Ion Ratio Failure Report
Manual Integration Report
Method Report
QC Standard Report
Qualitative Peak Report
Qualitative Summary Report
Quantitation Report
Quantitation Report - 2
Solvent Blank Report
Custom Report Types
•
•
•
•
•
•
•
•
•
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AltCalibrationReport
Alternate BatchReport
Alternate CalibrationReport
Alternate ConfirmationReport
Alternate MatrixSpikeReport
Alternate SampleReport
Alternate SummaryReport
BatchReport
BlankReport
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1 Introduction
Reporting Features
•
•
•
•
•
•
•
•
•
•
•
•
•
CalibrationDensityReport
CalibrationReport
CheckStandardReport
CompoundCalibrationReport
ConfirmationReport
ConfirmationReport2
HighDensitySampleReport1Long
HighDensitySampleReport2Long
HighDensitySampleReport3Long
HighDensitySampleReport4
HighDensitySampleReport5
QuantitationReport
SteroidAnalysisReport
Target Screening Report Types
Target Screening reports are available only when you install ToxID software and enable the
Target Screening features. For a detailed procedure for enabling target screening features, see
“Target Screening” on page 85.
• Target Screening Long Report
• Target Screening Summary Report
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Getting Started
This chapter includes the procedures for getting started with the TraceFinder application.
Contents
• Installing the TraceFinder Application
• Installing the Power Modules
• Installing the NIST and QED Libraries
• Launching the NIST Library Browser
• Launching the Qual Browser
• Converting Legacy Data
• Choosing a Mode
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Getting Started
Installing the TraceFinder Application
Installing the TraceFinder Application
Follow these instructions to install, start, and log in to the TraceFinder application.
 To install the TraceFinder application
1. Insert the TraceFinder CD, open the TraceFinder launcher, and click Next.
The InstallShield Wizard opens.
2. Click the TraceFinder 2.0 button, 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.
IMPORTANT If prompted to install Thermo Foundation, click Yes, and then when
prompted to restart your computer, click OK.
The wizard continues the installation.
3. When prompted, choose to install either the GC or LC version of the software.
4. When the installation completes, do not launch the TraceFinder application.
5. Open the TraceFinder launcher again, and click Next.
6. Click the ToxID 2.1.2 button, and follow the instructions to install ToxID.
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2 Getting Started
Installing the TraceFinder Application
7. Click the NIST Library button, and follow the instructions to install the NIST library
(required for ToxID).
When the wizard prompts you to select a destination folder, select C:\Program
Files\NISTMS.
8. Install the appropriate device drivers, and configure the instruments in the Thermo
Foundation Instrument Configuration dialog box.
9. You can now start your TraceFinder application.
 To install example data
(Optional) Click the Example Data button, and follow the instructions to install an
example project that contains example batch data.
 To start the TraceFinder application
1. Configure your instruments.
You cannot configure your instruments while the TraceFinder application is running.
2. Double-click the TraceFinder icon on your desktop, or go to Start > All Programs >
Thermo TraceFinder > TraceFinder.
By default, user security is not enabled and the application does not require a password.
To enable user security, see “User Security” on page 85.
 To log in to the TraceFinder application (when user security is enabled)
1. Enter your assigned user name.
Before you can log in to the TraceFinder application, a system administrator must set up a
user account for you. The administrator assigns you a user name and password and gives
you permission to access specific modes.
IMPORTANT If you are the administrator logging in for the first time with user
security enabled, use Administrator/Password as the username/password.
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 dashboard opens. See “TraceFinder Dashboard” on page 33.
4. To exit the TraceFinder application without logging in, click Exit TraceFinder.
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Getting Started
Installing the TraceFinder Application
Figure 2.
TraceFinder login screen
Table 1. Login screen parameters
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TraceFinder User Guide
Parameter
Description
Username
The user’s assigned user name.
Password
The assigned password for the user name.
Login
Verifies the user name and password, and displays the dashboard.
Exit TraceFinder
Closes the TraceFinder application without logging in.
Thermo Scientific
2 Getting Started
Installing the Power Modules
Installing the Power Modules
Follow these instructions to install and enable the TraceFinder power modules for
multiplexing.
 To install the power modules
1. Follow the instructions to install the TraceFinder application.
See “Installing the TraceFinder Application” on page 10.
2. Open the TraceFinder launcher again, and click Next.
3. Click the TraceFinder Power Modules button, and follow the instructions to install the
multiplexing module.
4. License the power modules.
Licensing for the power modules follows the same procedures as the TraceFinder
application licensing. See “System Activation” on page x.
 To enable the power modules
1. Start the TraceFinder application.
2. Go to the Configuration mode.
3. Click Application Configuration in the navigation pane.
4. Click Optional Features.
5. On the Optional Features page, select the Multiplexing check box.
For detailed instructions, see “Multiplexing” on page 87.
6. Click Apply.
A message prompts you to restart the TraceFinder application so that your changes can
take effect.
7. Click Yes.
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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, follow these instructions to install the
NIST and QED libraries.
 To install the NIST library
1. Launch the XInstall executable file.
2. Click the NIST button.
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.
 To install the QED library
1. On your desktop, double-click the Xcalibur icon,
.
The Thermo Xcalibur Roadmap opens.
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2 Getting Started
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 library in 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. Start the TraceFinder application.
9. Go to the Method Development mode.
10. Click Method View in the navigation pane.
11. 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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2 Getting Started
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 Go > Launch Library Browser from the 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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Getting Started
Launching the Qual Browser
Launching the Qual Browser
Use the Qual Browser to view chromatograms and spectra from raw data files or qualitative
processing results.
 To open the Qual Browser
Choose Go > Launch Qual Browser from the main menu.
The Thermo Xcalibur Qual Browser opens.
For detailed instructions about using the Qual Browser, refer to the Qual Browser Help.
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2 Getting Started
Converting Legacy Data
Converting Legacy Data
Use the TraceFinder Legacy Data Converter to convert methods, batches, method templates,
or batch templates from TraceFinder, EnviroLab Forms, QuanLab Forms, or ToxLab Forms
source versions to compatible TraceFinder 2.0 target versions.
Table 2. Version compatibility
Source
TraceFinder 2.0 target
General
EFS
ClinTox
TraceFinder 2.0 General


TraceFinder 1.1 EFS

TraceFinder 1.1 General


TraceFinder 1.0.1

EnviroLab Forms 3.1

QuanLab Forms 3.1




ToxLab Forms 3.1

EnviroLab Forms 2.5.2
QuanLab Forms 2.5.2



ToxLab Forms 2.5.2


 To open the TraceFinder Legacy Data Converter
Choose Go > Launch Legacy Data Converter from the main menu.
The TraceFinder Legacy Data Converter window opens.
Follow these procedures:
• To convert a method
• To convert a batch
• To convert a method template
• To convert a batch template
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Getting Started
Converting Legacy Data
 To convert a method
1. In the Data Type list, select Method.
The TraceFinder Legacy Data Converter displays the interface for converting methods.
2. In the Source Version list, select the version of the method you will convert.
The Methods to be Converted list 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 the Source Folder icon,
.
The application adds a Source Folder box to the window.
b. Click Browse and locate a method folder.
You can select a specific method folder or a folder that contains multiple methods.
c. Click OK in the Browse for Folder dialog box.
The application displays the selected folder in the Methods to be Converted list.
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 you are converting to.
The list displays only TraceFinder configurations with compatible data. See “Version
compatibility” on page 19.
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2 Getting Started
Converting Legacy Data
5. In the Target Drive list, select a fixed drive.
You cannot write the converted files to a mapped drive.
6. (Optional) In the New Name column, change the default new name for each method that
you want converted.
When you populate the Methods to be Converted list, the application checks each
method to see if a method with this name exists in the target folder.
• If it exists, the default new name is the old name with “_1” appended.
• If it does not exist, the default new name is blank and the converted method keeps
the original name.
IMPORTANT The conversion cannot overwrite an existing file name. If the new name
is identical to an existing method file, the conversion will fail. When you manually
enter a new name, you must verify that the name does not already exist.
7. Select the check box for each method 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 C:\Thermo\TargetVersion\Methods folder.
Note If a method conversion fails, the Status column displays an error icon. Hold
your cursor over the icon to display the error message.
8. 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 3.
Thermo Scientific
Sample log file for converting a method
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Getting Started
Converting Legacy Data
 To convert a batch
1. In the Data Type list, select Batch.
The TraceFinder Legacy Data Converter displays the interface for converting batches.
2. In the Source Version list, select the version of the batch you will convert.
The Batches to be Converted list displays all batches in the Projects folder for the selected
source version.
IMPORTANT A valid batch file (.btx) must be inside a folder with the same name. For
example:
3. To convert a batch that is not in the default list, do the following:
a. Click the Source Folder icon,
.
The application adds a Source Folder box to the window.
b. Click Browse and locate a batch folder.
You can select a specific batch folder or a project or subproject folder that contains
multiple batches.
c. Click OK in the Browse for Folder dialog box.
The application displays the selected folder and all batches in that folder in the Batches to
be Converted list.
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2 Getting Started
Converting Legacy Data
When you select a project or subproject folder that contains multiple batch folders, the
application displays all the batches.
4. In the Target Version list, select the version you are converting to.
The list displays only TraceFinder configurations with compatible data. See “Version
compatibility” on page 19.
5. In the Target Drive list, select a fixed drive.
You cannot write the converted files to a mapped drive.
6. Do one of the following to create a project and subproject for the converted batch:
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.
7. (Optional) In the New Name column, change the default new name for each batch that
you want converted.
When you populate the Batches to be Converted list, the application checks each batch to
see if a batch with this name exists in the target folder.
• If it exists, the default new name is the old name with “_1” appended.
• If it does not exist, the default new name is blank and the converted batch keeps the
original name.
IMPORTANT The conversion cannot overwrite an existing file name. If the new name
is identical to an existing batch folder, the conversion will fail. When you manually
enter a new name, you must verify that the name does not already exist.
8. Select the check box for each batch 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.
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Converting Legacy Data
When the Status column reports that a batch is successfully converted, the application
writes the converted batch to the C:\Thermo\TargetVersion\Projects folder using either
the original project and subproject names or the new names you entered.
Note If a batch conversion fails, the Status column displays an error icon. Hold your
cursor over the icon to display the error message.
9. 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 4.
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Sample log file for converting a batch
Thermo Scientific
2 Getting Started
Converting Legacy Data
 To convert a method template
1. In the Data Type list, select Method Template.
The TraceFinder Legacy Data Converter displays the interface for converting method
templates.
2. In the Source Version list, select the version of the method template you will convert.
The Method Templates to be Converted list displays the method templates in the
Templates folder for the selected source version. The application verifies that the method
template file is the .pmtx file format.
3. To convert a method template that is not in the default list, do the following:
a. Click the Source Folder icon,
.
The application adds a Source Folder box to the window.
b. Click Browse and locate a template folder.
You can select a specific template folder or a folder that contains multiple templates.
c. Click OK in the Browse for Folder dialog box.
The application displays the selected folder in the Method Templates to be Converted
list.
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 you are converting to.
The list displays only TraceFinder configurations with compatible data. See “Version
compatibility” on page 19.
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Getting Started
Converting Legacy Data
5. In the Target Drive list, select a fixed drive.
You cannot write the converted files to a mapped drive.
6. (Optional) In the New Name column, change the default new name for each method
template that you want converted.
When you populate the Method Templates to be Converted list, the application checks
each method template to see if a method template with this name exists in the target
folder.
• If it exists, the default new name is the old name with “_1” appended.
• If it does not exist, the default new name is blank and the converted method template
keeps the original 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.
7. Select the check box for each method template 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
C:\Thermo\TargetVersion\Templates\Methods folder.
Note If a template conversion fails, the Status column displays an error icon. Hold
your cursor over the icon to display the error message.
8. 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 5.
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Sample log file for converting a method template
Thermo Scientific
2 Getting Started
Converting Legacy Data
 To convert a batch template
1. In the Data Type list, select Batch Template.
The TraceFinder Legacy Data Converter displays the interface for converting batch
templates.
2. In the Source Version list, select the version of the batch template you will convert.
The Batch Templates to be Converted list displays the batch templates in the Templates
folder for the selected source version.
IMPORTANT A valid batch template file (.btx) must be inside a folder with the same
name. For example:
3. To convert a batch template that is not in the default list, do the following:
a. Click the Source Folder icon,
.
The application adds a Source Folder box to the window.
b. Click Browse and locate a template folder.
You can select a specific batch template folder or a folder that contains multiple batch
templates.
c. Click OK in the Browse for Folder dialog box.
The application displays the selected folder in the Batch Templates to be Converted list.
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Getting Started
Converting Legacy Data
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 you are converting to.
The list displays only TraceFinder configurations with compatible data. See “Version
compatibility” on page 19.
5. In the Target Drive list, select a fixed drive.
You cannot write the converted files to a mapped drive.
6. (Optional) In the New Name column, change the default new name for each batch
template that you want converted.
When you populate the Batch Templates to be Converted list, the application checks each
batch template to see if a batch template with this name exists in the target folder.
• If it exists, the default new name is the old name with “_1” appended.
• If it does not exist, the default new name is blank and the converted batch template
keeps the original 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.
7. Select the check box for each batch template 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
C:\Thermo\TargetVersion\Templates\Batches folder.
Note If a template conversion fails, the Status column displays an error icon. Hold
your cursor over the icon to display the error message.
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2 Getting Started
Converting Legacy Data
8. 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 6.
Thermo Scientific
Sample log file for converting a batch template
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Getting Started
Choosing a Mode
Choosing a Mode
When user security is enabled, the dashboard provides the current user with options
applicable to the role assigned to that user. The following table shows the available modes for
each user role.
Table 3. User roles and mode access
User role
Method
Development
Acquisition
Analysis
Configuration




LabDirector

ITAdmin
Supervisor

Technician




QAQC

Note When user security is not enabled, all modes are available to all users.
Follow these procedures:
• To choose a mode
• To display a log of instrument errors
• To monitor instrument status
• To watch the real-time display from the dashboard
 To choose a mode
1. From the dashboard, click the mode where you want to work.
The dashboard shows only the modes that you have permission to use. See “TraceFinder
Dashboard” on page 33.
2. To change modes from within any of the TraceFinder application modes, click a mode
button in the navigation pane.
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Getting Started
Choosing a Mode
 To display a log of instrument errors
1. Right-click the status light in the lower right corner of any mode.
2. Select Instrument Log.
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 you cleared the message log.
3. 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\2.0\General\Logs\TraceFinder.log
• Click OK to dismiss the Instrument Log dialog box.
 To monitor instrument status
Look at the status light in the lower 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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Getting Started
Choosing a Mode
 To watch the real-time display from the dashboard
Click Real Time Status.
The real-time status is displayed at the bottom of the dashboard.
For descriptions of all the features of the real-time display, see “Real-Time Display” on
page 249.
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Getting Started
Choosing a Mode
TraceFinder Dashboard
A dashboard without user security or for a user in the LabDirector role looks like this:
Table 4. TraceFinder dashboard screen parameters (Sheet 1 of 2)
Parameter
Description
Real Time Status
Opens the real-time display for the current acquisition. The acquisition
progress is displayed within the current mode window.
Help
Opens the TraceFinder Help.
Log Off
Logs off the current user and displays the login screen. This function is
available only when user security is enabled. See “User Security” on
page 85.
Acquisition
Opens the Acquisition mode where you can create and review batches,
batch data, reports, and local methods. See Chapter 5, “Using the
Acquisition Mode.”
This mode is available only when you select the Acquisition Batch
Wizard style in the Configuration mode. See “Batch Wizard Style” on
page 87.
Analysis
Thermo Scientific
Opens the Analysis mode where you can review batches, batch data,
reports, and local methods. See Chapter 6, “Using the Analysis Mode.”
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Choosing a Mode
Table 4. TraceFinder dashboard screen parameters (Sheet 2 of 2)
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Parameter
Description
Method
Development
Opens the Method Development mode where you can create a master
method, an instrument method, or a development batch. See
Chapter 4, “Using the Method Development Mode.”
Configuration
Opens the Configuration mode where you can set permissions, assign
users to roles, configure available reports and import new reports, and
maintain the various databases, including the Compound Datastore.
See Chapter 3, “Using the Configuration Mode.”
Thermo Scientific
3
Using the Configuration Mode
This chapter discusses the configuration tasks assigned to the ITAdmin and LabDirector roles
when user security is enabled. When user security is not enabled, all users have access to all
features in the Configuration mode except the User Administration tasks.
Contents
• User Administration
• Project Administration
• Compound Datastore
• Application Configuration
Users in the ITAdmin or LabDirector role are responsible for the following:
• Handling the databases
• Applying roles to users
• Understanding security, users, and groups
• Creating local users and network groups
• Creating projects and subprojects
• Maintaining compounds in the compounds datastore
 To access the Configuration mode
Click Configuration from the dashboard or the navigation pane.
The Configuration mode navigation pane opens.
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Using the Configuration Mode
Figure 7.
Configuration mode navigation pane
Available only to users in the LabDirector or ITAdmin role.
Available only when the Acquisition Batch Wizard is selected.
Table 5.
Configuration mode navigation pane functions
Function
Description
User Administration
Opens the User Administration view where you can add, remove, or edit user accounts
and permissions. See “User Administration” on page 37.
When user security is not enabled, this task pane is not available. When user security is
enabled, this task pane is available only to users in the LabDirector or ITAdmin role. See
“Application Configuration” on page 64.
Project Administration
Opens the Project Administration view where you can create and manage projects and
subprojects. See “Project Administration” on page 46.
Compound Datastore
Opens the Compound Datastore view where you can manage the definition of
compounds in the current datastore. See “Compound Datastore” on page 52.
This task pane is available only when you have selected the Compound Datastore option
on the Optional Features page of the Application Configuration view. See “Application
Configuration” on page 64.
Application Configuration
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Opens the Application Configuration view where you can specify available reports,
application defaults, and detection algorithms. You can also enable the user security,
target screening, compound datastore, multiplexing, and batch wizard features. See
“Application Configuration” on page 64.
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3
Using the Configuration Mode
User Administration
User Administration
In the User Administration view of the Configuration mode (when user security is enabled),
users in the LabDirector or ITAdmin role can add, remove, or edit user accounts and
permissions.
For detailed descriptions of each user role and the permissions and responsibilities for each
role, see “Choosing User Roles” on page 43.
Follow these procedures:
• To open the User Administration view
• To add a user
• To edit user information
• To change a user password
• To remove a user
 To open the User Administration view
1. Click Configuration from the dashboard or the navigation pane.
The Configuration navigation pane opens.
Note The User Administration view is available only when you enable user security.
Follow the instructions “To turn on user security” on page 85.
2. Click the User Administration task pane.
The User Administration view opens. See “User Administration view” on page 41.
 To add a user
1. Click the Add User icon,
.
The application enables the parameters in the User area at the bottom of the view.
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User Administration
2. Type a unique name in the Username field.
3. Select a role from the Role list.
A user in the LabDirector or ITAdmin role must assign each user to one of these defined
roles. For detailed information about the permissions allowed for each role, see “Choosing
User Roles” on page 43.
4. Type the user’s password and type it again to confirm it.
Make sure to communicate the password to the user.
5. (Optional) Type the user’s full name, account number, phone number, and e-mail
address.
6. To enable this user login, select the Enabled check box.
You can disable a user login without deleting the user’s information. Follow the
instructions “To edit user information” on page 38.
7. Do one of the following:
When all the user information is correct, click the Save Changes icon,
.
The TraceFinder application adds the new user to the User Listing table, and the
parameters in the User area are unavailable.
–Or–
To discard all information and not create a new user from
the parameter values you entered, click the Cancel Changes icon,
.
The application discards all information and the parameters in the User area are
unavailable.
 To edit user information
1. In the User Listing table, select a user.
Note Clicking anywhere in the row selects the user.
The user information populates the parameter fields in the User area.
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2. Click the Edit User icon,
Using the Configuration Mode
User Administration
.
The application enables the parameters in the User area.
3. Edit any of the parameter values.
If you are editing your own user name, the Enabled check box is unavailable because you
cannot make your own account unavailable.
4. Do one of the following:
When all the user information is correct, click the Save Changes icon,
.
The TraceFinder application adds the new parameter values to the User Listing, and the
parameters in the User area are unavailable.
– Or–
To discard all changes and not save the edits, click the Cancel Changes icon,
.
All changes are discarded, and the parameters in the User area are unavailable.
 To change a user password
1. In the User Listing table, select a user.
The user information populates the parameter fields in the User area.
2. Click the Edit User icon,
.
The parameters in the User area are enabled.
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User Administration
3. Click Reset Password.
The application makes the password and confirming password visible as a string of
asterisks ******.
4. In the Password box, select ****** and type a new password.
5. In the Confirm Password box, select ****** and retype the new password.
6. Click the Save Changes icon,
.
Make sure to communicate the new password to the user.
 To remove a user
1. In the User Listing table, select a user.
Note Clicking anywhere in the row selects the user.
The user information populates the parameter fields in the User area.
2. Click the Remove User icon,
.
If you select your current user name, the Remove User icon is unavailable. You cannot
remove yourself.
3. When prompted, confirm that you want to remove this user.
If the user is currently logged on to the TraceFinder application, the user’s current session
is not affected.
4. Click OK.
Note Rather than completely removing the user, you can disable a user login without
removing all the user information from the system. Follow the instructions “To edit user
information” on page 38.
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Figure 8.
Using the Configuration Mode
User Administration
User Administration view
Table 6. User Administration view parameters (Sheet 1 of 2)
Parameter
Description
Security Groups
All permission levels defined in the TraceFinder application. For detailed descriptions of
user permissions, see “Choosing User Roles” on page 43.
User Listing
Username
User login names.
Role
Security group that defines user permissions.
Account number
User account numbers.
Phone number
User telephone numbers.
Email address
User e-mail addresses.
Enabled
Available or unavailable status for the user account.
User
Username
Login name for the current user.
Role
Security group that defines the current user’s permissions.
Password
Login password for the current user.
Full name
The current user’s actual name.
Account number
Optional account number for the current user.
Phone number
Optional telephone number for the current user.
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User Administration
Table 6. User Administration view parameters (Sheet 2 of 2)
Parameter
Description
Email address
E-mail address for the current user. Used to notify user of a randomly generated
password.
Enabled
Allows or disallows access for this user. When this user is currently logged on, disallowing
takes effect after the user logs off.
Reset Password
Makes the password visible as a string of asterisks that you can select and change.
Icon
Function
Add user
Enables the fields in the User area where you can enter information for a new user.
Remove user
Deletes all information for the selected user.
Edit user
Enables the User area where you can edit any of the parameters for the selected user.
Save changes
Adds the new parameter values to the User Listing table and disables the parameters in
the User area.
Cancel changes Discards all new or edited information.
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User Administration
Choosing User Roles
This section describes the responsibilities for five different user roles when user security is
enabled: LabDirector, ITAdmin, Supervisor, Technician, and QAQC.
IMPORTANT User roles are in effect only when user security is enabled. When user
security is not enabled, all users have access to all modes.
TraceFinder Mode Access
A laboratory director or an IT administrator assigns you to a role that gives you access to
specific modes of the TraceFinder application. When you log on, the dashboard displays links
to only the modes that you can access.
Table 7. User roles and mode access
User role
Method
Development
Acquisition
Analysis
Configuration




LabDirector

ITAdmin
Supervisor
Technician





QAQC

LabDirector
In the LabDirector role, you review graphically applicable data and manipulate data, batches,
methods, and instruments.
A laboratory director is responsible for these tasks:
• Creating or editing methods for new levels of detection or adding new compounds to the
existing database
• Reviewing data from the mass spectrometer
• Running samples and reviewing data collected by others
• Reporting the data
• Understanding the results and giving final approval of the released data before archiving
ITAdmin
In the ITAdmin role, you set security, manage users into roles, and manipulate the various
databases. You are responsible for adding compounds into the various compound databases.
An IT administrator is responsible for these tasks:
• Handling the databases
• Applying roles to users
• Understanding security, users, and groups
• Creating local users and network groups
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User Administration
Supervisor
In the Supervisor role, you are responsible for setting up the instrument samples and using
previously built sequences and methods for processing and acquiring data. You also develop
and edit methods for processing and acquiring data, review the data, and distinguish between
the need to rerun samples or pass reports up to the lab manager for final review. On a daily
basis, you establish the priority for a list of samples to run and create the sequence of events.
A supervisor is responsible for these tasks:
• Submitting samples
• Creating and submitting batches
• Reporting the data to management
• Creating or editing methods for new levels of detection or adding new compounds to the
existing database
• Reviewing data from the mass spectrometer
• Understanding the results, who ran the batch, and who passed along the results before
giving intermediate approval and sending the data to management
• Modifying new compounds or adjusting methods for specific result sets
Technician
In the Technician role, you are responsible for setting up the instrument samples and using
previously built sequences and methods for processing and acquiring data. You also edit
existing methods for processing and acquiring data, review collected data, and distinguish
between the need to rerun samples or pass reports up to the supervisor. On a daily basis, you
are responsible for gathering the list of samples to run and creating the sequence of events.
A technician is responsible for these tasks:
• Submitting samples
• Creating and submitting batches
• Creating data to be reviewed by management
• Receiving instructions for new sets of samples for the TraceFinder application to analyze
after finishing the current analysis
• Reviewing data from the mass spectrometer
• Understanding the resulting data, making integration changes, and passing those changes
up for further approval
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User Administration
QAQC
In the QAQC role, you review graphically applicable data and interpret the data, but you do
not manipulate the data.
A QAQC technician is responsible for these tasks:
• Reviewing data from the mass spectrometer
• Understanding the results and who ran and passed along the results before giving
intermediate approval and sending the data to management
• Receiving instructions for new sets of samples for the TraceFinder application to analyze
after finishing the current analysis
Note In the QAQC role, you have access only to the Analysis mode.
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Using the Configuration Mode
Project Administration
Project Administration
When user security is enabled, users in the LabDirector or ITAdmin role can create and
manage projects and subprojects on fixed or network drives in the Project Administration
view of the Configuration mode.
This section includes the following topics:
• Working with Drives
• Working with Projects
 To open the Project Administration view
1. Click Configuration from the dashboard or the navigation pane.
The Configuration navigation pane opens. See “Configuration mode navigation pane” on
page 36.
2. In the Configuration navigation pane, click Project Administration.
The Project Administration view opens.
By default, all projects are created under a main Projects folder on the C: drive:
C:\Thermo\TraceFinder\2.0\General\Projects
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Project Administration
Working with Drives
Drives can be any of the following:
• Fixed: Directly connected to your computer.
• Network: Either a remote box or a mapped drive. A shared folder that is mapped to a
drive letter might physically exist on your computer, but because it is mapped, it is
considered to be a Network drive.
• Removable: Temporary drives such as a 3.5-inch disk or a USB drive.
Follow these procedures:
• To choose a drive
• To change the default drive
• To hide a drive from display
• To refresh the drives display
 To choose a drive
1. In the Available Drives area, click any drive other than the default C: drive.
If you have not created a Projects directory on this drive, you see this message:
2. Click Create Projects Directory.
The TraceFinder application adds a new Projects directory to the selected drive. To create
projects and subprojects on this drive, see “To create projects or subprojects” on page 49.
 To change the default drive
Select the check box in the Default column.
You can set only fixed drives as the default drive. The default drive is the only drive that
you can use to acquire data.
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Project Administration
 To hide a drive from display
Clear the check box in the Show column.
The application does not list the hidden drive in drive lists. You cannot hide the default
drive.
 To refresh the drives display
Right-click and choose Refresh from the shortcut menu.
The Available Drives table refreshes to show any drives that have changed, for example, if
you have inserted a USB drive. You can now configure any new drives.
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Project Administration
Working with Projects
When you create a batch, the application stores the data files, local method, and reports in a
project and subproject that you create in the C:\Thermo\TraceFinder\2.0\General\Projects
folder.
If you installed the TraceFinder example data, the main Projects folder includes an Examples
project folder that contains subprojects with example batches that you can use to experiment.
To install the example data from the InstallShield Wizard, see the instructions “To install
example data” on page 11.
Follow these procedures:
• To create projects or subprojects
• To delete projects or subprojects
• To remove all empty folders
• To copy the folder hierarchy from another drive
 To create projects or subprojects
1. Select the top-level project.
You can select the main Projects folder and create a new project under it, or you can select
one of the existing projects and create a subproject under it.
When you select a project folder, the application enables the plus sign icon,
indicating that you can create a folder within the selected folder.
,
2. Click the plus sign.
The TraceFinder application creates a new, unnamed project folder under the selected
project.
3. While the new project is still highlighted, type a new name.
Project names are limited to 30 characters and can contain spaces and special characters,
except for the following special characters: \ / : * ? " < > |
Note After you add a subproject to a project, you cannot rename the project.
4. To save the new name, press ENTER or click anywhere in the view.
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Project Administration
 To delete projects or subprojects
1. Select the project or subproject you want to delete.
You can delete projects that do not have subprojects. You can delete subprojects that do
not have batches. When the selected project or subproject is available for deletion, the
application enables the minus sign icon,
.
2. Click the minus sign, or right-click and choose Remove Project from the shortcut menu.
3. At the prompt, click Yes to remove the selected project or subproject.
 To remove all empty folders
1. Select the project or subproject that contains empty folders.
2. Right-click and choose Remove All Empty Child Folders from the shortcut menu.
A dialog box asks if you want to remove all empty folders.
3. Click OK.
The application removes all folders that have no folders or files. There is no undo for this
command.
 To copy the folder hierarchy from another drive
1. Select the top-level Projects directory in the Project Administration area.
When you copy the hierarchy from the drive to your Projects folder, the application will
add new folders to the current hierarchy, but it will not remove folders.
2. Right-click and choose Copy Folder Hierarchy from Drive from the shortcut menu.
3. Choose a drive from the list of available drives.
At the prompt, you must confirm that you want to create a folder hierarchy that matches
that of the specified drive.
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4. Click OK.
To replicate the hierarchy from the specified drive, the application will add new folders to
the current hierarchy, but it will not remove folders.
IMPORTANT The Copy Folder Hierarchy from Drive command copies only the
project and subproject folders; it does not copy batches within the folders.
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Compound Datastore
Compound Datastore
When user security is enabled, users in the LabDirector or ITAdmin role can manage
compound definitions in the current datastore in the Compound Datastore view.
This section includes the following topics:
• Opening and Saving a Datastore
• Adding Compounds, Quantitation Peaks, and Confirming Ions to a Datastore
• Choosing Experiment Types
For a description of all the parameters in the Compound Datastore view, see “Compound
Datastore view” on page 56.
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Compound Datastore
Opening and Saving a Datastore
You can use the default datastore or you can create your own datastore. The Compound
Datastore task pane is available only when the Compound Datastore feature is enabled. See
“Enabling Optional Features” on page 84.
Follow these procedures:
• To open the Compound Datastore editor
• To open a compound datastore
• To create a new compound datastore
• To save a datastore
• To save a datastore to a new name
 To open the Compound Datastore editor
1. Click Configuration from the dashboard or the navigation pane.
The Configuration navigation pane opens. See “Configuration mode navigation pane” on
page 36.
2. Click the Compound Datastore task pane.
The current datastore opens in the Compound Datastore view. For a detailed list of all
parameters and functions in the Compound Datastore view, see “Compound Datastore
view” on page 56.
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Compound Datastore
 To open a compound datastore
1. Click Load Compound Datastore in the Compound Datastore task pane.
The Open Compound Datastore dialog box opens.
2. Double-click the name of the datastore you want to open.
The selected datastore opens in the Compound Datastore view. See “Compound
Datastore view” on page 56.
 To create a new compound datastore
Click New Compound Datastore in the Compound Datastore task pane.
A new, empty datastore opens in the Compound Datastore view.
You can import a file of compounds into the new datastore (following the instructions, To
import compounds), or you can manually add compounds one at a time (following the
instructions, To add a compound to the datastore).
 To save a datastore
1. Click Save Compound Datastore in the Compound Datastore task pane.
The application stores the database as
…\Thermo\TraceFinder\2.0\General\Databases\filename.xml
If the datastore contains any compounds that do not have associated quantitation peaks,
the Invalid Compound Datastore Not Saved dialog box opens, listing the compounds.
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Compound Datastore
2. To add a quantitation peak row to the listed compounds, click Continue.
The application returns you to the Compound Datastore view.
3. Add quantitation peaks to the incomplete compounds before you save the datastore.
See “To add a quantitation peak to a compound” on page 61.
 To save a datastore to a new name
1. Click Save As Compound Datastore in the Compound Datastore task pane.
The Save Compound Datastore dialog box opens.
2. Type a file name for the new compound datastore.
3. Click Save.
The application stores the database as
…\Thermo\TraceFinder\2.0\General\Databases\filename.xml
Figure 9.
Save Compound Datastore dialog box
Table 8. Save Compound Datastore dialog box parameters
Thermo Scientific
Parameter
Description
Compound Datastore
name
Lists the file name for the new datastore.
Overwrite
Overwrites the selected datastore.
OK
Writes the new datastore to the Databases folder.
Cancel
Closes the dialog box and makes no changes to the datastore.
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Compound Datastore
Figure 10. Compound Datastore view
Table 9. Compound Datastore view parameters (Sheet 1 of 3)
Parameter
Description
Function icons
Adds a new compound row.
Removes the selected row and all quantitation peak and confirming ion rows within it.
Adds a new quantitation peak row to the compound. Each compound requires at least one
quantitation peak.
Removes the selected row and all confirming ion rows within it.
Adds a new confirming ion row to the quantitation peak.
Removes the selected confirming ion row.
Select experiment types
to display
Specifies one of these experiment types that each use a different structure for the mass
filter. See “Choosing Experiment Types” on page 63.
• SRM: Selected Reaction Monitoring
• XIC: Extracted Ion Chromatogram
• SIM: Single Ion Monitoring
Compound parameters
Compound Name
Alphanumeric name assigned to the compound.
Experiment Type
Experiment type: SRM, XIC, or SIM.
Category
(Optional) Alphanumeric identifier.
Ionization
(Optional) Alphanumeric identifier.
Valid values: None, ESI, APCI, EI, CI, APPI
Default: None
Chemical Formula
(Optional) Alphanumeric chemical identifier.
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Table 9. Compound Datastore view parameters (Sheet 2 of 3)
Parameter
Description
Quantitative peak parameters
Precursor Mass
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.
In confirming ion rows, the precursor mass is a noneditable copy of the quantitation peak
precursor mass.
Available only for SRM experiments.
Default: 0.0
Range: 10.000 to 2999.999
Product Mass
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.
Available only for SRM experiments.
Default: 0.0
Range: 10.000 to 2999.999
Mass
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.
Available only for XIC and SIM experiments.
Default: 0.0
Range: 10.000 to 2999.999
Collision Energy
The energy used when ions collide with the collision gas.
Available only for SRM experiments.
Range: –250.00 to 250.00
RT (min)
Retention time. The application uses 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
Window (sec)
The application uses RT and Window values to determine the start and stop time for the
acquisition.
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
Polarity
+ (positive) or – (negative)
Lens
(Optional) Range: –400 to 400
Energy Ramp
(Optional)
Available only for SRM experiments.
Range: 0.00 to 200.00
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Table 9. Compound Datastore view parameters (Sheet 3 of 3)
Parameter
Description
Confirming ion parameters
Precursor Mass
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.
Available as a noneditible field only for SRM experiments.
Default: 0.0
Range: 10.000 to 2999.999
Product Mass
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.
Available only for SRM experiments.
Default: 0.0
Range: 10.000 to 2999.999
Mass
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.
Available only for XIC and SIM experiments.
Default: 0.0
Range: 10.000 to 2999.999
Collision Energy
The energy used when ions collide with the collision gas.
Available only for SRM experiments.
Range: –250.00 to 250.00
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Compound Datastore
Adding Compounds, Quantitation Peaks, and Confirming Ions to a Datastore
In the Compound Datastore view, you can import compounds into the datastore, add or
remove compounds from the datastore, add quantitation peaks and confirming ions to a
compound, or remove quantitation peaks or confirming ions from a compound.
Follow these procedures:
• To import compounds
• To add a compound to the datastore
• To remove a compound
• To add a quantitation peak to a compound
• To remove a quantitation peak
• To add a confirming ion to a quantitation peak
• To remove a confirming ion
 To import compounds
1. Click Import Compounds in the Compound Datastore task pane.
2. Browse to a .csv or .xml compounds file and click Open.
The TraceFinder application imports the compounds from the imported file, adds them
to any compounds already in the datastore, and alphabetically sorts them.
When the application imports a compound that contains multiple quantitation peaks and
confirming ions, it lists all the peaks under a single compound name, as in this example
for Monuron:
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Compound Datastore
 To add a compound to the datastore
1. Click the Add Compound button,
, or right-click the compounds list and choose
Add Compound from the shortcut menu.
The application adds a new, empty compound row to the compounds table.
2. Click the first table cell, and enter the required Compound Name parameter.
3. (Optional) Change the value for the Experiment Type.
The default is SRM. For descriptions of available experiment types, see “Choosing
Experiment Types” on page 63.
After you add a quantitation peak to the compound, you cannot change the experiment
type, even if you cancel the quantitation peak.
4. (Optional) Type a value or select a value from the Category list.
You can use any alphanumeric string. After you type a new Category value, that value is
available from the list.
5. (Optional) Change the values for Ionization.
The default is None.
6. (Optional) Type a value for the Chemical Formula.
You can use any alphanumeric string.
Each compound requires at least one quantitation peak.
 To remove a compound
1. Select the compound row you want to delete.
2. Click the Remove Compound button,
Compound from the shortcut menu.
, or right-click and choose Remove
3. If you are sure you want to delete the selected row, at the prompt, click OK.
The application removes the selected row and all quantitation peak and confirming ion
rows within it.
Tip If you add a row of compound information and do not complete all the column
required values, you can right-click and choose Cancel to remove the entire row. You
can cancel only an incomplete compound row.
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Compound Datastore
 To add a quantitation peak to a compound
1. Select the compound.
2. Click the Add Quan Peak button,
from the shortcut menu.
, or right-click and choose Add Quan Peak
The application adds a new quantitation peak row to the compound. A quantitation peak
includes quantitative values for the compound. Each compound requires at least one
quantitation peak.
quantitation peak row
3. Enter all required parameters.
For a list of required and optional parameters, see the list of “Compound Datastore view
parameters” on page 56.
Tip You cannot add another new compound or save the compound datastore until
you enter all required quantitation peak parameters or remove incomplete
quantitation peaks from the compound.
4. Repeat steps 2 through 3 to add as many as six quantitation peaks to the compound.
 To remove a quantitation peak
1. Select the row of the quantitation peak you want to delete.
2. Click the Remove Quan Peak button,
Peak from the shortcut menu.
, or right-click and choose Remove Quan
3. If you are sure you want to delete the selected row, at the prompt, click OK.
The application removes the selected row and all confirming ion rows within it.
Tip If you add a row of quantitation peak information and do not complete all the
required values, you can right-click and choose Cancel to remove the entire row. You
can cancel only incomplete quantitation peak rows.
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Compound Datastore
 To add a confirming ion to a quantitation peak
1. Click the Add Confirming Ion icon,
, or right-click the quantitation peak row and
choose Add Confirming Ion from the shortcut menu.
The application adds a new confirming ion row to the quantitation peak. A confirming
ion includes a mass value.
Confirming ion row
2. Type the required column values for the confirming ion.
The required confirming ion values differ for each experiment type. See “Choosing
Experiment Types” on page 63.
3. Repeats steps 1 through 2 to add as many as 10 confirming ions to the quantitation peak.
 To remove a confirming ion
1. Select the confirming ion row you want to delete.
2. Click the Remove Confirming Ion icon,
Confirming Ion from the shortcut menu.
, or right-click and choose Remove
3. If you are sure you want to delete the selected row, at the prompt, click OK.
The application removes the selected confirming ion row.
Tip If you add a row of confirming ion information and do not complete all the
required values, you can right-click and choose Cancel to remove the entire row. You
can cancel only incomplete confirming ion rows.
 To filter a list
Click the funnel icon,
, in the column header.
For each column, the application displays filterable criteria (compound names,
experiment types, categories, or ionization methods) in a list. In all lists, you can choose
to view all criteria or a specific type of criterion for that column.
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Compound Datastore
Choosing Experiment Types
The TraceFinder application uses three experiment types: SRM, XIC, and SIM.
A compound datastore 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 ions include values for product mass, collision energy, and a noneditable
precursor mass.
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 ions include a single mass value.
SIM – Single Ion Monitoring
The SIM experiment type supports single quadrupole LC/MS and Exactive™ systems. The
mass filter includes narrow mass ranges to identify product masses.
Confirming ions include a single mass value.
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Application Configuration
Application Configuration
When user security is enabled, users in the LabDirector or ITAdmin role can enable features
such as available reports, user security, compound datastore, reporting defaults, multiplexing,
detection algorithms, and target screening. You can also choose the reports that are available
to users, the application defaults, and the defaults used for peak detection.
This section includes the following tasks:
• Specifying the Reports Configuration
• Specifying Configuration Defaults
• Specifying Detection Parameters
• Enabling Optional Features
 To open the Application Configuration view
1. Click Configuration from the dashboard or the navigation pane.
The Configuration navigation pane opens. See “Configuration mode navigation pane” on
page 36.
2. Click Application Configuration.
The Application Configuration view opens.
Table 10. Application Configuration pages
Page
Reports
See “Specifying the Reports Configuration” on page 65.
Defaults
See “Specifying Configuration Defaults” on page 70.
Detection
See “Specifying Detection Parameters” on page 72.
Optional Features
See “Enabling Optional Features” on page 84
3. In the Application Configuration list, click the type of information you want to
configure.
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Application Configuration
Specifying the Reports Configuration
When user security is enabled, users in the LabDirector or ITAdmin role can configure a list
of reports that are available to all users when they generate reports from the Method
Development, Analysis, and Acquisition modes. From the Reports page, you can configure
the standard, custom, or target screening reports.
Example PDFs of report formats are located in the following folder:
C:\Thermo\TraceFinder\2.0\General\ExampleReports
Follow these procedures:
• To open the Reports page
• To specify which reports are available
• To import new reports
 To open the Reports page
In the Application Configuration view, click Reports.
The Reports page of the Application Configuration view opens. For a list of reports, see
“Reports” on page 67.
 To specify which reports are available
1. Use the directional arrows to move reports from the Installed Reports pane to the
Displayed Reports pane.
Tip Use the CTRL or SHIFT keys to select multiple reports.
In the Method Development, Analysis, and Acquisition modes, users can access all
reports in the Displayed Reports pane.
2. To create a single composite report for an entire batch (rather than separate reports for
each sample), select the Batch Level check box for the report.
Rather than creating separate reports for each sample, the application uses a composite of
the data from all the samples to create a single report for the entire batch. Batch-level
reports are prepended with a B to differentiate them.
Note Only reports that can aggregate data at the batch level have the Batch Level
check box enabled. By default, the application selects the Batch Level feature for all
these reports.
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Application Configuration
3. Do one of the following:
Apply the current selections as follows:
a. Click Apply.
A message prompts you to restart the TraceFinder application so that a user can access
the reports you selected for the Method Development, Analysis, and Acquisition
modes.
b. To restart the TraceFinder application now, click Yes, or to remain on the Reports
page, click No.
–Or–
To return the report selections to their original state (when you first opened this page),
click Undo Changes.
 To import new reports
1. Click Import.
2. In the browser, locate a Crystal Reports .dll or Custom Reports .xltm file and open the
file.
The application writes the imported report to the TraceFinder installation directory and
displays the new report in the Installed Reports pane.
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Reports
The application uses the following standard, custom, and target screening reports. For
descriptions of the parameters on the Reports page, see “Reports page parameters” on page 69.
Figure 11. Reports page showing standard reports
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Figure 12. Reports page showing custom reports
Figure 13. Reports page showing target screening reports
Note Target screening reports are available only when you install ToxID and enable the
target screening features. See “Enabling Optional Features” on page 84.
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Table 11. Reports page parameters
Thermo Scientific
Parameter
Description
Installed Reports
All reports listed in this pane are potentially available but are not
selected for use in the application.
Displayed Reports
All reports listed in this pane are selected for use in the
application.
>>
Moves all reports from the Installed Reports list to the Displayed
Reports list.
>
Moves the selected reports from the Installed Reports list to the
Displayed Reports list.
<
Moves the selected reports from the Displayed Reports list to the
Installed Reports list.
<<
Moves all reports from the Displayed Reports list to the Installed
Reports list.
Import
Opens a browser where you can select a report file to add to the
Installed Reports list.
Undo changes
Returns the report selections to their original state (when you
first opened this page).
Apply
Applies the current selections, and prompts you to restart the
TraceFinder application so that a user can access the reports you
selected for the Method Development, Analysis, and Acquisition
modes.
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Application Configuration
Specifying Configuration Defaults
Use the Application Configuration view of the Configuration mode to specify the default
laboratory and instrument names, the mass precision, and the intensity scale to use for
reporting. When user security is enabled, only users in the LabDirector or ITAdmin role can
access these features.
Follow these procedures:
• To open the Application Defaults page
• To specify a default laboratory name and instrument name
• To specify default mass precision and the intensity scale
 To open the Application Defaults page
In the Application Configuration view, click Defaults.
The Application Defaults page of the Application Configuration view opens.
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 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 General page of the Master 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.
3. In the Application Configuration view, click Apply.
The application does not apply this default instrument name to previously created
batches. By default, the instrument name is Thermo Scientific Instrument.
4. Click Yes.
 To specify default mass precision and the intensity scale
1. In the Display Mass Precision box, set the mass precision decimal places value to an
integer from 0 to 5, inclusive.
The default mass precision is 2. The TraceFinder application uses this mass precision
value 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)
– Qualitative Summary Report (all m/z values)
– 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
2. Select Relative or Absolute from the Chromatogram Intensity Scale list.
This sets the default display type for both quantitation and qualitative chromatograms
displayed in data review and reports.
3. In the Application Configuration view, click Apply.
4. Click Yes.
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Application Configuration
Specifying Detection Parameters
When user security is enabled, users in the LabDirector or ITAdmin role can specify detection
parameters for the Genesis, ICIS, or Avalon detection algorithms. Use the Peak Detection
Defaults page to specify a peak detection algorithm and its options and to determine the area
under a curve.
This section includes procedures for specifying the following detection algorithms:
• Genesis Detection Method
• ICIS Detection Method
• Avalon Detection Method
 To specify common detection parameters
1. In the Application Configuration view, click Detection.
The Peak Detection Defaults page opens. See “Common peak detection areas” on
page 73.
2. In the Detector Type list, select a detector type.
3. In the Mass Tolerance area, do the following:
a. Select the unit of measure you want to use.
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.
4. 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.
5. In the Ion Ratio Parameters area, do the following:
a. In the Window Type box, 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.
6. In the Peak Detection Parameters area, select one of the detection algorithms: Genesis,
ICIS, or Avalon.
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Figure 14. Common peak detection areas
Table 12. Common peak detection parameters
Parameter
Description
Detector Type
Reserved for future releases.
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
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.
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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Application Configuration
Genesis Detection Method
The TraceFinder application provides the Genesis peak detection algorithm for backward
compatibility with Xcalibur 1.0 studies.
Figure 15. Genesis peak detection page
Table 13. Genesis peak detection page parameters (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. The ICIS peak detection algorithm uses this value.
Range: Any odd integer from 1 through 15 points
Default: 1
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Table 13. Genesis peak detection page parameters (Sheet 2 of 3)
Parameter
Description
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
enables 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 13. Genesis peak detection page parameters (Sheet 3 of 3)
Parameter
Description
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
Valley S/N
Specifies a value to evaluate the valley bottom. Using this parameter ensures that the
surrounding measurements are higher.
Range: 1.0 to 100.0
Default: 2.0
# 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 16. ICIS peak detection page
Table 14. ICIS peak detection page parameters (Sheet 1 of 3)
Parameter
Description
Sensitivity
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.
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
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Table 14. ICIS peak detection page parameters (Sheet 2 of 3)
Parameter
Description
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
Peak height (%)
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
enables the Peak Height (%) and Tailing Factor options.
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
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.
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Table 14. ICIS peak detection page parameters (Sheet 3 of 3)
Parameter
Description
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
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.
Figure 17. Avalon peak detection page
Table 15. Avalon peak detection page parameters
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.
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
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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.
Edit
Opens the Avalon Event List dialog box where you can edit the
Time/Event/Value parameters. See “Avalon Event List” on
page 81.
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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”
on page 82.
Figure 18. Avalon Event List dialog box
Table 16. 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” on page 82.
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 19. Event types
Table 17. Event type definitions (Sheet 1 of 2)
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Parameter
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 17. Event type definitions (Sheet 2 of 2)
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Parameter
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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Application Configuration
Enabling Optional Features
In the Application Configuration view of the Configuration mode, you can enable the
following features:
• User Security
• Target Screening
• Quick Acquisition
• Compound Datastore
• Delay Calibration Calculation
• Batch Wizard Style
• Multiplexing
• Acquisition Submission Options
 To open the Optional Features page
In the Application Configuration view, click Optional Features.
The Optional Features page of the Application Configuration view opens.
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Application Configuration
User Security
When user security is enabled, all users must log on to the TraceFinder application for access
to only those modes assigned to their user role. See “Choosing User Roles” on page 43.
 To turn on user security
1. Select the User Security check box.
When this check box is selected, all users must log on to the TraceFinder application for
access to the modes assigned to their user role. See “Choosing User Roles” on page 43.
When user security is enabled, only users in the LabDirector or ITAdmin roles can access
the Configuration mode.
When this check box is cleared, users are not required to log on to the TraceFinder
application. When they start the application, the dashboard is the first screen that users
see and all modes are available to them. The User Administration view in the
Configuration mode is hidden from all users except those assigned the LabDirector or
ITAdmin role.
IMPORTANT If you are the administrator logging on with user security enabled, you
can use Administrator/Password as the username/password.
2. Click Apply.
A message prompts you to restart the TraceFinder application so that your changes can
take effect.
3. Click Yes.
Target Screening
You must have the ToxID application installed on your computer before you can generate
Target Screening reports.
 To enable target screening
1. Select the Target Screening (ToxID) check box.
2. Click Apply.
A message prompts you to restart the TraceFinder application so that your changes can
take effect.
3. Click Yes.
For a list of available target screening reports, see “Reports” on page 67.
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Application Configuration
Quick Acquisition
The quick acquisition option enables the Quick Acquisition feature in the Acquisition,
Analysis, or Method Development mode.
Note The Quick Acquisition feature is not available when you enable multiplexing. See
“Multiplexing” on page 87.
 To enable quick acquisition
1. Select the Quick Acquisition (EnviroLab/ToxLab/QuanLab Forms) check box.
2. Click Apply.
A message prompts you to restart the TraceFinder application so that your changes can
take effect.
3. Click Yes.
For a description of the Quick Acquisition features, see “Working with Master Methods” on
page 94.
Compound Datastore
 To enable the compound datastore
1. Select the Compound Datastore check box.
By default, the Compound Datastore option is not selected.
2. In the Application Configuration view, click Apply.
3. Click Yes.
The application implements the following changes:
• Displays the Acquisition List page on the Compounds page in the Master Method
View. See “Editing the Compounds Page” on page 120.
• Displays the Compound Datastore task pane on the Configuration mode navigation
pane. See “Compound Datastore” on page 52.
• Enables the Export SRM Data command in the Method Development mode. See
“Exporting SRM Data” on page 196.
Delay Calibration Calculation
Use the Delay Calibration Calculation... option to make the application wait until it processes
the last calibration sample in a batch before it calculates the calibration curve (faster) instead
of recalculating the calibration curve after each calibration sample (more responsive).
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 To delay calculation of a calibration curve
1. Select the Delay Calibration Calculation... check box.
By default, this option is selected.
2. In the Application Configuration view, click Apply.
3. Click Yes.
Batch Wizard Style
Use the Batch Wizard Style option to choose one of two styles for your batch wizard.
 To select a wizard style
1. In the Batch Wizard Style list, select a wizard style:
• Acquisition Batch Wizard: Adds the Acquisition mode to the navigation pane. This
mode is similar to the Acquisition mode in the TraceFinder 1.1 application. See
Chapter 5, “Using the Acquisition Mode.”
When you enable multiplexing, the application automatically enables this wizard
style.
• Batch Template Wizard: The default wizard style that is similar to the acquisition
wizard in the EnviroLab Forms, ToxLab Forms, and QuanLab Forms applications.
See “Creating a Batch Using the Batch Wizard” on page 290.
Note The Batch Template Wizard feature is not available when you enable
multiplexing. See “Multiplexing” on page 87.
2. Click Apply.
A message prompts you to restart the TraceFinder application so that your changes can
take effect.
3. Click Yes.
Multiplexing
The Multiplexing options are available only when you have installed the Power Modules. See
“Installing the Power Modules” on page 13.
 To specify multiplexing features
1. Select the Multiplexing check box.
2. Choose 2 Channels or 4 Channels.
3. When you are using 2 channels, select a 1- or 2-arm autosampler configuration.
The 1 arm configuration enables channels 1 and 3; the 2 arm configuration enables
channels 2 and 4.
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4. Click Apply.
A message prompts you to restart the TraceFinder application so that your changes can
take effect.
5. Click Yes.
When you enable multiplexing, the following optional features are not available:
• Quick Acquisition
• Batch Template Wizard
• Single Sample Submission (Intelligent Sequencing)
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 225) or monitor an
acquisition (see “Devices Page” on page 252).
Acquisition Submission Options
To control acquisitions, you can enable full-sequence or single-sample submission options.
When you submit batches from the Acquisition mode, development batches from the
Method Development 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 are using Full Sequence Submission, priority batches always run immediately
after the currently acquiring batch completes.
• When you are using Single Sample Submission, priority batches always run immediately
after the currently acquiring sample completes.
 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 preparation for all sample
injections when the pre-run condition begins. All samples in the batch must
complete before other batches (even higher priority batches) can begin.
• 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 enable
multiplexing. See “Multiplexing” on page 87.
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Application Configuration
2. Click Apply.
A message prompts you to restart the TraceFinder application so that your changes can
take effect.
3. Click Yes.
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Using the Method Development Mode
This chapter includes method development tasks assigned to the Supervisor or LabDirector
roles when user security is enabled.
Contents
• Working with Master Methods
• Working with Instrument Methods
• Working with Development Batches
• Using Quick Acquisition
From the Method Development mode, you can create a master method, an instrument
method, or a simple development batch to test your instrument method.
You can also use the Quick Acquisition feature to quickly submit a single sample from any
view in the Method Development mode.
 To access the Method Development mode
Click Method Development from the dashboard or the navigation pane.
The Method Development navigation pane opens. For a detailed description of all the
features on the Method Development navigation pane, see “Method Development
navigation pane” on page 92.
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Figure 20. Method Development navigation pane
Available only when you enable the Compound
Datastore feature in the Configuration mode.
Available only when you select the Acquisition
Batch Wizard in the Configuration mode.
Table 18. Method Development navigation pane functions (Sheet 1 of 2)
Function
Description
Method View
See “Working with Master Methods” on page 94.
Create method
Opens the Create Master Method dialog box where you can choose the process you want to
use to begin your master method.
Open method
Opens the Open Master Method dialog box where you can choose a master method to
open.
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Table 18. Method Development navigation pane functions (Sheet 2 of 2)
Function
Description
Import Published
Method
Opens the Import Published Method dialog box where you can select a published method
to import.
Export SRM data
Writes the selected reaction monitoring (SRM) table to the following file:
…\Thermo\TraceFinder\2.0\General\Methods\methodname.xml
You can use the data in this file in the instrument method editor when you open the TSQ
2.1 application. This command is displayed only when you enable the Compound
Datastore option in the Configuration mode. See “Compound Datastore” on page 86.
The compounds in the Acquisition List must contain at least one SRM experiment type.
Recent Files
Displays recently saved master methods.
Instrument View
See “Working with Instrument Methods” on page 197.
New instrument
method
Opens the Instrument View where you can specify instrument settings for your configured
instruments.
If the instrument you want to use is not configured, close the TraceFinder application,
configure the instrument, and then reopen the application. You cannot configure an
instrument while the TraceFinder application is running.
Open instrument
method
Opens a browser where you can choose an instrument method to open.
Development Batch
See “Working with Development Batches” on page 204.
Select batch location
Specifies a location to store temporary development batch raw data files.
New sample list
Removes acquired samples from your development batch, so you can begin a new sample
list.
Open Qual Browser
Opens the Thermo Xcalibur Qual Browser where you can view the acquired raw data files.
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Working with 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.
A 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 evaluates 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.
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 data.
This section includes instructions for the following tasks:
• Creating a New Master Method
• Editing a Master Method
• Creating a Method Template
• Importing Published Master Methods
• Exporting SRM Data
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Creating a New Master Method
To begin a master method, follow any of four different procedures in the Create Master
Method dialog box:
• Creating a New Method with Method Forge
• Importing an Xcalibur Master Method
• Associating a Raw Data File
• Selecting Compounds from the Compound Datastore
With each procedure, you begin the method in a specific way and then use the common
features of the Master Method View to complete and save your master method.
Figure 21. Create Master Method dialog box
Available only when you enable the Compound
Datastore feature in the Configuration mode.
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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 a detailed description of all the Method Forge parameters, see “Method
Forge dialog box parameters” on page 102.
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.
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 Method View task pane, click Create Method.
The Create Master Method dialog box opens. See “Create Master Method dialog box” on
page 95.
2. Select the Use Method Forge option and click OK.
The Method Forge dialog box opens. For a detailed description of all the features on the
Method Forge dialog box, see “Method Forge dialog box” on page 101.
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.
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3. In the Method Forge dialog box, do one of the following:
Select the Use the Default Template option.
–Or–
Select the Select a Custom Template option and highlight your custom template in the
Method template table.
For detailed instructions on creating a custom method template, see “Creating a Method
Template” on page 186.
4. Select the Name the Master Method check box and type a name for your master method.
You can enter an existing method name and overwrite it when you create the method. If
you do not specify a name, the application names the method for the raw data file used to
create the method.
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, choose Use an Existing Raw Data File.
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, choose Acquire a New Raw Data File.
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. If you chose to acquire a new raw data file, do one of the following:
Choose Manual Injection.
–Or–
Specify the autosampler settings by doing the following:
a. Choose Use Autosampler.
b. In the Vial Position box, type a vial position.
c. In the Injection Volume box, type an injection volume.
The minimum injection volume allowed is 0.1 μL; the maximum injection volume
allowed is 5000 μL.
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8. To automatically create the master method, click OK (or Overwrite).
As the Method Forge creates the method, it displays the following status:
The Method Forge process searches the NIST library and displays the identified
compound names instead of peak times.
When the acquisition completes, Method Forge performs peak detection, datastore
searching, and characteristic ion and reference spectrum identification. Method Forge
then loads this information into a new master method. This process occurs immediately if
you selected a previously acquired raw data file.
If the compounds in the raw data file you used to create the method are not in the current
compound datastore, the TraceFinder application displays the compounds in the Edit
Compound Dependent Parameters dialog box.
9. (Optional) Select the compounds that you want to add to the compound datastore and
click Add to CDS.
The selected compounds are added to the current compound datastore.
Note You must click the Add to CDS button before you continue to the method.
10. To use these compounds in your method and close the dialog box, click Continue to
Method.
The TraceFinder application uses all compounds found in the raw data file in your
method and displays the General page of the Master Method View. For a detailed
description of all the features on the General page, see “General page” on page 117.
11. From the Instrument Method list on the General page, select an instrument method.
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12. From the Qualitative Peak Processing Template list, select a method template for
performing peak detection on quantitative samples following target compound analysis.
13. 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.
14. 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 110.
 To manually select compounds to create a new method
1. From the Method View task pane, click Create Method.
The Create Master Method dialog box opens. See “Create Master Method dialog box” on
page 95.
2. In the Create Master Method dialog box, select the Use Method Forge option and click
OK.
The Method Forge dialog box opens. For a detailed description of all the features on the
Method Forge dialog box, see “Importing an Xcalibur Master Method” on page 103.
3. In the Method Forge dialog box, do one of the following:
Select the Use the Default Template option.
–Or–
Select the Select a Custom Template option and highlight your custom template in the
Method Template table.
For detailed instructions about creating a custom method template, see “Creating a
Method Template” on page 186.
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4. Select the Name the Master Method check box and type a name for your master method.
You can enter an existing method name and overwrite it when you create the method. If
you do not specify a name, the method is named for the raw data file used to create the
method.
5. Ensure that the Automatically Create the Master Method check box is not selected.
6. To select a raw data file, click the browse button and locate the file.
7. To manually create the master method, click OK (or Overwrite).
The Master Method View displays a list of possible matches in the Library Results pane.
The TraceFinder application displays the best match in the Compound Name list and
displays the peak spectrum for that compound.
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8. To use a compound other than the compound chosen by the TraceFinder application,
scroll to the spectrum for that compound and select the compound name in the header of
the spectrum pane.
Select
compound
9. After you manually select your compound, click Create to create the master method.
The TraceFinder application uses all compounds found in the raw data file in your
method and displays the General page of the Master Method View. For a detailed
description of all the features on the General page, see “General page” on page 117.
10. From the Instrument Method list on the General page, select an instrument method.
11. 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 110.
Figure 22. Method Forge dialog box
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Table 19. Method Forge dialog box parameters
Parameter
Description
Method template selection
Use the default
template
Creates a new method with the default template.
Select a custom
template
Lists all the available method templates.
Name the master
method
The name for the new master method.
Automatically create
the master method
When the acquisition completes, Method Forge performs peak detection, library searching,
and characteristic ion and reference spectrum identification. This information is loaded into
a new master method. This process occurs immediately when you specify an existing raw
data file.
For detailed instructions about creating a custom method template, see “Creating a Method
Template” on page 186.
Raw file selection
Use an existing raw
data file
Enables the Raw Filename box where you can select a raw data file used in creating the
master method.
Acquire a new raw data Enables functions to acquire data to create a raw data file used in creating the master
file
method.
Instrument
method
The saved method (.meth) file used for acquiring the data.
Raw filename
The file name where the TraceFinder application writes the raw data.
Path
The location where the TraceFinder application saves the raw data file.
Sample comment
(Optional) Comment about the acquired sample or the data file.
Manual injection
Performs a manual acquisition.
Use autosampler
Performs an autosampler acquisition.
Vial position
The tray vial number used for the autosampler acquisition.
Injection amount
The volume (in milliliters) injected by the autosampler acquisition.
Function button
Overwrite
Overwrites the specified master method name. This function is enabled only when the
specified master method name already exists.
OK
Creates a master method using the data and parameters you specified.
Cancel
Closes the 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. From the Method View task pane, click Create Method.
The Create Master Method dialog box opens. See “Create Master Method dialog box” on
page 95.
2. In the Create Master Method dialog box, select the Import Xcalibur Processing Method
option and click OK.
The Import an Xcalibur Method dialog box opens.
3. Click the browse button for the Xcalibur Method to Import box, browse to the Xcalibur
processing method file, and open the file.
The TraceFinder application imports the compound information from the Xcalibur
method file.
4. (Optional) Click the browse button for the Raw Data File to Associate box, browse to the
raw data file, and open the file.
5. (Optional) Change the number of decimal places in the Mass Precision box.
You can set the mass precision decimal places to any integer between 0 and 5, inclusive.
Note When you associate a raw data file, the application reads the mass precision
from the file and this parameter is unavailable.
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6. Click OK.
If the compounds in the imported Xcalibur method file are not in the Compound
Datastore, the TraceFinder application displays the compounds in the Edit Compound
Dependent Parameters dialog box.
7. (Optional) Select the compounds you want to add to the Compound Datastore and click
Add to CDS.
The selected compounds are added to the current compound datastore.
To add these compounds to the datastore, you must click the Add to CDS button before
you continue to the method. When you click Continue to Method, the Edit Compound
Dependent Parameters dialog box closes and you cannot return to add the compounds.
8. To add these compounds to your method and close the dialog box, click Continue to
Method.
The TraceFinder application adds all compounds found in the imported Xcalibur method
and displays the General page of the Master Method View. For a detailed description of
all the features on the General page, see “General page” on page 117.
9. From the Instrument Method list on the General page, select an instrument method.
10. 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 110.
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Associating a Raw Data File
You can use the compounds in a previously acquired raw data file to create a new master
method.
Follow these procedures:
• To associate a raw data file with the method
• To add compounds to the method
 To associate a raw data file with the method
1. From the Method View task pane, click Create Method.
The Create Master Method dialog box opens. See “Create Master Method dialog box” on
page 95.
2. In the Create Master Method dialog box, select the Associate a Raw Data File option
and click OK.
The Associate a Raw Data File dialog box opens.
3. Click the browse button and locate a raw data file to associate with the method.
4. To set a reference spectrum, select the Yes option.
The TraceFinder application adds all compounds found in the raw data file to your
method and displays the General page of the Master Method View. For a detailed
description of all the features on the General page, see “General page” on page 117.
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5. From the Instrument Method list on the General page, select an instrument method.
6. To save the new method, choose File > Save from the main menu.
If the compounds in the associated raw data file are not found in the Compound
Datastore, you cannot save the method. Follow the instructions “To add compounds to
the method” on page 106.
For a detailed description of how to modify a master method, see “Editing a Master
Method” on page 110.
 To add compounds to the method
1. Click the Compounds tab.
The Detection page is selected by default.
Note When the Compound Datastore is enabled, the Compounds page includes an
Acquisition List tab. See “Enabling Optional Features” on page 84.
The Detection page shows an empty Compound list and displays the chromatographic
data for the compounds in the raw data file.
2. Select a filter from the Filter list.
3. Click the peak in the chromatogram that represents the compound you want to add to
the method.
4. 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 quan peak, and the second and third largest ions as the confirming ions.
If the name of the first match is already in the library, the Add New Compound dialog
box opens.
5. (Optional) In the Add New Compound dialog box, 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.
Select
compound
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b. In the Type of Compound to Add list, select a compound type.
c. Click OK.
6. Repeat this procedure for each compound you want to add to the method.
For a detailed description of all the features on the Detection page, see “Editing the
Compounds Page” on page 120.
For a detailed description of how to modify a master method, see “Editing a Master
Method” on page 110.
Selecting Compounds from the Compound Datastore
You can select compounds from the compound datastore to create a new master method. This
method for creating a master method is available only when the compound datastore is
enabled. See “Compound Datastore” on page 86.
 To select compounds from the datastore
1. From the Method View task pane, click Create Method.
The Create Master Method dialog box opens.
2. In the Create Master Method dialog box, select the Select Compounds from CDS
option and click OK.
The Select Compounds to Add dialog box opens, listing all the compounds defined in the
compound datastore.
3. Select the check box for each of the compounds you want to add to the method.
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4. To quickly select multiple compounds, right-click and use any of the commands on the
shortcut menu.
Table 20. Select Compounds to Add shortcut menu
Command
Description
Select All
Selects all compounds in the compound datastore.
Deselect All
Clears all compounds in the compound datastore.
Copy Down
Copies the state (checked or cleared) of the currently selected
compound to all compounds below it in the compound list.
5. Click Apply.
The TraceFinder application adds the selected compounds to the method.
Note After you add a compound to a method, the compound is no longer enabled in
the Select Compounds to Add dialog box. You cannot remove the applied compounds
from the method by returning to this dialog box. To remove a compound from a
method, see “Acquisition List” on page 120.
6. From the Instrument Method list on the General page, select an instrument method.
7. 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 110.
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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 in the method.
This section includes instructions for the following tasks:
• Opening a Master Method
• Editing the General Page
• Editing the Compounds Page
• Editing the QAQC Page
• Editing the Groups Page
• Editing the Reports Page
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 legacy TraceFinder, EnviroLab Forms,
QuanLab Forms, or ToxLab Forms applications. To convert legacy methods, see “Converting
Legacy Data” on page 19.
 To open a saved master method
1. Click Method Development from the dashboard or the navigation pane.
The Method Development navigation pane opens.
2. In the Method View task pane, do one of the following:
Click Open Method.
–Or–
Click a method name in the Recent Files list.
When you save a method, the application adds it to the Recent Files list. The Recent Files
list displays a list of your most recently saved master method files.
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The Open Master Method dialog box opens.
The Open Master Method dialog box displays all available methods.
3. Select a master method and click Open.
The TraceFinder application copies all components of the selected method including its
associated instrument method.
The General page for the selected method opens in the Method View. For a detailed
description of all the features on the General page, see “General page” on page 117.
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Editing the General Page
The General page defines basic information about the master method. For a detailed
description of all the features on the General page, see “General page” on page 117.
Follow these procedures:
• To specify general information for a master method
• To edit the instrument method parameters
• To select a qualitative peak processing template
• To set automated background subtraction options
• To specify a chromatogram reference sample
• To specify mass tolerance
 To specify general 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.
3. From the Injection Volume box, select the injection volume (in 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 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 calibration levels on the Compounds page,
see “Editing the Compounds Page” on page 120.
5. From the Qualitative Peak Processing Template box, select a template for performing
peak detection on quantitative samples following target compound analysis.
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 To edit the instrument method parameters
1. From the Instrument Method list on the General page, select an instrument method.
2. To edit the instrument method for this master method, click Edit.
The Thermo Xcalibur Instrument Setup dialog box opens. This example instrument
setup shows multiple configured instruments.
3. Edit the values on the instrument page for your instrument.
4. From the main menu on the Thermo Xcalibur Instrument Setup dialog box,
choose File > Save and then choose File > Exit.
The TraceFinder application returns you to the General page.
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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 Xcalibur Method: Overwrites the instrument method in the
C:\Xcalibur\methods folder with the current instrument method.
• Get From Xcalibur Method: Overwrites the current instrument method with the
instrument method in the C:\Xcalibur\methods folder.
• Cancel: Make no changes to the instrument method in the current master method.
 To select a qualitative peak processing template
In the Qualitative Peak Processing Template list, select the template you want to use to
perform peak detection on quantitative samples following compound analysis.
The application lists all method templates (.pmtx file format) in the following folder:
C:\Thermo\TraceFinder\2.0\General\Templates\Methods
 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 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.
2. In the Number of Scans to Subtract box, enter a number.
This is the number of scans that the TraceFinder application subtracts from the
background after averaging. If you specified to subtract scans from both sides of the peak,
the application subtracts this number of scans from each side of the peak.
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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. For example:
If you specified to subtract 3 scans before the peak 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.
 To specify a chromatogram reference sample
1. In the Set Chromatogram Reference Sample list, select External.
2. Click Select.
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 this 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, it must have been processed with the current master
method.
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7. Click Open.
The selected sample is displayed as the chromatogram reference sample in the Master
Method View.
Tip To clear the reference sample from the master method, select None in the Set
Chromatogram Reference Sample list.
 To specify mass tolerance
1. Select the units of measure 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.
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Figure 23. General page
Table 21. General page parameters (Sheet 1 of 3)
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 Configuration Defaults” on
page 70.
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).
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Table 21. General page parameters (Sheet 2 of 3)
Parameter
Description
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 through 5000 μL
Ion range calc method
The TraceFinder application uses the selected ion range calc method 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 120.
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 Xcalibur Method: Overwrites the Xcalibur method with the current
instrument method.
• Get From Xcalibur Method: Overwrites the current instrument method with the
Xcalibur method.
Qualitative peak
processing template
The TraceFinder application uses the qualitative peak processing template to perform peak
detection on quantitative samples following compound analysis.
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.
Set chromatogram
reference sample
Valid values: None, External
Default: None
Set Reference sample
This parameter is enabled only when Set Chromatogram Reference Sample is set to
External. Click the Select button to choose a reference sample from the project folders.
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Table 21. General page parameters (Sheet 3 of 3)
Parameter
Description
Mass Tolerance
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.
Notes
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Editing the Compounds Page
Use the Compounds page to set all parameters for the identification, detection, and
quantification for the target compound list.
From the Compounds page of the Master Method View, you can access the following pages:
• Acquisition List
• Identification
• Detection
• Calibration
• Calibration Levels
• QC Levels
• Real Time Viewer
Each page on the Compounds page (except the Acquisition List page) uses a right-click
shortcut menu. See “Using the Shortcut Menu Commands” on page 162.
Acquisition List
The Acquisition List page displays all compounds defined for the current method. From this
page, you can add or delete compounds from the method. For a detailed description of all the
features on the Acquisition List page, see “Acquisition List page” on page 122.
The Acquisition List page is displayed only when you enable the Compound Datastore option
in the Configuration mode. See “Compound Datastore” on page 86.
Follow these procedures:
• To filter the compound list
• To delete a compound from the list
• To add a compound to the list
 To filter the compound list
1. To display a filtered list of compounds, click the funnel icon,
, in the column header.
The application displays a list of filterable criteria. In all lists, you can choose to filter by
All, Blanks, NonBlanks, or by custom filter criteria. Other filter criteria are specific to the
individual columns.
2. To create a custom filter based on compound values in a specific column, choose Custom
from the column list.
For detailed instructions about creating a custom filter, see Appendix C, “Using Filter
Criteria.”
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 To delete a compound from the list
1. Select the compound to remove from the list.
2. Click the Remove Compound icon,
Compound from the shortcut menu.
, or right-click and choose Remove
A confirmation dialog box opens, listing the compound to be removed.
3. To confirm the deletion, click Yes.
The selected compound is removed from the acquisition list, which has no effect on the
compound datastore.
 To add a compound to the list
1. Click the Add Compound icon,
the shortcut menu.
, or right-click and choose Add Compound from
The Select Compounds to Add dialog box opens, listing all the compounds defined in the
compound datastore.
2. Select the check box for each of the compounds you want to add to the method.
3. To quickly select multiple compounds, right-click and use any of the commands on the
shortcut menu.
Table 22. Select Compounds to Add shortcut menu
Command
Description
Select All
Selects all compounds in the compound datastore.
Deselect All
Clears all compounds in the compound datastore.
Copy Down
Copies the state (checked or cleared) of the currently selected
compound to all compounds below it in the compound list.
4. Click Apply.
The TraceFinder application adds the compounds to the Acquisition List and
Compounds pages of the Master Method View.
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Figure 24. Acquisition List page
Table 23. Acquisition List page parameters (Sheet 1 of 2)
Parameter
Description
Function Icons
Opens the Select Compounds to Add dialog box that lists all the compounds defined in the
compound datastore.
Deletes the selected compound. The icon is unavailable when no row is selected. If you used
the filters to display a subset of compounds, the selected compound might not be visible on
the Acquisition List page.
Compound parameters
Compound Name
Alphanumeric name assigned to the compound.
Experiment Type
Experiment type: SRM, XIC, or SIM.
Category
(Optional) Alphanumeric identifier.
Ionization
(Optional) Alphanumeric identifier.
Valid values: ESI, APCI, EI, CI, APPI
Chemical Formula
(Optional) Alphanumeric chemical identifier.
Quantitation peak parameters
Precursor Mass
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.
Available only for SRM experiments.
Range: 10.000 to 2999.999
Product Mass
The mass-to-charge ratio of the quan ion. The location of the center of a target quan-ion
peak in mass-to-charge ratio (m/z) units.
Available only for SRM experiments.
Range: 10.000 to 2999.999
Mass
The mass-to-charge ratio of the quan ion. The location of the center of a target quan-ion
peak in mass-to-charge ratio (m/z) units.
Available only for XIC and SIM experiments.
Range: 10.000 to 2999.999
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Table 23. Acquisition List page parameters (Sheet 2 of 2)
Parameter
Description
Collision Energy
The energy used when ions collide with the collision gas.
Range: –250 to 250
Lens
(Optional) Range: –400 to 400
Polarity
+ (positive) or – (negative)
RT (min)
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
Window (sec)
Acquisition window. The TraceFinder application uses the RT and Window values to
determine the start and stop time for the acquisition.
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
Energy Ramp
Available only for SRM experiments.
Range: 0.00 to 200.00
Confirming ion parameters
Precursor Mass
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.
Available as a read-only field for SRM experiments only.
Range: 10.000 to 2999.999
Product Mass
The mass-to-charge ratio of the quan ion. The location of the center of a target quan-ion
peak in mass-to-charge ratio (m/z) units.
Available only for SRM experiments.
Range: 10.000 to 2999.999
Mass
The mass-to-charge ratio of the quan ion. The location of the center of a target quan-ion
peak in mass-to-charge ratio (m/z) units.
Available only for XIC and SIM experiments.
Range: 10.000 to 2999.999
Collision Energy
The energy used when ions collide with the collision gas.
Available only for SRM experiments.
Range: –250.00 to 250.00
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Identification
The Identification page lists the compounds that are targeted for analysis, reporting, and other
compound-specific values. For a description of all values on the Identification page, see
“Identification page” on page 125.
 To filter the displayed compounds
From the Show list, select the type of compounds you want to display in the compounds
list.
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Compound type
Description
Quan compounds
Displays only quan compounds, such as target
compounds, internal standards, and surrogates.
Target compounds
Displays only target compounds.
Internal Standards
Displays only internal standard compounds.
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Figure 25. Identification page
Table 24. Identification 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.
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
A list of compounds that have been identified. To customize the compound names, click the
cell and type a new name. To display a filtered list of compounds, use the Show list.
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 to 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.
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
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.
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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
• Signal
• Detect
• Spectrum
• Ratios
On the Detection page (see “Detection page” on page 134), 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 quantification peak, mass range, or
confirming ion. The TraceFinder application automatically uses the first match it finds as the
compound name, the base peak of the mass spectrum as the quan peak, and the second and
third largest ions as the confirming ions.
Follow these procedures:
• To filter the displayed compounds
• To add compounds to the method
• To change the compound reference spectrum
• To replace a quan mass
• To add a mass to the existing quan mass ranges
• To add a quan peak
• To add a mass as a new compound
• To replace a confirming ion
• To add a mass as a new confirming ion
• To save the new method
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 To filter the displayed compounds
From the Show list, select the type of compounds you want to display in the compounds
list.
Compound type
Description
Quan compounds
Displays only quan compounds, such as target
compounds, internal standards, and surrogates.
Target compounds
Displays only target compounds.
Internal Standards
Displays only internal standard compounds.
 To add compounds to the method
1. From the main menu, choose Master Method > Associate a Raw Data File.
The Associate a Raw Data File dialog box opens.
2. Browse to a raw data file to associate with the method and open the file.
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.
This feature is available only when you have set background subtraction values on the
General page of the Master Method View. See “Editing the General Page” on page 112.
6. Click OK.
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The TraceFinder application displays the chromatographic and spectrum data for the
compounds in the selected raw data file.
7. Select a filter from the Filter list.
8. Click to select the peak in the chromatogram that represents the compound you want to
add to the method.
9. 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 quan peak, and the second and third largest ions as the confirming ions.
If the name of the first match is already in the library, the Add New Compound dialog
box opens.
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Figure 26. Add New Compound dialog box
10. (Optional) 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
11. In the Type of Compound to Add list, select a compound type.
12. Click OK.
13. Repeat this procedure for each compound you want to add to the method.
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 To change the compound reference spectrum
1. In the raw data file chromatogram pane, click a peak.
The TraceFinder application displays the spectrum for the selected peak in the spectrum
pane.
2. In the raw data file spectrum pane, right-click and choose Use This Spectrum for
Compound Reference Spectrum from the shortcut menu.
The TraceFinder application replaces the spectrum on the Spectrum page of the quan
peak pane with this spectrum.
 To replace a quan mass
1. Click the pane for the quan mass 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 Mass as Quan Mass 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 ions. See
“Ratios” on page 154.
 To add a mass to the existing quan mass ranges
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 Mass to Existing Quan Mass 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 quan 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 ions. See “Ratios” on page 154.
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 To add a quan peak
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 Mass as New Quan Peak from the shortcut menu.
The application adds a new quan peak to the compound.
You can use the shortcut menu on the spectrum pane for this new quan peak to perform
any of the tasks you could perform on the original quan peak.
 To add a mass 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 Mass 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 quan peak, and the second and third largest ions as the confirming ions.
If the name of the first match is already in the library, the Add New Compound dialog
box opens with the matching compound selected.
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Figure 27. Add New Compound dialog box
3. (Optional) In the Add New Compound dialog box, make any of the following changes:
a. Change the name for the compound in the Name of New Compound box.
b. 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
c. In the Type of Compound to Add list, select a compound type.
4. Click OK.
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 To replace a confirming ion
1. Click the pane for the confirming ion 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 Mass as Confirming Ion from the shortcut menu.
The TraceFinder application replaces the confirming ion with the selected mass.
 To add a mass as a new confirming ion
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 Mass as New Confirming Ion from the shortcut menu.
The TraceFinder application adds the confirming ion to the quan peak.
You can use the shortcut menu on the spectrum pane for this new confirming ion to
perform any of the tasks you could perform on the original confirming ions.
 To save the new method
1. Choose File > Save.
The Save Master Method 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 data in the following folder:
…\Thermo\TraceFinder\2.0\General\Methods
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Figure 28. Detection page
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Table 25. Detection page parameters
Parameter
Description
Compound list
Lists all compounds in the master method.
Quan peak
Displays a chromatogram for the quan peak and its confirming ions. The quan peak and
confirming ion panes include additional pages for retention time, signal, detection,
spectrum, and ratio parameters.
Filter
Displays the filter used for the raw data file.
Reference
chromatogram and
spectra
Displays a reference chromatogram and spectra for the raw data file.
Additional pages
Times
Defines the retention time and window for a quan peak.
See “Times” on page 136.
Signal
Defines the detector and its parameters used to display each chromatogram trace. See
“Signal” on page 137.
Detect
Defines the peak detection algorithm and its options.
See “Detect” on page 140.
Spectrum
Defines a reference mass spectrum for a quan peak or compound. See “Spectrum” on
page 149.
Ratios
Defines the criteria for evaluating, confirming, or qualifying ions. See “Ratios” on page 154.
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Times
Use the Times page to define the retention time and window for a quan peak.
Figure 29. Times page
Table 26. Times page parameters
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Parameter
Description
Expected RT (min)
Expected retention time. The time after injection when the
compound elutes. The total time that the compound is retained
on the column.
Window (sec)
Width of the window (in seconds) to indicate how far around the
expected retention time the system looks for a peak apex.
View width (min)
Viewable size 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.
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Signal
Use the Signal page to define the detector and its parameters as you display each
chromatogram trace. For a detailed description of all the features on the Signal page, see
“Signal page parameters” on page 138.
 To specify ranges of ions for detection and integration
1. In the Ranges area, click Edit.
The Edit Mass Ranges dialog box opens where you can enter rows using a center of mass
or a range.
Figure 30. Edit Mass Ranges dialog box
2. Enter a value in the Center Mass box and click Add.
The application adds a row with this value to the ranges grid. Center mass values are listed
in the Start m/z column. The application uses a range of one amu centered on this value.
3. 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.
4. 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.
5. Click Apply.
When you are editing a master method, the application applies the entries to the list of
ranges.
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Figure 31. Signal page
Table 27. Signal page parameters (Sheet 1 of 2)
Parameter
Description
Detector
MS: Mass spectrometers.
Analog: Supplemental detectors (for example, FID, ECD).
AD 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.
Filter
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.
Trace
Represents a specific range of the data. In conjunction with the filter, the TraceFinder application
uses the trace to identify the characteristic ions for a compound. The options are: Mass Range, TIC,
or Base Peak.
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Table 27. Signal page parameters (Sheet 2 of 2)
Parameter
Description
Ranges
Edit
Opens the Edit Mass Ranges dialog box where you can specify a range of ions for detection and
integration. See “Edit Mass Ranges dialog box” on page 137.
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. On this page, you can specify how you want each mode to run.
For a detailed description of all the features on the Detect page for Genesis sensitivity,
see “Detect page parameters for Genesis” on page 142.
For a detailed description of all the features on the Detect page for ICIS sensitivity,
see “Detect page parameters for ICIS” on page 145.
For a detailed description of all the features on the Detect page for Avalon sensitivity,
see “Detect page parameters for Avalon” on page 147.
 To apply current peak detection settings to all peaks
1. Edit the parameters for either the Quan peak or a Confirming peak.
2. Right-click the Detect page and choose Apply to All Peaks in Method from the shortcut
menu.
The application updates all compounds in the method with the current settings on the
Detect page. These updates apply to both quan and confirming ions.
 To apply current peak detection settings to all peaks that use the same detection
mode
1. Edit the parameters for either the Quan peak or a Confirming peak.
2. Right-click the Detect page and choose Apply to All Peaks with Like Sensitivity Setting
from the shortcut menu.
The application uses the current settings on the Detect page to update all compounds in
the method that use the same sensitivity mode (Genesis, ICIS, or Avalon). These updates
apply to both quan and confirming ions that use the same sensitivity mode.
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Figure 32. Detect page for Genesis
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Table 28. Detect page parameters for Genesis (Sheet 1 of 2)
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.
Range: Any odd integer from 1 through 15 points
Default: 1
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
enables 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 28. Detect page parameters for Genesis (Sheet 2 of 2)
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
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.
Range: 1.0 to 100.0
Default: 2.0
# 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.
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Figure 33. Detect page for ICIS
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Table 29. Detect page parameters for ICIS (Sheet 1 of 2)
Parameter
Description
Sensitivity
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.
Smoothing
Determines the degree of data smoothing to be performed on the active component peak
prior to peak detection and integration.
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.
Range: 1 through 500
Default: 5
Peak noise factor
The noise level multiplier used to determine the potential peak signal threshold.
Range: 1 through 1000
Default: 10
Baseline window
The TraceFinder application looks for a local minima over this number of scans.
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
enables 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 29. Detect page parameters for ICIS (Sheet 2 of 2)
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
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.
Range: 0 to 100 scans
Default: 3
Multiplet resolution
The minimum separation in scans between the apexes of two potential peaks. This is a
criterion to determine if two peaks are resolved.
Range: 1 to 500 scans
Default: 10
Area tail extension
The number of scans past the peak endpoint to use in averaging the intensity.
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
146
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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Figure 34. Detect page for Avalon
Table 30. 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 30. 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.
Range: Any odd integer from 1 through 15 points
Default: 1
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 81.
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Spectrum
Use the Spectrum page to store a reference mass spectrum for a quan peak or compound.
For a detailed description of all the shortcut menu commands on the Spectrum page, see
“Spectrum shortcut menu functions” on page 153.
Follow these procedures:
• To update confirming ion ratios
• To change the quantitation mass used for a quan peak
• To add ions together to get an accumulated signal
• To add a quan 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 update confirming ion ratios
1. Click a peak in the quan 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.
 To change the quantitation mass used for a quan 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 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 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 quan peak and a quan peak with an updated quan
mass.
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Figure 35. Original quan peak mass example
Original quan peak mass
The TraceFinder application replaces the original quan mass with the selected mass.
Figure 36. Updated quan peak example
New quan peak mass
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 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 quan peak signal.
 To add a quan 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 quan peak.
New quan peak mass
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 To add one or more confirming ions to an existing compound
1. Click the 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 quan
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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Figure 37. Spectrum page
Table 31. Spectrum shortcut menu functions
Functions
Description
Update confirming ion Updates the confirming ion ratios using the selected peak.
ratios with this spectrum
Set this mass as quan
mass
Adds the quan mass of the selected ion to the quantitation mass used for the quan peak.
You can choose to update the ion ratios or not update the ion ratios using this reference
spectrum.
Add this mass to
Adds the selected mass to your existing quan mass range. You can choose to update the ion
existing quan mass range ratios to adjust the confirming ion comparisons to the new summed quan peak signal.
Set this mass as new
quan peak
Adds a new quan peak to an existing compound.
Add this mass as new
confirming ion
Adds one or more confirming ions to an existing compound.
Reset scaling
Returns the chromatogram or spectrum display to its original size.
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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 on reports.
For a detailed description of all the features on the Ratios page, see “Ratios page parameters”
on page 155.
 To specify ion ratio criteria
1. Select the Enable check box to enable 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 is 41.02 to 81.02%.
• If, instead, 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 is 48.82 to 73.22%.
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Figure 38. Ratios page
Table 32. 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.
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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.
Figure 39. Calibration page
Table 33. 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.
Compound type
Displays the compound type as a Target Compound or Internal Standard.
Standard type
Specifies Internal or External standards.
Response via
The use of area or height.
Curve type
Specifies Linear, Quadratic, or AverageRF curve types.
Origin
The origin treatment as Ignore, Include, or Force. The Origin and Weighting columns are
active only when you are using Linear or Quadratic curve types.
Weighting
Specifies the weighting as Equal, 1/X, 1/X^2, 1/Y, or 1/Y^2.
Units
The units to be displayed with the calculated values.
ISTD
The internal standard (ISTD) for a target compound or surrogate if the standard type is set
to Internal. If you set the standard type to External, this field is inactive.
Amount
The amount of the internal standard for ISTD compounds.
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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.
 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 TraceFinder 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
level for each compound.
4. To enter the concentrations to 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 you want to
copy, right-click, and choose Copy Down from the shortcut menu.
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Figure 40. Calibration Levels page
Table 34. 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.
cal1-caln
User-defined calibration levels for the compound.
Manage Calibration
levels
Defines values for each of the calibration level values for the selected compound.
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QC Levels
Use the QC levels page for a master method to define the standards for QC levels. You can
edit QC levels for master methods only. The contents of this page are read-only when you are
editing a local method. For a detailed description of all the features on the QC Levels page, see
“QC levels page parameters” on page 160.
 To specify QC levels and concentrations
1. Select the compound whose QC levels, percentage test values, and concentrations you
want to define.
2. In the QC Levels area, type a name for the first QC level.
The TraceFinder application adds a new, empty QC 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 QC level.
4. Continue adding QC levels and values for the percentage test.
When you finish adding QC levels, you can specify the concentrations for each level for
each compound.
5. To enter the concentration values to the table, do the following:
a. Select the first QC 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 QC levels associated with the first compound.
7. To specify the same concentration values for all compounds, select the value you want to
copy, right-click, and choose Copy Down from the shortcut menu.
Figure 41. QC Levels page
Table 35. QC 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.
QC1-QCn
User-defined quality control levels for the compound.
QC levels
Level
User-defined quality control level names.
% Test
A value for the acceptable difference (as a percentage) between the known amount and
calculated (measured) amount of each QC level.
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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 or when you acquire a development
batch in the Method Development mode. See “Real-Time Display” on page 249.
Figure 42. Real Time Viewer page
Table 36. Real Time Viewer page parameters (Sheet 1 of 2)
Parameter
Description
Show Quan Peaks
Only
Displays only quan peaks in the compounds list. Quan peaks are indicated with a dot in the
Quan Peak column.
Displayable Traces
Quan Peak
Checks indicate quan peak traces. Unchecked traces indicate confirming ions.
Compound Name
Names of all compounds in the method.
Trace
Lists the simple mass or precursor mass for all traces—both quan peak and confirming
ion—for each compound.
Moves the selected trace to the Traces to Display in Real Time Viewer pane.
Moves the selected trace to the Displayable Traces pane.
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Table 36. Real Time Viewer page parameters (Sheet 2 of 2)
Parameter
Description
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 (0/25)
List the traces to be displayed and the display order in the real-time viewer in the
Acquisition mode. 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.
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.
Using the Shortcut Menu Commands
Each page on the Compounds page (except the Acquisition List page) 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 37. Compounds page shortcut menu (Sheet 1 of 2)
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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 B, “Using Copy Down and
Fill Down.”
Display retention time
column
Displays or hides the RT column in the compound list.
Delete compound from
method
Removes the selected compound from the current master
method.
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Table 37. Compounds page shortcut menu (Sheet 2 of 2)
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Command
Description
Copy
Copies the data in the selected rows or columns to the Clipboard.
Use this command to copy compound information to another
application, such as an Excel spreadsheet. 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 another application, such as an
Excel spreadsheet. You cannot paste this data back into the
method development compound list.
Paste
Pastes a single column of copied data from another application,
such as an Excel spreadsheet, 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.
Export to CSV file
Opens the Save As dialog box where you can save the current
compound list to a .csv file.
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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.
From the QAQC page of the Master Method View, you can access these additional pages:
• Limits
• Calibration
• Chk Std
• Matrix Blank
• ISTD
• Solvent Blank
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Limits
Use the Limits page to define levels of review for quantified results. Quantified results appear
on printed and electronic reports. You can also define when a quantified value is reported
instead of reporting less than a particular limit.
Figure 43. Limits page
Figure 44. 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
Thermo Scientific
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 makes the evaluation by comparing the initial calibration results for each
compound found in the sample to the values defined on this page.
On the Calibration report, the application flags the calculated values for internal standard
compounds that exceed these limits.
Figure 45. Calibration page
Table 38. 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).
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).
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Chk Std
Use the Chk Std page to review the calibration on an ongoing basis. The TraceFinder
application makes the evaluation by comparing the quality check standard results for each
compound in the sample to the initial calibration using values defined on this page.
On the Check 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 Chk Std sample versus the theoretical value is set on the QC Levels page of the
Compounds page.
Figure 46. Chk Std page
Table 39. 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
Chk Std sample and the average response factor from the
calibration (when in average RF mode).
Min RF
The minimum response factor for the Chk Std sample (when in
average RF mode).
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Matrix Blank
Use the Matrix Blank page to define acceptable levels of target compounds in blank samples.
The TraceFinder application makes the evaluation by comparing 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.
On 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 47. Matrix Blank page
Table 40. 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 (if
available). The TraceFinder application makes the evaluation by comparing 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 you have not identified
any compounds as internal standards, this page does not show any values.
Figure 48. ISTD page
Table 41. 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
makes the evaluation by comparing the calculated response for each compound in the sample
to the maximum response defined on this page.
On the Solvent Blank report, the TraceFinder application flags the calculated values for target
compounds that exceed these limits.
Figure 49. Solvent Blank page
Table 42. 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 quan ion only
(Quan Ion RT) or a summed response for the quan 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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Editing the Groups Page
Use the Groups page of the Master Method View to organize compounds into functional or
logical groups. You can use these groups for creating a subset of target compounds. For a
detailed description of all the features on the Groups page, see “Groups page parameters” on
page 172.
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 create a group
1. From the Show list, select the type of compounds you want to view.
2. At the bottom of the Groups area, click Add Group.
The Add a New Group dialog box opens.
3. Type a name for the new group and click OK.
The new group appears in the Groups area.
4. Drag a compound from the Compounds area onto a group name (as if you were moving
files into a folder).
5. 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.
6. To remove a single compound, right-click the compound name in the group and choose
Remove from Group from the shortcut menu.
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Figure 50. Groups page
Table 43. Groups page parameters
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.
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 Reports Page
Use the Reports page to specify how you want to save or print your reports. For a detailed
description of the features on the Reports page, see “Reports page parameters” on page 174.
For the Quantitation Report type, you can modify quan report, user interface, quan flag, and
surrogate correction options in the Report Options pane.
This section includes instructions for the following tasks:
• Specifying Report Formats
• Specifying Quan Report Settings
• Specifying Target Screening Settings
Specifying Report Formats
• For each standard report, you can create a hardcopy printout, a PDF file, or an XML file.
• For each custom report, you can create a hardcopy printout or an Excel Macro-Enabled
Workbook (.xlsm) file.
• For each target screening report, you can create a hardcopy printout or a PDF file.
In addition to the report type, you can specify a report description for each of your reports.
The default report description is the report name.
 To specify report types and output formats
1. Click the Reports tab.
The Reports page displays the following columns for all configured reports:
• Example: Click the magnifying glass icon to open an example PDF of the report type
• Report Name, Report Description, and Report Type
• For standard report types: Options to create a hardcopy, PDF file, or XML file
• For custom report types: Options to create a hardcopy or Excel Macro-Enabled
Workbook file
• For target screening report types: Options to create a hardcopy or PDF file
• Batch Level: Option that indicates which reports are batch-level reports
For information about configuring which reports are available when you create a master
method or which reports create a batch-level report, see “Specifying the Reports
Configuration” on page 65.
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2. To edit the Report Description, double-click the name and type your new description.
The TraceFinder application uses this description for all reports that use this master
method. You cannot edit the Report Description from other report views.
3. To specify the type of report output to create for each report type, select the check box in
the appropriate column.
4. To duplicate the 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.
Figure 51. Reports page
Table 44. Reports page parameters (Sheet 1 of 2)
Parameter
Description
Example
Opens a PDF that displays an example of the report type.
Report Name
The name of a report.
Report Description
The user-defined description to be used on a report.
Report Type
The type of report: Standard, Custom, or Target Screening.
Print
Sends reports to the printer.
Create PDF
Saves reports as PDF files.
Available only for standard and target screening reports.
Create XML
Exports reports in XML format.
Available only for standard reports.
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Table 44. Reports page parameters (Sheet 2 of 2)
Parameter
Description
Create XLSM
Exports reports in Excel Macro-Enabled Workbook (.xlsm) format.
Available only for custom reports.
Batch Level
Rather than creating separate reports for each sample, the application uses a composite of
the data from all the appropriate samples to create a single report for the entire batch.
Batch-level reports are prepended with a B to differentiate them.
You cannot select this option from the Reports page. You must select the Batch Level option
for the report in the report configuration. See “Specifying the Reports Configuration” on
page 65.
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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 standard report types.
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 164.
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 on 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 7 calibration standards, select the Use Alternate
Calibration Report Format check box.
4. To display flags and a legend on high density reports, select the Display Quan Flags and
Legend check box.
 To specify quantitation flag options
Select the values you want to display in the report.
Values are above or below the limits defined on the Quan page.
These flags appear on a variety of reports and are defined in the “Quan Report Settings
page parameters” on page 178.
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Figure 52. Quan Report Settings page
Table 45. 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 on the quantitation report.
Display compounds
above set limit
Prints only the positive compounds in a sample. If a compound is above the specified Quan
Flag Options limits, the TraceFinder application reports the compound.
User Interface Options
Shade row when
sample is outside of
evaluation criteria
Shades a compound row on any of the reports if a value fails one of the criteria used for
evaluation.
Separate ion overlay
display
Separates the ion overlay pane from the confirming ion plots in data review.
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 7 calibration standards).
Display Quan flags and Displays manual flags, confirming manual flags, quan flags, and a legend on high density
legend
reports.
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Table 45. Quan Report Settings page parameters (Sheet 2 of 2)
Parameter
Description
Quan Flag Options
Values that are above or below limits defined on the Limits page. These flags appear on 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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Specifying Target Screening Settings
Use the options on the Target Screening Settings page to set the parameters required to
produce Target Screening reports. For a detailed description of the features on the Target
Screening Settings page, see “Target Screening Settings page parameters” on page 183.
The TraceFinder application use these parameters to process a raw data file and create a report
similar to a ToxID report. See “Example Target Screening Summary Report” on page 185.
Follow these procedures:
• To specify the default parameters
• To calculate and report semi-quantitative results
• To specify the ion ratio calculation method
• To specify the exact mass window
• To specify the Exactive parameters
 To specify the default parameters
1. Click the Processing Configuration File browse button and select a configuration file
(.csv).
2. From the Screening Method list, select one of these compound screening methods.
• (Default) Auto Detect
• Based on Full MS2 scans
• Based on SRM and MS2 scans
• Based on MS2 and MS3 scans
• Based on MS3 scans
• Based on accurate mass scans
• Based on SRM scans
• Based on Exactive screening method
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3. Type the name of the company to print on the report.
4. Type the name of the laboratory to print on the report.
5. Click the Company Logo browse button and select a graphic file (.jpg, .gif, or .bmp) to
print on the report.
6. In the m/z Window box, enter a value for the window above and below the m/z value for
the compounds.
7. In the RT Window box, enter a value for the window above and below the retention time
value for the compounds.
8. In the MS2 Search Library boxes, type the names of as many as three search libraries for
searching MS/MS spectra.
9. In the MS3 Search Library boxes, type the names of as many as three search libraries for
searching MS3 spectra.
10. Select the Use Full MS Scan to Confirm check box if you want to confirm library search
results with parent ion peak detection in the full scan.
When the application does not detect a peak in the full scan, the compound is not
reported as a hit.
 To calculate and report semi-quantitative results
1. In the Semi Quantitative area, do the following:
a. Select the Report Semi-Quantitative Result check box.
b. Type the measurement units.
The measurement units are used only for labeling purposes.
2. Select either the Scan Intensity or Peak Area option.
• Scan Intensity: The application measures the intensity of the MS/MS peak without
performing background subtraction.
• Peak Area: The application measures the peak area of the reconstructed full scan
chromatogram peak of the parent ion. When you select Peak Area, the Use Full MS
Scan to Confirm check box is automatically selected.
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 To specify the ion ratio calculation method
1. Select the Use Scan at Peak Apex or Use Average Scan option.
• Use Scan at Peak Apex: The application calculates the ion ratio based on the peak
apex scan spectrum.
• Use Average Scan: The application calculates the ion ratio based on the average scan
spectrum over the range of the peak’s half height. The relative intensity in the
configuration file must use the selected scan method.
2. In the Ion Ratio Window (%) box, type the acceptable percentage of the intensity of the
qualifier ion to the quan ion.
For example, when the Ion Ratio Window is 20% and the quan ion has an
intensity/height of 100, the specified confirming ion/mass must have a height of at least
80 to be considered found.
 To specify the exact mass window
Type a total window width value in parts per million for the Exact Mass Window.
For example, when you expect a mass of 50 with a window of 2, the algorithm creates an
XIC based on the responses of all masses from 49 to 51.
 To specify the Exactive parameters
1. Type values for Adduct 1, Adduct 2, and Adduct 3.
These values identify the adducts listed in and applied throughout the configuration file.
Adducts are polarity sensitive. For negative ionization, enter negative adduct values.
These values default to H+, NH4+, and Na+, respectively.
2. To search the entire raw data file for the specified peak, do the following:
a. Select the No Specified Retention Time check box.
b. Select either the First Peak or Highest Peak option.
When the search finds more than one m/z match in the raw data file, the application
uses the specified peak for processing.
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3. Select the Report All Compounds Listed in Configuration File check box to report all
compounds in the configuration file whether or not matches are found for them.
The default reports on only those compounds where matches are found in the raw data
file. This option applies to the Exactive™ experiment only.
Figure 53. Target Screening Settings page
Table 46. Target Screening Settings page parameters (Sheet 1 of 2)
Parameter
Description
Processing
Configuration File
Specifies a configuration file (.csv).
Screening Method
Specifies one of the following screening methods:
• (Default) Auto Detect
• Based on Full MS2 scans
• Based on SRM and MS2 scans
• Based on MS2 and MS3 scans
• Based on MS3 scans
• Based on accurate mass scans
• Based on SRM scans
• Based on Exactive screening method
Note Using the Auto Detect method, the ToxID application can identify the screening
experiment implemented in the acquired data file.
Company Name
Specifies the name of the company to print on the report.
Laboratory Name
Specifies the name of the laboratory to print on the report.
Company Logo
Specifies a graphic file (.jpg, .gif, or .bmp) to print on the report.
m/z Window (mu)
Specifies a value for the window above and below the m/z value for the compounds.
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Table 46. Target Screening Settings page parameters (Sheet 2 of 2)
Parameter
Description
RT window (min)
Specifies a value for the window above and below the retention time value for the
compounds.
MS2 Search Library
Specifies the names of as many as three search libraries for searching MS/MS spectra.
MS3 Search Library
Specifies the names of as many as three search libraries for searching MS3 spectra.
Use Full MS Scan to
Confirm
Specifies that the application confirms library search results with parent ion peak detection
in the full scan. When the application does not detect a peak in the full scan, the compound
is not reported as a hit.
Semi Quantitative
Report
Semi-Quantitative
Result
Measurement Unit
Calculation based on
Specifies one of the following calculation methods:
• Scan Intensity: Specifies that the application measures the intensity of the MS/MS peak
without performing background subtraction.
• Peak Area: Specifies that the application measures the peak area of the reconstructed full
scan chromatogram peak of the parent ion. When you select Peak Area, the Use Full MS
Scan to Confirm check box is automatically selected.
Ion Ratio Calculation Method (In SRM Experiment)
Use Scan at Peak Apex
Specifies that the application calculates the ion ratio based on the peak apex scan spectrum.
Use Average Scan
Specifies that the application calculates the ion ratio based on the average scan spectrum
over the range of the peak’s half height. The relative intensity in the configuration file must
use the selected scan method.
Ion Ratio Window(%)
Accurate Mass Experiment
Exact Mass Window
Specifies a value in parts per million for the accurate mass experiment.
Exactive
Adduct 1–n
Specifies the adducts listed in and applied throughout the configuration file. Adducts are
polarity sensitive. For negative ionization, enter negative adduct values.
Defaults: Adduct 1: H+, Adduct 2: NH4+, and Adduct 3: Na+
No Specified Retention Specifies either First Peak or Highest Peak to use for processing when the search finds more
Time
than one m/z match in the raw data file.
Report All Compounds Specifies that in an Exactive experiment, the application reports all compounds in the
Listed in Configuration configuration file whether or not matches are found for them.
File
Default: Reports only those compounds where matches are found in the raw data file.
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Figure 54. Example Target Screening Summary Report
Your Company Name
Summary Report
Raw File Name: C:\Xcalibur\examples\ToxID\Exact_Mass\Exact_Mass_Test.RAW
Config File Name: C:\Xcalibur\examples\ToxID\Exact_Mass\ConfigFile_Exact_mass.csv
Sample Name:
Laboratory: Your Lab Name
Acquistion Start Time: 3/24/2008 4:46:43 PM
Screening Conditions: Based on accurate mass scans. Exact mass window (ppm): 30, RT window(min): 0.50.
Peak 1
50
Peak 2
NL: 2.03E5
m/z= 240.15580-240.16300
F: FTMS + c ESI Full ms
[120.00-1000.00]
2.58
2.52
100
1.99 2.39
0
100
2.84 4.16
4.66
NL: 1.26E7
m/z= 250.17665-250.18415
F: FTMS + c ESI Full ms
[120.00-1000.00]
4.69
50
Peak 3
4.82
5.19
4.06
0
100
7.68
9.47
NL: 1.18E7
m/z= 278.18643-278.19477
F: FTMS + c ESI Full ms
[120.00-1000.00]
50
Peak 4
1.53
0
100
4.12
3.57
50
Peak 5
0
100
3.49
3.13
0.87
5.36
10.15
NL: 2.12E6
m/z= 328.14938-328.15922
F: FTMS + c ESI Full ms
[120.00-1000.00]
3.80
4.18
12.50
50
Peak 6
0
100
3.98
4.33
11.50
50
0
Peak
Number
Thermo Scientific
Compound Name
3.72
2
NL: 4.59E6
m/z= 342.16507-342.17533
F: FTMS + c ESI Full ms
[120.00-1000.00]
NL: 9.08E6
m/z= 337.20734-337.21746
F: FTMS + c ESI Full ms
[120.00-1000.00]
4.12
4
6
Time (min)
Expected Detected
m/z
m/z
8
10
Delta
(mDa)
12
Delta
(ppm)
Expected Actual RT
RT
Intensity
1
Albuterol
240.15940 240.15939
-0.0
-0.0
2.58
2.58
199505
2
Alprenolol
250.18040 250.18039
-0.0
-0.0
4.50
4.66
12604499
3
Amitriptyline
278.19060 278.19061
0.0
0.0
5.00
5.19
11769755
4
6-Acetylmorphine
328.15430 328.15433
0.0
0.1
3.30
3.57
2112090
5
6-Acetylcodeine
342.17020 342.17035
0.1
0.4
4.10
4.18
4593306
6
Acebutolol
337.21240 337.21246
0.1
0.2
3.80
3.98
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Creating a Method Template
In the TraceFinder application, you can create a processing method using a method template
that contains common settings.
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 enter a note for the method
• To save the method template
 To open the Method Template Editor
1. Click Method Development from the dashboard or the navigation pane.
The Method Development navigation pane opens.
2. Click Method View in the navigation pane.
3. From the main menu, choose File > New > Method Template.
The Method Template Editor opens. For a complete description of the Method Template
Editor, see “Method Template Editor dialog box” on page 192.
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 To specify peak criteria
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 is provided for 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
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
1. In the Use these Libraries box, select the libraries 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. This value defaults to 2 because you typically perform a 3-ion experiment
with one quan 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, all weighting values are unavailable except for Equal.
• Quadratic: All other settings are available with this exception: When you select
Include in the Origin list, all weighting values are unavailable except for Equal.
• Average RF: No selections in the Weighting or Origin lists are available. The
Weighting list is set to Equal, and the Origin list is set to Ignore.
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 you specify. For additional information about the Genesis
algorithm, see “Genesis Detection Method” on page 74.
2. Select or clear the Exclude Matching Quan Peaks check box and specify a value for the
exclusion window.
The application excludes quan peaks in a range plus/minus the value you specify.
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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.
In addition to the peak information, the TIC Report and TIC Summary Report display
information about the data-dependent filtered data. See Appendix A, “Reports.”
 To enter a note for the method
Type in the Notes box, or paste text from another application using CTRL+V.
You can add a note to your method template to explain what makes this template unique.
 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:
…\Thermo\TraceFinder\2.0\General\Templates\Methods
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Figure 55. Method Template Editor dialog box
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Table 47. Method Template Editor dialog box parameters (Sheet 1 of 2)
Parameter
Description
Find the peaks
Sensitivity
Defines how extensively the peak detector algorithm searches for low-level peaks.
Limit the retention time Min RT specifies the beginning of the range. Max RT specifies the end of the range.
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 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/ Specifies the number of confirming ions, which are other ions in the spectrum whose ratio
Number of confirming is compared to the quantitation ion to identify the compound.
ions
This value defaults to 2 because you typically perform a 3-ion experiment with one quan
mass and two confirming ions.
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 Includes the peak spectrum in the processing method. Use this setting to perform a spectra
spectrum as reference
comparison in Data Review.
spectrum
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 47. Method Template Editor dialog box parameters (Sheet 2 of 2)
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
peaks
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
Window range.
Exclusion window
Defines a range plus/minus the Exclusion Window value you specify.
Use data dependent
scans
Constrains the Qual Mode view in the Data Review to only data-dependent scan spectra.
See “Qual Mode” on page 313. In addition to the peak information, the TIC Report and
TIC Summary report display information about the data-dependent filtered data.
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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\2.0\General\Published Master Methods
 To import a published master method
1. From the Method View task pane, click Import Published Method.
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:
…\Thermo\TraceFinder\2.0\General\Methods
You can use any of the Open Method commands to open this method just as you would a
method you created.
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Exporting SRM Data
In the TraceFinder application, you can export your selected reaction monitoring (SRM) data
to an XML file. The Export SRM Data command is displayed only when you enable the
Compound Datastore option in the Configuration mode. See “Compound Datastore” on
page 86.
 To export SRM data to an XML file
1. Open the master method whose SRM data you want to export.
2. From the Method View task pane, click Export SRM Data.
The TraceFinder application writes the data in the SRM table to the following file:
…\Thermo\TraceFinder\2.0\General\Methods\methodname.xml
The data in this file matches the TSQ .xml data, which you can use in the instrument
method editor of the TSQ application.
Figure 56. SRM TSQ Quantum™ example
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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 dashboard or the navigation pane.
The Method Development navigation pane opens.
2. Click the Instrument View task pane.
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 To create a new instrument method
1. Click New Instrument Method in the Instrument View task pane.
The Thermo Xcalibur Instrument Setup window opens.
Figure 57. Example instrument setup showing multiple configured instruments
2. Click the icon for the instrument 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. Click New Instrument Method in the Instrument View task pane.
The Thermo Xcalibur Instrument Setup window opens.
Figure 58. Example instrument setup showing a configured multiplexed instrument
2. Click the icon for the instrument 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 you want to use for acquisition. For example:
5. From the main menu in 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
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 To open an instrument method
1. Click Open Instrument Method on the Instrument View task pane.
An instrument method browser opens.
2. In the browser, select an instrument method from the list and open the file.
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 to another name.
Note To open Help for any of your configured instruments, click Help on the
instrument page.
Figure 59. Example instrument setup showing multiple configured instruments
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 To import an instrument method
1. From the Instrument View task pane, click 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 you want to import.
For instructions for importing the master methods, see “Importing Published Master
Methods” on page 195.
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.
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Working with Development Batches
In the Development Batch view, you can test your instrument method in real time by creating
and acquiring test samples. Development batches let you test different instrument methods
and optimize parameters, such as MS source parameters and autosampler variables, to find the
best conditions for a master method. Development batches are not designed for high
throughput in everyday analysis.
This section includes instructions for the following tasks:
• Creating a Development Batch
• Editing Samples in a Development Batch
• Acquiring Samples in a Development Batch
Creating a Development Batch
You create a development batch to test your instrument method and use it to acquire samples
only once. You cannot save a development batch; you can save only the raw data files created
when you acquire the samples in the batch.
Follow these procedures:
• To open the Development Batch view
• To specify a location for development batch data
• To add samples to the development batch
• To insert samples into the development batch
• To copy a sample
 To open the Development Batch view
1. Click Method Development from the dashboard or the navigation pane.
The Method Development navigation pane opens.
2. In the Method Development navigation pane, click Development Batch.
The Development Batch view opens a new, empty batch.
Note The Channel column is available only when you have enabled multiplexing in
the Configuration mode. See “Multiplexing” on page 87.
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 To specify a location for development batch data
1. To specify a location for the files, click Select Batch Location in the Development Batch
task pane.
By default, the TraceFinder application writes the temporary files, raw data files, and .sld
method file to the following folder:
…\Thermo\TraceFinder\2.0\General\Temp
2. In the browser, do one of the following:
Locate the folder you want to use for the development batch files and click OK.
–Or–
Create a new folder:
a. Locate and select the folder where you want to create a new folder for the batch
files.
b. Click Make New Folder.
The TraceFinder application creates a new folder in the selected folder.
c. Right-click the New Folder file name and choose Rename from the shortcut
menu.
d. Type the name for the folder.
e. Click OK.
The TraceFinder application creates all development batch files in the specified folder.
 To add samples to the development batch
Do one of the following:
Right-click and choose Add Sample from the shortcut menu.
–Or–
To add multiple sample rows, enter the number of rows and click the Add Sample icon.
The application adds the specified number of new, empty samples to the end of the
sample list.
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 To insert samples into the development batch
1. Select the sample above which you want to insert empty samples.
2. Do one of the following:
Right-click and choose Insert Sample from the shortcut menu.
–Or–
To insert multiple sample rows, enter the number of rows and click the Insert Sample
icon.
The TraceFinder application inserts new, empty samples above the selected sample.
Note You cannot insert samples into an empty batch. You must have at least one
sample to select before you can use this icon.
 To copy a sample
1. Select the sample you want to copy.
2. Right-click and choose Insert Copy Sample from the shortcut menu.
The TraceFinder application adds a copy of the sample above the selected sample.
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Editing Samples in a Development Batch
A development batch requires fewer parameters than a real batch, but the mechanism for
managing the information is the same.
For detailed instructions about using the Copy Down or Fill Down commands to enter
column values, see Appendix B, “Using Copy Down and Fill Down.”
Follow these procedures:
• To enter column values
• To resize or reorganize the columns
• To remove selected samples from the list
• To remove all samples from the list
 To enter column values
1. Double-click the Filename column and type a file name for the raw data file.
2. (Optional) Enter values for the Sample Name or Sample ID columns.
3. Enter a vial position for each sample.
4. Enter an injection volume for each sample.
The minimum injection volume value allowed is 0.1 μL; the maximum injection volume
value allowed is 5000 μL.
5. To enter an instrument method for each sample, click the down arrow in the Instrument
Method column and select a method from the list.
This list contains all the available instrument methods.
6. To enter a channel for each sample, click the down arrow in the Channel column and
select a channel from the list.
You cannot specify the auto channel selection in a development batch.
Note The Channel column is available only when you have enabled multiplexing in
the Configuration mode. See “Multiplexing” on page 87.
Figure 60. Completed Development Batch
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 To resize or reorganize the columns
1. To resize a column, drag the header separator on the right side of the column.
2. To move a column, drag the column header.
You cannot move the Filename column.
 To remove selected samples from the list
1. Select the samples you want to remove.
Use the first column to ensure that the samples are selected.
Selected samples
2. Right-click and choose Remove Selected Samples from the shortcut menu.
 To remove all samples from the list
1. Click New Sample List in the Development Batch task pane.
One of the following happens:
• If the samples in the current batch have all been acquired, the list is cleared.
• If the samples in the current list have not been acquired, a message confirms that you
want to clear them and start a new list.
2. To create a new empty list, click Yes.
Note You cannot save a development batch when you create a new one; you can only
create, acquire, and discard each batch after you use it. The TraceFinder application
saves only the generated raw data files in the specified batch location.
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Acquiring Samples in a Development Batch
In a development batch, you can submit the entire batch for acquisition or submit only
selected samples.
Follow these procedures:
• To acquire selected samples
• To acquire the batch
 To acquire selected samples
1. Select the samples you want to acquire.
2. Right-click and choose Submit Selected Samples from the shortcut menu,
or click the Submit Selected Samples icon,
.
The TraceFinder application creates a raw data file for each selected sample. It writes the
raw data files and all temporary working files to the following folder:
…\Thermo\TraceFinder\2.0\General\Temp
When the acquisition is complete, the application deletes all the temporary working files.
Only the raw data files and a MethodDevelopment.sld file remain in the folder.
If you acquire a sample more than once, the application time-stamps the subsequent raw
data files with the acquisition time.
 To acquire the batch
Right-click and choose Submit Batch from the shortcut menu, or click the Submit
Batch icon,
.
The TraceFinder application creates a raw data file for each sample in the batch and
an .sld method file. The TraceFinder application writes the raw data files, the .sld method
file, and all temporary working files to the specified folder.
When the acquisition is complete, the application deletes all the temporary working files.
Only the raw data files and a MethodDevelopment.sld file remain in the folder.
If a sample is acquired more than once, the subsequent raw data files are time-stamped
with the acquisition time.
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Viewing Raw Data Files in the Qual Browser
You can view the chromatogram and spectra for completed samples in a development batch.
Follow these procedures:
• To open the Qual Browser
• To display the last completed raw data file in the Qual Browser
 To open the Qual Browser
In the Development Batch task pane, click Open Qual Browser.
The Thermo Xcalibur Qual Browser window opens.
For detailed instructions about using the Qual Browser, refer to the Qual Browser Help.
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 To display the last completed raw data file in the Qual Browser
In Acquisition page of the real-time viewer, right-click and choose View Last File in Qual
Browser from the shortcut menu.
The last completed file opens in the Qual Browser.
When all samples are completed, you can view the last raw data file for the batch.
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Using Quick Acquisition
You can use the quick acquisition feature to quickly submit a single sample from any view in
the Method Development mode.
Note The Quick Acquisition feature is available only when you enable it in the
Configuration mode. See “Enabling Optional Features” on page 84.
 To run a quick acquisition
1. Choose Go > Quick Acquire Sample from the main menu.
The Quick Acquisition dialog box opens.
2. Select an instrument method.
3. Type a name for the raw data file that you acquire.
4. Click the browse button and locate a folder where you want to write the acquired raw
data file.
5. Select either the manual injection or the autosampler option:
• To perform manual injection, do the following:
a. Select the Manual Injection option.
b. Click OK.
The application submits the sample to the Acquisition queue. See “Acquisition Page”
on page 250.
• To perform autosampler injection, do the following:
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.
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The minimum injection volume allowed is 0.1 μL; the maximum injection volume
allowed is 5000 μL.
d. Click OK.
The Quick Acquisition dialog box opens.
e. Select the Use check box for the device that you want to use for this acquisition.
f.
(Optional) Select the Start Device check box to indicate the device that will initiate
communication with the other instruments.
This is usually the autosampler.
g. (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
must wait for the last instrument to be ready.
h. (Optional) Select the Priority check box to place the sample immediately after any
currently acquiring sample.
i.
(Optional) Select a value for the Post-run System State: Unknown, On (default),
Off, or Standby.
The application sets the system to this state after it acquires the last sample.
j.
Click OK.
The application submits the sample to the Acquisition queue. See “Acquisition Page”
on page 250.
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Using the Acquisition Mode
This chapter describes the tasks associated with the Acquisition mode.
This mode is available only when you select the Acquisition Batch Wizard style in the
Configuration mode. See “Batch Wizard Style” on page 87.
Contents
• Working with Batches
• Using Quick Acquisition
• Real-Time Display
• 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.
Note When user security is enabled, only a user in the LabDirector or Supervisor role can
create a batch template.
If you have a master method, you can create a batch and run the samples. Batches represent
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 “Using Quick Acquisition” on page 247.
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Working with Batches
This section includes instructions for the following tasks:
• Opening and Navigating the Acquisition Mode
• Creating Batches
Opening and Navigating the Acquisition Mode
 To access the Acquisition mode
Click Acquisition from the dashboard or the navigation pane.
The Acquisition mode navigation pane opens.
The TraceFinder application does not use the navigation pane in the Acquisition mode in the
same way it uses the navigation pane in other modes. In the Acquisition mode, this pane
keeps track of your progress as you move through the views to create and submit a batch or a
batch template.
Figure 61. Task pane when you enter the Acquisition mode
The status of each view in the Acquisition mode shows you which tasks are completed and
which tasks are not.
Completed view
Incomplete required view
Current view
Unvisited view
As you complete each view, the task panes display the parameters you specified for your batch.
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Figure 62. Example task pane when you have completed the Acquisition mode
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 Batches
To create a batch, follow these major steps in Acquisition mode:
1. Selecting a Batch
2. Defining the Sample List
3. Selecting and Reviewing Reports
4. Submitting the Batch
The following workflows show the different Acquisition views required for each batch
creation approach. Depending on your approach to creating a batch, use one of these specific
workflows.
 To create an original batch
Batch and
Method
Samples
Reports
Finish
To create an original batch, start with the instructions “To start a new batch” on
page 220.
 To acquire a previously saved (.tbr) batch
Batch
Finish
Samples
To acquire a previously saved batch, start with the instructions “To select a
ready-to-acquire batch” on page 222.
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 To edit and process a previously acquired batch
Batch
Samples
Finish
To process a previously acquired batch, start with the instructions “To select a previously
acquired batch” on page 223.
 To create a batch template
Template and
Method
When user security is enabled, this
workflow is available only to users in the
LabDirector or Supervisor role.
Samples
Finish
To create a batch template, start with the instructions “To create a batch template” on
page 224 and then click Save on the Finish page.
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Selecting a Batch
In a Template Selection view of the Acquisition mode, you can choose to create a new batch in
any of your current projects/subprojects.
Follow these procedures:
• To start a new batch
• To start a new batch from a template
• To select a ready-to-acquire batch
• To select a previously acquired batch
• To create a batch template
 To start a new batch
1. Click the New Batch tab.
2. Select the project and subproject where you want to create the new batch.
3. Type a name for the new batch in the Batch Name box.
4. 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.
5. To continue to the next view, click Next.
The Sample Definition view opens. See “Defining the Sample List” on page 225.
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 To start a new batch from a template
1. Click the New Batch tab.
2. 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 the date and time
stamp. You can change the default project, subproject, and method associated with this
template.
3. (Optional) Select a different project and subproject where you want to create the new
batch.
4. (Optional) Select a different method to use for the new batch.
5. To continue to the next view, click Next.
The Sample Definition view of the Acquisition mode opens. See “Defining the Sample
List” on page 225.
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 To select a ready-to-acquire batch
1. Click the Ready to Acquire tab.
All your unacquired, saved batches are displayed with the file extension .tbr (to be run).
The TraceFinder application stores all .tbr batches in the following folder:
…\Thermo\TraceFinder\2.0\General\Projects\projectname\subprojectname
2. Select the batch you want to acquire.
3. To continue to the next view, click Next.
The Finish view of the Acquisition mode opens. From the Finish view, you can save the
batch, submit the batch for acquisition, or go to the Sample Definition view to edit the
samples 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. Alternatively, you can browse in a
new raw data file to replace the corrupt file.
4. Do one of the following:
To prepare the batch for acquisition, click Submit.
For detailed instructions, see “Submitting the Batch” on page 238.
–Or–
To edit the samples list, click Previous.
For detailed instructions, see “Defining the Sample List” on page 225.
–Or–
To save the batch to the Ready to Acquire list, click Save.
The TraceFinder application saves your batch as a to-be-run (.tbr) file, closes the
Acquisition mode, and returns you to the application dashboard.
The application saves the .tbr batches in the following folder:
…\Thermo\TraceFinder\2.0\General\Projects\projectname\subprojectname
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 To select a previously acquired batch
1. Click the Acquired Batches tab.
From this page, you can resubmit a previously acquired batch, edit the batch, or save it to
be acquired later.
2. In the Project pane, select a project name.
All subprojects included in the selected project are displayed in the Subproject pane.
3. In the Subproject pane, select a subproject name.
The Batch pane displays all previously acquired batches included in the selected
subproject.
4. In the Batch pane, select the batch you want to reacquire.
5. To continue to the next view, click Next.
The Sample Definition view of the Acquisition mode opens. See “Defining the Sample
List” on page 225.
• 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. Alternatively, you can browse in a new raw data file to replace the corrupt
file.
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 To create a batch template
1. Click the Template tab.
Note When user security is enabled, this page is available only to users in the
LabDirector or Supervisor role.
2. Select the project and subproject where you want to create the new batch template.
3. Type a name for the new batch template in the Template Name box.
4. Select a method from the Method Selection list.
5. 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 view, click Next.
7. The Sample Definition view of the Acquisition mode opens. See “Defining the Sample
List” on page 225.
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Defining the Sample List
In the Sample Definition view of the Acquisition mode, you can create a list of samples for the
batch. You can add samples, insert samples, import a sample list, or remove samples from the
list. See “Sample Definition view” on page 232.
As you enter sample values, you can use the Copy Down and Fill Down commands to enter
column values. For detailed instructions on using Copy Down and Fill Down to enter column
values, see Appendix B, “Using Copy Down and Fill Down.”
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
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, the Report Selection view opens. See “Selecting and Reviewing Reports”
on page 234.
• When you are editing a previously acquired batch or a .tbr batch, the Finish Selection
view opens. See “Submitting the Batch” on page 238.
 To add samples to the list
1. Select the number of sample rows to add and click Add,
.
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
Unknown
Cal Std
QC Std
Unknown/Qual
For a detailed description of each sample type, see “Sample Types” on page 262.
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4. For each Cal Std or Chk Std sample, select a level from the Level list.
The sample levels are defined in the master method. If there is nothing 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 click Update.
For detailed instructions, see Chapter 4, “Using the Method Development Mode.”
5. Type a vial position in the Vial Position column for each sample.
Tip Use the Fill Down command to make entering vial positions easier.
6. 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.
7. (Optional) Type or edit the values for the remaining columns.
Note When you use the horizontal scroll bar at the bottom of the samples list, the
Status, Filename, Sample Type, and Level columns stay fixed while the other columns
scroll right and left.
For instructions to automatically copy or fill values in these columns, see Appendix B,
“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 click Insert,
.
The application inserts the Unknown samples above the selected sample.
Inserted
samples
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3. Type a file name in the Filename column for each sample.
Each file name must be unique.
4. Select a sample type from the Sample Type list for each sample.
For a detailed description of each sample type, see “Sample Types” on page 262.
Available sample types
Matrix Blank
Solvent
Unknown
Cal Std
QC Std
Unknown/Qual
5. For each Cal Std or Chk Std sample, click the Level cell and select a level from the list.
The sample levels are defined in the master method. If there are no levels to select from
the Level list, ask a user with Supervisor or LabDirector permissions to edit the method
and specify the levels.
For detailed instructions about defining sample levels, see Chapter 4, “Using the Method
Development Mode.”
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 horizontal scroll bar at the bottom of the samples list, the
Status, Filename, Sample Type, and Level columns stay fixed while the other columns
scroll right and left.
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 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, .xml, or .sld file.
2. Click Browse and select a .csv, .xml, or .sld file that contains the sample definitions 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 specified samples are added to the
Samples 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. For each Cal Std or Chk Std sample, click the Level cell and select a level from the list.
The sample levels are defined in the master method. If there are no levels to select from
the Level list, ask a user with Supervisor or LabDirector permissions to edit the method
and specify the levels.
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For detailed instructions, see Chapter 4, “Using the Method Development Mode.”
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 horizontal scroll bar at the bottom of the samples list, the
Status, Filename, Sample Type, and Level 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 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 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 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 enabled multiplexing in the
Configuration mode. See “Multiplexing” on page 87.
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 mode. See “Enabling Optional
Features” on page 84.
Disabling 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 you disabled.
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 To assign a specific channel to a sample
1. Scroll to the Channel column (the rightmost column in the sample list).
Note The Channel column is available only when you have enabled multiplexing in
the Configuration mode. See “Multiplexing” on page 87.
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 view.
The incorrect sample is marked with an error flag.
b. Correct the channel selection.
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Figure 63. Sample Definition view
Table 48. Sample Definition view parameters (Sheet 1 of 2)
Parameter
Definition
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 where you can import samples defined in a .csv file or
an .xml file.
Multiplexing Channels
These features are available only when you have enabled multiplexing in the Configuration
mode. See “Multiplexing” on page 87.
All Channels
Uses all configured channels to acquire this batch.
Channel 1-n
Uses only the selected channels to acquire this batch.
Previous
Returns you to the previous Acquisition mode view.
Cancel
Confirms that you want to exit the Acquisition mode. When you cancel out of the
Acquisition mode, your edits are not saved.
Save
Saves this batch as a to-be-run (.tbr) batch.
Next
Takes you to the next Acquisition mode view.
Shortcut menu
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 228.
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 B, “Using Copy Down and Fill Down.”
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Table 48. Sample Definition view parameters (Sheet 2 of 2)
Parameter
Definition
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 B, “Using Copy Down and Fill Down.”
Modify columns
Opens the Modify Columns dialog box. See “Column Display” on page 286.
Copy
Copies the data in the selected rows or columns to the Clipboard. Use this command to
copy sample information to another application, such as an Excel spreadsheet. 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 another application, such as
an Excel spreadsheet. You cannot paste this data back into the Acquisition mode sample
list.
For example:
Copy With Headers
from TraceFinder
Paste into Excel spreadsheet
Paste
Pastes a single column of copied data from another application, such as an Excel
spreadsheet, 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.
Status color codes
Sample is not acquired.
Sample is acquired but not processed.
Sample is acquired and processed.
Sample is currently acquiring.
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Selecting and Reviewing Reports
On the Report Selection view, you can specify the types of reports you want to create. See
“Report Selection view” on page 236. For a complete list of report types and examples of
output files, see Appendix A, “Reports.” In addition to the report type, you can specify a
report description for each of your reports.
For each standard report you generate, you can create a hardcopy printout, a PDF file, or an
XML file.
For each custom report you generate, you can create a hardcopy printout or an XLSM file.
For each target screening report you generate, you can create a hardcopy printout or a PDF
file.
When you have finished specifying your report options, click Next to go to the Finish view
and submit your batch. See “Submitting the Batch” on page 238.
The application writes the resulting output files for your reports to the following folder:
…\TraceFinder\2.0\General\Projects\projectname\subprojectname\batchname\Reports
Follow these procedures:
• To edit a report description
• To preview a standard report
• To specify a standard report in print format or as a PDF, XML, or XLSM file
• To export reports to a specific folder
 To edit a report description
Select the Report Description column and edit the default description.
The default report description is the same as the report name.
 To preview a standard report
1. Click the magnifying icon,
, to view an example of the report type as a PDF file.
The right pane of the view displays an example PDF report with typical PDF viewer
buttons.
2. To minimize the PDF viewer, click the minimize icon,
.
Note Only Standard report types have preview documents.
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 To specify a standard report in print format or as a PDF, XML, or XLSM file
1. For each type of report you want to create, select the check box in the Print, Create PDF,
Create XML, or Create XLSM columns.
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.
 To specify a custom report in hardcopy or XLSM format
1. For each custom report that you want to create, select the check box in the Print or Create
XLSM columns.
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.
 To specify a target screening report in hardcopy format or as a PDF file
1. For each target screening report that you want to create, select the check box in the Print
or Create PDF columns.
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.
 To export reports to a specific folder
1. Select the Export Results check box at the bottom of the view.
The Browse For Folder dialog box opens.
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2. Locate and select the folder where you want to save the reports.
3. To create a new reports folder within the selected folder, click Make New Folder and type
the new folder name.
4. Click OK.
The application writes all reports to the specified folder in addition to the batch Reports
folder.
Figure 64. Report Selection view
Table 49. Report Selection parameters (Sheet 1 of 2)
Parameter
Description
Displays an example PDF for the report type. This example provides a model of the report
type only; it does not reflect your specific data. This is available for standard reports only.
Report Name
The name of a report.
Report Description
User-editable description to be used on a report.
Report Type
The type of report: Standard, Custom, or Target Screening.
Print
Reports to be sent to the printer.
Create PDF
Reports to be saved as PDF files.
Available only for standard and target screening reports.
Create XML
Reports to be exported in XML format.
Available only for standard reports.
Create XLSM
Reports to be exported in Excel Macro-Enabled Workbook (.xlsm) format.
Available only for custom reports.
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Table 49. Report Selection parameters (Sheet 2 of 2)
Parameter
Description
Batch Level
Rather than creating separate reports for each sample, the application uses a composite of
the data from all the samples to create a single report for the entire batch. Batch-level reports
are prepended with a B to differentiate them.
You cannot select this option from the Report Selection page. You must select the Batch
Level option for the report in the report configuration. See “Specifying the Reports
Configuration” on page 65.
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 view 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 view” on page 245.
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 .calx
calibration file.
2. To add calibration data from the current batch to the selected calibration file, select the
Extend Calibration option.
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 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 50. Instrument states
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.
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.
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 To save a batch for later acquisition
From the Finish view, click Save.
The TraceFinder application saves your batch as a to-be-run (.tbr) file, closes the
Acquisition mode, and returns you to the application dashboard.
 To start an acquisition
1. Click Submit.
The Submit Options dialog box opens. For a detailed description of the parameters, see
“Submit Options dialog box” on page 242.
2. (Optional) Select the Create Reports check box.
Note By default, the application acquires and processes data when you submit the
batch.
3. Select the Use check box for the device that you want to use for this acquisition.
4. (Optional) Select the Start Device check box to indicate the device that will initiate
communication with the other instruments.
This is usually the autosampler.
5. (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.
6. (Optional with multiplexing enabled) Select the Priority Sequence check box.
The application acquires the priority batch on the next available channel or the assigned
channel.
7. (Optional without multiplexing enabled) 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.
8. Do one of the following:
To start the selected processes, click OK.
The selected processes begin, and the TraceFinder application returns you to the
dashboard and shows the real-time display at the bottom of the dashboard.
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The real-time display is visible from the dashboard and all modes. 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.
Figure 65. Submit Options dialog box
Table 51. Submit Options dialog box parameters (Sheet 1 of 2)
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Parameter
Description
User Name
Name of the current user.
Acquire Data
(Default) Submits the current batch to acquisition.
Process Data
(Default) Processes the data for the current batch.
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Table 51. Submit Options dialog box parameters (Sheet 2 of 2)
Parameter
Description
Create Reports
Creates reports for the current batch.
Acquisition pane
Device Name
Lists all configured instruments.
If the instrument 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.
Use
Specifies the instruments used for this acquisition.
Start Device
Specifies the instrument that initiates the communication
with the other instruments. This is usually the autosampler.
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.
Priority Sequence
With multiplexing enabled, places the batch immediately after
the currently acquiring batch.
Without multiplexing enabled, 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.
Post-run system
state
Thermo Scientific
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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Working with Batches
 To view the output files
• The TraceFinder application writes saved batches to the subproject folder with the file
extension .tbr (to be run):
…\TraceFinder\2.0\General\Projects\projectname\subprojectname
• For each acquired sample, the application writes an RSX file to the batch Data folder:
…\projectname\subprojectname\batchname\Data
• The application saves method information to the batch Methods folder:
…\projectname\subprojectname\batchname\Methods\methodname
• The application writes the reports to the batch Reports folder:
…\projectname\subprojectname\batchname\Reports
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Figure 66. Finish view
Table 52. Finish view parameters (Sheet 1 of 2)
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 samples in the batch
• Number of standard and custom reports to be printed and saved as PDF, XML, or
XLSM files
• Local method and instrument method used for the batch
• Number of compounds in the method
System Startup
Method
The instrument method that runs before the batch. No autosampler injection takes place.
This feature is not available for all instruments.
System Shutdown
Method
The instrument method that runs after the batch. No autosampler injection takes place.
This feature is not available for all instruments.
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Table 52. Finish view parameters (Sheet 2 of 2)
Parameter
Description
Auto TSRM Update
Updates the TSQ method with mass transitions, collision energy, and other appropriate data
for TSRM functionality.
Calibration
• 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 to-be-run (.tbr) file.
Submit
Opens the Submit Options dialog box where you can optionally choose to generate reports.
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Using Quick Acquisition
The quick acquisition feature lets you quickly submit a single sample from any view of the
Acquisition mode.
Note The quick acquisition feature is available only when you enable it in the
Configuration mode. See “Enabling Optional Features” on page 84.
 To run a quick acquisition
1. Choose Go > Quick Acquire Sample from the main menu.
The Quick Acquisition dialog box opens.
2. Select an instrument method.
3. Type a name for the raw data file that you acquire.
4. Click the browse button and locate a folder where you want to write the acquired raw
data file.
5. Select either the manual injection or the autosampler option:
• To perform manual injection, do the following:
a. Select the Manual Injection option.
b. Click OK.
The application submits the sample to the Acquisition queue. See “Acquisition Page”
on page 250.
• To perform autosampler injection, do the following:
a. Select the Use Autosampler option.
b. In the Vial Position box, type a vial position.
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c. In the Injection Volume box, type an injection volume.
The minimum injection volume allowed is 0.1 μL; the maximum injection volume
allowed is 5000 μL.
d. Click OK.
The Quick Acquisition dialog box opens.
e. Select the Use check box for the device that you want to use for this acquisition.
f.
(Optional) Select the Start Device check box to indicate the device that will initiate
communication with the other instruments.
This is usually the autosampler.
g. (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
must wait for the last instrument to be ready.
h. (Optional) Select the Priority check box to place the sample immediately after any
currently acquiring sample.
i.
(Optional) Select a value for the Post-run System State: Unknown, On (default),
Off, or Standby.
The application sets the system to this state after it acquires the last sample.
j.
Click OK.
The application submits the sample to the Acquisition queue. See “Acquisition Page”
on page 250.
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Real-Time Display
Real-Time Display
You can access the real-time display from the dashboard and from any mode in the
TraceFinder application.
 To access the real-time display from the dashboard
Click Real Time Status.
The real-time status displays at the bottom of the dashboard.
 To access the real-time display from all modes
Click Real Time Status.
The real-time status displays at the bottom of the current view.
Figure 67. Real Time Status display
The real-time status display 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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Real-Time Display
Acquisition Page
Use the Acquisition page to monitor the progress as the application acquires the samples.
 To pause or stop the batches in the queue
Use the Start,
, Stop,
Acquisition queue.
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, or Pause,
, buttons to control batches in the
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Real-Time Display
Instrument Page
Use the Instrument page to monitor the currently acquiring sample.
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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 access the Aria multiplexing controls
• To control the channels
• To view the pressure trace
 To pause the autosampler
1. Click Hold Autosampler.
The autosampler finishes the current autosampler step and then pauses. The LC pumps
and autosampler continue.
2. To restart the autosampler, click Hold Autosampler again.
 To access the Aria multiplexing controls
Click Direct Control.
The AriaMuxVi Direct Ctl dialog box opens.
For a detailed description of the features in this dialog box, refer to the Transcend Systems
with Xcalibur Software User Guide.
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 To control the channels
Right-click the channel name and choose a command from the shortcut menu.
Table 53. Autosampler shortcut menu commands
Parameter
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.
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.
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 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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Queues Page
Use the Queues page to monitor and control the Acquisition, Processing, and Reporting
queues:
• Use the Queue-Level Commands to pause or remove batches in any of the queues.
• Use the Batch-Level Commands to pause or remove entire batches or samples within
batches from any of the queues.
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 257.
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 enabled, 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.
Figure 68. Queue-level shortcut menu
Table 54. Queue-level shortcut menu commands (Sheet 1 of 2)
Thermo Scientific
Parameter
Description
Pause Queue
After the current sample completes, the application pauses the
specified queue. Only the selected queue is affected.
Stop Active Batch
Removes all pending samples from the specified queue. The active
sample is not affected.
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Table 54. Queue-level shortcut menu commands (Sheet 2 of 2)
Parameter
Description
Stop All Batches
Removes all pending samples and batches from the specified
queue. The active sample is not affected.
Remove Pending
Batches
Removes all pending batches from the specified queue. The active
batch is not affected.
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” on page 259.
Follow these procedures:
• To stop a batch
• To remove a pending batch
• To remove pending samples from a batch
• To remove a single pending sample from a batch
 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.
 To remove 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.
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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.
 To remove a single pending sample from a batch
1. Select a pending sample.
2. Right-click 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.
Figure 69. Batch-level shortcut menu
Table 55. Batch-level shortcut menu commands
Parameter
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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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 display 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 Viewer” on page 161.
 To display multiple traces
Right-click the chromatogram pane and choose the number of traces you want 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.
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Real-Time Display
Figure 70. Real-time 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. To view example standard reports specific to a sample type, see Appendix A,
“Reports.”
Figure 71. Sample type definitions
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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.
Unknown/Qual
Used for quantitative and qualitative analysis of samples.
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Using the Analysis Mode
This chapter includes instructions for using the features of the Analysis mode.
Contents
• Using Quick Acquisition
• Working in the Batch View
• Creating a Batch Using the Batch Wizard
• Working in Data Review View
• Working in the Report View
• Working in the Local Method View
• Working in the Batch Template Editor
In the Analysis mode, you can
• Submit a single sample for quick acquisition
• Submit batches for acquisition, processing or reports
• Review batches, batch data, reports, and local methods
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Using the Analysis Mode
 To access the Analysis mode
Click Analysis from the dashboard or the navigation pane.
The Analysis navigation pane opens.
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Using Quick Acquisition
Using Quick Acquisition
With the quick acquisition feature, you can quickly submit a single sample from any view of
the Analysis mode.
Note The quick acquisition feature is available only when you enable it in the
Configuration mode. See “Enabling Optional Features” on page 84.
 To run a quick acquisition
1. Choose Go > Quick Acquire Sample from the main menu.
The Quick Acquisition dialog box opens.
2. Select an instrument method.
3. Type a name for the raw data file that you acquire.
4. Click the browse button and locate a folder where you want to save the acquired raw data
file.
5. Select either the manual injection or the autosampler option:
• To perform manual injection, do the following:
a. Select the Manual Injection option.
b. Click OK.
The application submits the sample to the Acquisition queue. See “Acquisition Page”
on page 250.
• To perform autosampler injection, do the following:
a. Select the Use Autosampler option.
b. In the Vial Position box, type a vial position.
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c. In the Injection Volume box, type an injection volume.
The minimum injection volume allowed is 0.1 μL; the maximum injection volume
allowed is 5000 μL.
d. Click OK.
The Quick Acquisition dialog box opens.
e. Select the Use check box for the device that you want to use for this acquisition.
f.
(Optional) Select the Start Device check box to indicate the device that will initiate
communication with the other instruments.
This is usually the autosampler.
g. (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
must wait for the last instrument to be ready.
h. (Optional) Select the Priority check box to place the sample immediately after any
currently acquiring sample.
i.
(Optional) Select a value for the Post-run System State: Unknown, On (default),
Off, or Standby.
The application sets the system to this state after it acquires the last sample.
j.
Click OK.
The application submits the sample to the Acquisition queue. See “Acquisition Page”
on page 250.
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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.
This section contains information about the following topics:
• Batch View Panes
• Creating a New Batch
• Editing a Batch
• Editing Report Output Formats
• Submitting a Batch
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Working in the Batch View
Batch View Panes
The Batch View is divided into three panes:
• Use the sample list to create a batch. See “Creating a New Batch” on page 271.
• Use the Automated Batch Reports pane to select the type of output formats you want to
generate for the reports. See “Editing Report Output Formats” on page 282.
• Use the Compound Active Status pane to make specific compounds active or inactive. See
“Setting Compound Active Status” on page 284.
Use the Batch View toolbar or shortcut menu to create the sample list and submit samples for
acquisition. See “Batch View Toolbar” on page 269 or “Batch View Shortcut Menu” on
page 269.
Sample list
Automated Batch Reports pane
Compound Active Status pane
Tip To resize the panes, drag the separators that divide the panes.
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Batch View Toolbar
The Batch View includes this toolbar for creating and submitting a batch.
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 272.
Inserts a new, empty sample or samples above the selected sample. See
the instructions “To insert samples into the list” on page 273.
Removes the selected samples from the samples list. See the
instructions “To remove samples from the list” on page 274.
Adds imported samples from a .csv, .xml, or .sld file to the samples
list. See the instructions “To import samples into the list” on
page 273.
Submits only the selected samples for acquisition, processing, or
report generation. See the instructions “To submit selected samples”
on page 287.
Submits the batch for acquisition, processing, or report generation.
See the instructions “To submit all samples in the batch” on page 286.
Batch View Shortcut Menu
The Batch View includes a shortcut menu for creating a batch.
Table 56. Batch View shortcut menu commands (Sheet 1 of 2)
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 273.
Browse in raw file
Opens a dialog box where you can select a raw data file to use for the sample row.
Map raw files to samples Opens a dialog box where you can select raw data files to use for the sample rows.
Copy down
Thermo Scientific
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.
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Table 56. Batch View shortcut menu commands (Sheet 2 of 2)
Command
Description
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 308.
Copy
Copies the data in the selected rows or columns to the Clipboard. Use this command to
copy sample information to another application, such as an Excel spreadsheet. You cannot
paste this data back into the Batch View 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 another application, such as
an Excel spreadsheet. You cannot paste this data back into the sample list.
For example:
Copy With Headers
from TraceFinder
Paste into Excel spreadsheet
Paste
Pastes a single column of copied data from another application, such as an Excel
spreadsheet, 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.
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Working in the Batch View
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
 To create a new batch
1. Click New Batch in the Batch View task pane or choose File > New > Batch.
The Create a New Batch dialog box opens.
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2. Select a master method from the Method list.
3. Select a drive from the Storage Location list.
The project list displays all projects, subprojects, and batches on the selected drive.
Tip The application does not display drives that do not have a project and subproject.
You cannot use network drives to acquire data. For more information about network
drives, see “Working with Drives” on page 47.
4. Select a project and a subproject and type a name for your new batch.
Tip To enable the Save button, you must select a subproject and enter a unique batch
name. If the Save button is not enabled, either you have entered a name that is already
used or you have not selected a subproject.
5. Click Save.
A new, unnamed batch opens with one Unknown sample.
 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
button,
.
The application adds the specified number of new, empty samples to the end of the
sample list.
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 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 button
.
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
button,
.
The Sample Import Tool dialog box opens.
From this dialog box, you can import samples from a .csv, .xml, or .sld file.
2. Click Browse and select a .csv, .xml, or .sld file that contains the samples you want to
import.
3. From the Imported Samples Will Be list, select Appended to the End of the List or
Inserted at the Selected Row.
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4. Click Import.
The Sample Import Tool dialog box closes, and the application adds the specified samples
to the samples 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 enabled multiplexing in
the Configuration mode. See “Multiplexing” on page 87.
 To remove samples from the list
1. Select the samples 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 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 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 same sample are numbered INJ002, INJ003,
and so forth.
The TraceFinder 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
Unknown
Cal Std
QC Std
Unknown/Qual
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 is nothing 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, see Chapter 4, “Using the Method Development Mode.”
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4. Type a vial position in the Vial Position column for each sample.
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 horizontal scroll bar at the bottom of the samples list, the
Status, Filename, Sample Type, and Level columns stay fixed while the other columns
scroll right and left.
For instructions to automatically copy or fill values in these columns, see Appendix B,
“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 inserts any additional browsed in files above 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 inserts all browsed in files above 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 57. Modify Columns dialog box buttons
Button
Description
Moves all columns to the Displayed Columns pane.
Moves the selected column to the Displayed Columns pane.
Moves the selected column to the Available Columns pane. You cannot
move the Status, Filename, Sample Type, or Level columns.
Moves all columns except Status, Filename, Sample Type, or Level to
the Available Columns pane.
Moves the selected column name in the Displayed Columns pane one
row up in the column order. You cannot move the Status, Filename,
Sample Type, or Level columns.
Moves the selected column name in the Displayed Columns pane one
row down in the column order. You cannot move the Status, Filename,
Sample Type, or Level columns.
2. Use the arrow buttons to move all the columns you want to display to the Displayed
Columns pane.
All the columns you select are displayed after the Status, Filename, Sample Type, or Level
columns.
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3. To arrange the order of the columns, do the following:
a. In the Displayed Columns pane, select a column name.
b. Use the Up and Down buttons 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; 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, or Level 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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Editing a Batch
In the Batch View, you can open a saved batch and edit the samples 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 to-be-run (.tbr) 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 submit all samples in the batch
• To submit selected samples
 To open a saved batch
1. From the Batch View task pane, click Open Batch.
The Open Batch dialog box opens.
2. Select a drive from the Storage Location list.
The project list displays all projects, subprojects, and batches on the selected drive.
3. Select a project, subproject, and batch.
4. Click Open.
The selected batch opens in the Batch View.
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 To open a recent batch
Click a batch name in the Recent Files list.
The selected batch opens in the Batch View.
Tip To view the drive, project, and subproject for a recent batch, hold your cursor
over the batch name.
 To edit samples in a batch
Use the commands described in “Working in the Batch View” on page 267.
You can edit samples, add new samples, reinject acquired samples, or delete samples.
 To reinject a sample from a previously acquired batch
1. In the sample list, select the sample 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 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 all samples in this batch, the application acquires all samples (including
previously acquired samples).
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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 .tbr batch. You can open this batch from the Ready to Acquire
page in the Acquisition mode and submit the batch. The application acquires all
submitted samples—both the reinjection samples and the previously acquired samples.
The application appends a timestamp to the acquired raw data files to differentiate each
acquisition.
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Editing Report Output Formats
In the Automated Batch Reports pane, you can view the reports that are selected for this batch
and modify which output formats are generated for each report.
 To edit the sample-level output formats
1. Click the Sample Level tab.
The application displays reports and the output formats as they were specified in the
method.
For detailed instructions for specifying which reports and output formats are generated,
see “Specifying the Reports Configuration” on page 65.
2. Select or clear any of the check boxes for your reports.
3. To duplicate an output format for all reports for this sample, 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. You can duplicate the output type only for reports that have this
output format available.
4. To duplicate the output format for all samples in the batch, right-click the cell and choose
Apply Selection to All Samples from the shortcut menu.
Tip In the Batch View, you can change the output formats but you cannot change
which reports are available.
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 To edit the batch-level output formats
1. Click the Batch Level tab.
The application displays the reports and the output formats as they were specified in the
method.
For detailed instructions for specifying which reports and output formats are generated
and which reports are batch-level, see “Specifying the Reports Configuration” on page 65.
2. Select or clear any of the check boxes for your reports.
3. To duplicate the output format 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. You can duplicate the output type only for reports that have this
output format available.
Tip In the Batch View, you can change the output formats but you cannot change
which reports are available.
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Setting Compound Active Status
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 samples 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 settings in the local method. See
“Identification” on page 124.
2. Select or clear the Active check box for the compound.
When you specify a compound as inactive in this pane, it becomes inactive in the
Compounds pane in the Data Review view. Inactive compounds are grayed out:
For instructions for changing the active/inactive status in the Data Review view, see
“Inactive and Excluded Compounds” on page 312.
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Compound Active/Inactive Status
You can specify which compounds are active or inactive in the Local Method View, the Batch
View, or the Data Review view.
Figure 72. Active and inactive compounds in the Local Method View
For details about setting the status on the Identification page, see “Identification” on
page 124.
Figure 73. Active and inactive compounds in the Batch View
For details about setting the status in the Batch View, see “Setting Compound Active Status”
on page 284.
Figure 74. Active and inactive compounds in the Data Review view
Inactive
For details about setting the status in the Data Review view, see “Inactive and Excluded
Compounds” on page 312.
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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 288.
Follow these procedures:
• To submit all samples in the batch
• To submit selected samples
For a description of commands on the shortcut menu, see “Batch View shortcut menu
commands” on page 269.
 To submit all samples in the batch
1. Click the Submit Batch button,
.
The Submit Options dialog box opens. See “Submit Options dialog box” on page 288.
2. Select the tasks you want to perform: acquire data, process data, or create reports.
3. (Optional) Click Show Details to display additional Acquisition parameters.
4. Select the Use check box for the device that you want to use for this acquisition.
5. (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.
6. (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.
7. (Optional with multiplexing enabled) Select the Priority Sequence check box.
The application acquires the priority batch on the next available channel or the assigned
channel.
8. (Optional without multiplexing enabled) 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.
9. To start the selected processes, click OK.
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 To submit selected samples
1. Select the samples you want to submit.
2. Click the Submit Selected Samples button,
.
The Submit Options dialog box opens. See “Submit Options dialog box” on page 288.
3. Select the tasks you want to perform: acquire data, process data, or create reports.
4. Select the Use check box for the device that you want to use for this acquisition.
5. (Optional) Click Show Details to display additional Acquisition parameters.
6. (Optional) Select the Start Device check box to indicate the device that will initiate
communication with the other instruments.
This is usually the autosampler.
7. (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.
8. (Optional with multiplexing enabled) Select the Priority Sequence check box.
The application acquires the priority batch on the next available channel or the assigned
channel.
9. (Optional without multiplexing enabled) 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.
10. To start the selected processes, click OK.
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Figure 75. Submit Options dialog box
Table 58. Submit Options dialog box parameters (Sheet 1 of 2)
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Parameter
Description
User Name
Name of the current user.
Samples
Reports the range of samples to be acquired, processed, or
reported.
Acquire Data
(Default) Submits the current batch to acquisition.
Process Data
(Default) Processes the data for the current batch.
Create Reports
Creates reports for the current batch.
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Table 58. Submit Options dialog box parameters (Sheet 2 of 2)
Parameter
Description
Acquisition pane
Device Name
Lists all configured instruments.
If the instrument you want to use is not configured, close the
TraceFinder application, configure the instrument, and then
reopen the application. You cannot configure an instrument while
the TraceFinder application is running.
Use
Specifies the instruments used for this acquisition.
Start Device
Specifies the instrument that will initiate communication with the
other instruments. This is usually the autosampler.
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.
Priority Sequence
With multiplexing enabled, places the batch immediately after the
currently acquiring batch.
Without multiplexing enabled, 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.
Post-run system
state
Specifies the system state after it acquires the last batch.
On (default), Standby, or Off.
Buttons
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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
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Creating a Batch Using the Batch Wizard
Using the Batch Wizard, you can define a sequence composed of various sample types to be
assembled into a batch of samples. Before you can create a batch with the Batch Wizard, you
must have a master method and a batch template. See “Creating a New Master Method” on
page 95 and “Working in the Batch Template Editor” on page 370.
Note This batch wizard is available only when you select the Batch Template Wizard
(EnviroLab/ToxLab/QuanLab forms) batch wizard style in the Configuration mode. See
“Application Configuration” on page 64.
Follow these procedures in the Batch Wizard to create and submit a batch:
• Selecting a Batch Template
• Specifying a Batch
• Submitting the Batch
• (Optional) Selecting Calibration Files and Compounds
The Batch Wizard workflow uses the following pages:
Batch Template Selection
Batch Specification
Finish
Calibration and Compound
Selection
 To open the Batch Wizard
Choose File > New > Batch Using Wizard from the main menu in the Analysis mode,
or click the Batch Wizard button,
.
The Batch Template Selection page of the Batch Wizard opens.
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Selecting a Batch Template
From the Batch Template Selection page, you can create a list of samples to acquire or process.
For descriptions of the parameters on the Batch Template Selection page, see “Batch Template
Selection page” on page 292.
 To create a sample list
1. From the Project list, select a project.
2. From the Subproject list, select a subproject.
The Available Templates area lists all the templates in the specified subproject.
3. Select a starting vial position.
The default is vial position 1, but you can choose to start your acquisition at any vial
position.
4. (Optional) To simplify the sample list, select the Quick Mode check box.
Quick Mode limits the columns of information on the Batch Specification page to the
following:
• Sample Type
• Sample ID
• Injection Volume
• Conversion Factor
5. From the Available Templates list, select a template that defines the layout you want to
use.
The Template Layout area displays sample information in the selected batch template and
a list of methods that use the same assay type as your template.
6. Select an available method.
By default, the application selects the method used to create the batch template, but you
can choose any method in the Available Methods list.
7. To go to the next wizard page, click Next.
From the Batch Specification page of the wizard, you can customize the batch.
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Figure 76. Batch Template Selection page
Table 59. Batch Template Selection parameters (Sheet 1 of 2)
Parameter
Description
Starting vial position
The vial position where you want to begin acquiring samples.
Default: 1
Total batch rows
The number of sample rows in the batch template.
Assay type
The assay type specified in the master method used to create the batch template.
Quick mode
Limits the columns of information on the Batch Specification page to the following:
• Sample Type
• Sample ID
• Injection Volume
• Conversion Factor
Available Templates
All batch templates are saved in the following folder:
…\Thermo\TraceFinder\2.0\General\Templates\Batches
Template Layout
Displays sample information in the selected batch template.
Available Methods
Lists all master methods created with the same assay type as the selected batch template.
Help
Opens the “Creating a Batch Using the Batch Wizard” topic (this topic) in the application
Help tool.
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Table 59. Batch Template Selection parameters (Sheet 2 of 2)
Parameter
Description
Next
Returns you to the Batch Specification page where you can enter a sample ID, a sample
name, or a comment. You can also add or remove samples from the sample list or edit the
column values for the samples. See “Specifying a Batch” on page 293.
Cancel
Immediately exits the Batch Wizard and does not save the batch. There is no confirming
message.
Specifying a Batch
From the Batch Specification page, you must enter either a sample ID, sample name, or
comment. You can also add or remove samples from the sample list or edit the column values
for the samples. The batch template might contain many samples that you do not want to use
for your batch. If you do not enter a sample ID, sample name, or comment for these samples,
the application discards them when you save the batch. For descriptions of the parameters on
the Batch Specification page, see “Batch Specification page” on page 296.
 To enter a sample ID, sample name, or comment
1. In the Sample ID column, type an identifier.
The identifier can be any text string.
2. In the Sample Name column, type a name.
The name can be any text string.
3. In the Comment column, type a comment.
The comment can be any text string.
Note The application requires a value in at least one of these fields to acquire a sample.
When the batch begins acquisition, it discards any sample that does not have a value in at
least one of these fields.
 To simplify the sample list
Select the Quick Mode check box.
In Quick Mode, the Batch Specification page displays only the following columns:
• Sample Type
• Sample ID
• Injection Volume
• Conversion Factor
In Quick Mode, you cannot add or remove samples from the sample list. You can only
edit these four column values for the samples specified in the template.
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When you are not using Quick Mode, follow these procedures:
• To add samples to the batch
• To remove samples from the batch
• To insert samples into the batch
• To copy a sample
• To move a sample up or down in the sample list
• To browse in a raw data file
 To add samples to the batch
1. Right-click and choose Add Sample from the shortcut menu, or click the add sample
icon,
.
The application adds a new, Unknown sample to the end of the sample list.
2. In the Filename column for each sample, type a file name.
Note Or, you can right-click and choose Browse in Raw File from the shortcut
menu. Follow the instructions “To browse in a raw data file” on page 296.
3. Select a sample type from the Sample Type list for each sample.
Available sample types
Matrix Blank
Solvent
Unknown
Cal Std
QC Std
Unknown/Qual
4. For a detailed description of sample types, see “Sample Types” on page 262.
5. 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 from
the Level list, do the following:
a. Cancel the Batch Wizard.
b. Return to the Method Development mode.
c. Open the method.
d. Click the Compounds tab.
e. Click the Calibration Levels tab.
f.
Add the levels.
g. Save the method.
h. Return to the Analysis mode, open the Batch Wizard, and begin your batch again.
For detailed instructions about defining sample levels, see Chapter 4, “Using the Method
Development Mode.”
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6. In the Vial Position column for the new sample, type a vial position.
7. In the Injection Volume column for the new sample, type a volume.
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 This function is not available in Quick Mode.
 To remove samples from the batch
1. Select the samples you want to remove.
2. Right-click and choose Remove Selected Samples from the shortcut menu, or click the
remove samples icon,
.
The application removes the selected samples from the sample list.
Note This function is not available in Quick Mode.
 To insert samples into the batch
1. Select the sample above where you want to insert a new sample.
2. Right-click and choose Insert Sample from the shortcut menu.
The application inserts a new, Unknown sample above the selected sample.
Note This function is not available in Quick Mode.
 To copy a sample
1. Select the sample you want to copy.
2. Right-click and choose Insert Copy Sample from the shortcut menu.
The application inserts the copy above the selected sample.
Note This function is not available in Quick Mode.
 To move a sample up or down in the sample list
1. Select the sample you want to move.
2. Right-click and choose Move Sample Up or Move Sample Down from the shortcut
menu.
The application moves the selected sample up or down one row in the sample list.
Note This function is not available in Quick Mode.
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 To browse in a raw data file
1. Double-click the Filename column, or right-click and choose Browse in Raw File from
the shortcut menu.
A dialog box opens where you can select a raw data file to use for the sample. You can also
browse in multiple raw data files to create multiple samples.
2. Locate the raw data file to use for the sample and click Open.
Note This function is not available in Quick Mode.
Figure 77. Batch Specification page
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Table 60. Batch Specification parameters
Parameter
Description
Batch Template
Master Method
Batch File
Calibration File
Displays the path names of the batch template, master method, batch file, and calibration
file used to create this batch.
Adds a new, Unknown sample to the end of the sample list.
This function is not available in Quick Mode.
Removes the selected sample.
This function is not available in Quick Mode.
Quick mode
Limits the columns of information in the Batch Specification page to the following:
• Sample Type
• Sample ID
• Injection Volume
• Conversion Factor
In Quick Mode, the shortcut menu and add/remove sample icons are unavailable.
Help
Opens the “Creating a Batch Using the Batch Wizard” topic (this topic) in the application
Help tool.
Back
Returns you to the Batch Template Selection page where you can choose a different batch
template, master method, or starting vial position.
Next
Takes you to the Finish page where you can submit the batch for acquisition or processing.
See “Submitting the Batch” on page 298.
Cancel
Immediately exits the Batch Wizard and does not save the batch. There is no confirming
message.
Shortcut Menu
Add sample
Adds a single empty row to the sample list.
Insert sample
Inserts a new, Unknown sample above the selected row.
Insert copy sample
Copies the currently selected row and inserts a copy above the row.
Remove selected samples Removes selected samples from the sample list.
Move sample up
Moves the selected sample up one row in the sample list.
Move sample down
Moves the selected sample down one row in the sample list.
Browse in raw file
Opens a dialog box where you can select a raw data file to use for the sample row. You can
also browse in multiple raw data files to create multiple samples.
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 B, “Using Copy Down and Fill Down.”
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Creating a Batch Using the Batch Wizard
Submitting the Batch
From the Finish page, you can change the name of the batch, access the Calibration and
Compound Selection page to edit the calibration file or edit the list of compounds to identify,
or save the batch and open it in Batch View. For descriptions of the parameters on the Finish
page, see “Finish page” on page 299.
Follow these procedures:
• To change the name of the batch
• To save the batch
• To edit the calibration file
• To identify specific compounds or groups of compounds
 To change the name of the batch
Edit the name in the Batch Name box.
You cannot overwrite an existing batch name. If you enter a name for a batch that already
exists, when you click Finish, the Batch Save dialog box asks you to enter another name.
 To save the batch
Click Finish.
The application saves the batch and displays it in the Batch View. From the Batch View,
you can submit the batch for acquisition, processing, or report generation. See
“Submitting a Batch” on page 286.
 To edit the calibration file
1. Select the Modify Calibrations or Active Compounds by Group check box.
The application replaces the Finish button with a Next button.
2. Click Next.
The Calibration and Compound Selection page opens. See “Selecting Calibration Files
and Compounds” on page 300.
 To identify specific compounds or groups of compounds
1. Select the Modify Calibrations or Active Compounds by Group check box.
The application replaces the Finish button with a Next button.
2. Click Next.
The Calibration and Compound Selection page opens. See “Selecting Calibration Files
and Compounds” on page 300.
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Figure 78. Finish page
Table 61. Finish parameters (Sheet 1 of 2)
Parameter
Description
Modify Calibrations or
Active Compounds by
Group
Enables the Next button that lets you access the Calibration and Compound Selection
page.
Batch name
Name of the current batch in the form:
MasterMethodName_MMDDYYYY_
Help
Opens the “Creating a Batch Using the Batch Wizard” topic (this topic) in the application
Help tool.
Back
Returns you to the Batch Specification page where you can enter a sample ID, sample
name, or comment. You can also add or remove samples from the sample list or edit the
column values for the samples. See “Specifying a Batch” on page 293.
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If you have already used the Calibration and Compound Selection page, this option is not
available.
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Table 61. Finish parameters (Sheet 2 of 2)
Parameter
Description
Finish
Saves the batch and displays it in Batch View. From Batch View, you can submit the batch
for acquisition, processing, or report generation. See “Submitting a Batch” on page 286.
Next
Opens the Calibration and Compound Selection page where you can edit the calibration
file or edit the list of compounds you want to identify.
Available only when Modify Calibrations or Active Compounds by Group is checked.
Cancel
Immediately exits the Batch Wizard and does not save the batch. There is no confirming
message.
Selecting Calibration Files and Compounds
From the Calibration and Compound Selection page, you can edit the calibration file or edit
the list of compounds you want to identify. For descriptions of the parameters on the
Calibration and Compound Selection page, see “Calibration and Compound Selection Page”
on page 301.
Follow these procedures:
• To add calibration data to the calibration file
• To identify specific compounds or groups of compounds
 To add calibration data to the calibration file
1. To add calibration data from another batch to the current calibration file, click Extend
Calibrations.
The Select a Calibration File to Use dialog box opens. The dialog box lists only
calibration batches that use the same master method as the current batch.
2. Select a calibration file to append to the current calibration file and click OK.
The application appends the selected calibration file to the current file.
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3. To save calibration data from both files into a single file for this batch, click Create New.
4. When you are finished with the Calibration and Compound Selection page, click Next.
The Finish page opens. See “Submitting the Batch” on page 298.
 To identify specific compounds or groups of compounds
1. In the Compound Groups area, select the groups that include the compounds you want
to identify in the samples.
2. In the Included Compounds area, select the Active check box for each compound that
you want to identify in the samples.
3. When you are finished with the Calibration and Compound Selection page, click Next.
The Finish page opens. See “Submitting the Batch” on page 298.
Figure 79. Calibration and Compound Selection Page
Table 62. Calibration and Compound Selection parameters (Sheet 1 of 2) (Sheet 1 of 2)
Parameter
Description
Calibration File
Name of the current batch in the form:
MasterMethodName_MMDDYYYY_
Create New
Saves calibration data from all calibration files to the current calibration file.
Available only after you use Extend Calibrations to append calibration data from another
calibration file.
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Table 62. Calibration and Compound Selection parameters (Sheet 2 of 2) (Sheet 2 of 2)
Parameter
Description
Extend Calibrations
Adds calibration data from the current batch to the selected calibration file.
Compound Groups
Displays all available groups defined in the Groups page of the Master Method View. See
“Editing the Groups Page” on page 126.
Included Compounds
Displays all available compounds that you can identify in the samples. Compounds
marked as Active are identified in the batch samples.
Help
Opens the “Creating a Batch Using the Batch Wizard” topic (this topic) in the application
Help tool.
Back
Returns you to the Batch Specification page where you can enter a sample ID, sample
name, or comment. You can also add or remove samples from the sample list or edit the
column values for the samples. See “Specifying a Batch” on page 293.
Next
Opens the Finish page where you can change the name of the batch or save the batch to
the Batch View. See “Submitting the Batch” on page 298.
Cancel
Immediately exits the Batch Wizard and does not save the batch. There is no confirming
message.
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Working in Data Review View
In the Data Review view, you can view the data generated by the master method. Use the Data
Review view to verify the data for a sample-specific compound before you generate reports.
You can use the functions in the Data Review view to investigate and edit the quantification
values in a batch.
 To open the Data Review view
1. Do one of the following:
From the dashboard, click Analysis.
–Or–
Click Analysis in the navigation pane of the current mode.
2. In the Analysis navigation pane, click Data Review.
The Data Review view for the currently selected batch opens.
The Data Review view uses a samples list and one of two modes: Quan Mode or Qual Mode.
The Qual Mode is available only for Unknown/Qual sample types. When you view the data
for an Unknown/Qual sample type, you can switch between Qual Mode and Quan Mode.
This section includes the following topics:
• Samples List
• Quan Mode
• Qual Mode
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Samples List
Use the samples list to select a particular sample. To see the columns in a sample list and view
their descriptions, see “Samples list” on page 305.
Status indicators for each sample indicate if the sample is currently acquiring, not acquired,
acquired, or processed.
The samples list includes the following features:
• Column Display
• Status Indicators
• Caution Flags
• Compound Flags
• Inactive and Excluded Compounds
The samples list is the same in both Quan Mode and Qual Mode and displays all the
quantitative data for the samples of a batch.
• In Quan Mode, the samples list works with the Compounds pane to select a unique
sample and compound combination, which then has its textual and graphical values
displayed in the Quan Mode pane. The list of compounds that are available for a specific
method is displayed in the Compounds pane.
From the samples list, you can make a compound active or inactive. Switching a
compound to inactive status 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. For a
calibration standard, 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. It is no longer part of the result set.
• In Qual Mode, the samples list works with the peaks pane to select a unique sample and
peak combination, which then has its textual and graphical values displayed in the Qual
Mode pane.
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Figure 80. Samples list
Cells in the samples list that should not have a value, such as the theoretical concentration for
an unknown, are shaded and empty. Cells that should have a value, but none exists, report
N/A (not available). Results for compounds that are not detected display N/F (not found).
Table 63. Samples list columns (Sheet 1 of 3)
Parameter
Status
Description
Sample is not acquired.
Sample is acquired but not processed.
Sample is acquired and processed.
Sample is currently acquiring.
Flags
Displayed only when a compound within the sample has an error.
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, Unknown, or Unknown/Qual
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Table 63. Samples list columns (Sheet 2 of 3)
Parameter
Description
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.
Comment
A user-defined comment for the sample.
Vial Position
The tray vial number used for the autosampler acquisition.
Injection Volume
The injection volume in microliters of sample to be injected.
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 range displayed.
The Injection Volume value set in the master method overwrites the value in the instrument
method.
Range: 0.1 through 5000 μL
Integration Mode
Indicates whether the peaks have been manually integrated or integrated from the original
method.
Height
The distance from the peak maximum to the peak base, measured perpendicular to the
ordinate. When the Resp Ratio is specified as Height, this column displays an asterisk
(*Height).
Area
The area obtained by integrating peak intensities from the start to the end of the peak.
When the Resp Ratio is specified as Area, this column displays an asterisk (*Area).
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.
Expected RT
Expected retention time for the compound.
Calc Amt
The amount present in the sample, as determined using the calibration curve and the
response ratio.
Theo Amt
Theoretical amount of the compound expected in the sample.
Sample Amt
The injected volume multiplied by the correction 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 correction factor is 1000, and your sample
amount is 1000.
Resp 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.
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Table 63. Samples list columns (Sheet 3 of 3)
Parameter
Description
IS Amt
Amount of internal standard.
IS Resp
Response of the internal standard.
Active
Displays or hides a compound for a particular sample. 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. It is no longer part of the result set.
Excluded
Turns a compound on or off in the Calibration curve of the Qualification pane.
%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.
%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.
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 enabled multiplexing in the
Configuration mode. See “Multiplexing” on page 87.
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Column Display
The samples list can contain many columns of information. You can scroll to see all the
columns of information, and you can customize which columns you want to display and their
display order.
Follow these procedures:
• To scroll the samples list
• To customize the column display
 To scroll the samples list
Use the scroll bar at the bottom of the samples list to view all the information.
When you use the horizontal scroll bar at the bottom of the samples list, the Status, Flags,
Filename, and Sample Type columns stay fixed while the other columns scroll right and
left.
 To customize the column display
1. Right-click the Data Review sample list and choose Modify Columns from the shortcut
menu.
The Modify Columns dialog box opens. See “Modify Columns dialog box” on page 309.
2. Use the arrow buttons to move all the columns you want to display to the Displayed
Columns pane.
All the columns you select are displayed after the Status, Flags, Filename, and Sample
Type columns.
3. To arrange the order of the columns, do the following:
a. In the Displayed Columns pane, select a column name.
b. Use the Up and Down buttons 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; the last column in the list represents the rightmost column in the Batch View
sample list.
Note You cannot move the Status, Flags, Filename, and Sample Type 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. 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 Data Review view.
Figure 81. Modify Columns dialog box
Parameter
Description
Moves all columns to the Displayed Columns pane.
Moves the selected column to the Displayed Columns pane.
Moves the selected column to the Available Columns pane. You cannot
move the Status, Flags, Filename, and Sample Type columns.
Moves all columns except Status, Flags, Filename, and Sample Type to the
Available Columns pane.
Moves the selected column name in the Displayed Columns pane one row
up in the column order. You cannot move the Status, Flags, Filename, and
Sample Type columns.
Moves the selected column name in the Displayed Columns pane one row
down in the column order. You cannot move the Status, Flags, Filename,
and Sample Type columns.
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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
Caution Flags
The Flags column in the samples list displays a caution flag if the sample is not in compliance
with the method criteria.
Sample caution flags remain static when you switch between compounds for chromatogram
review until a change is completed, for example, when a compound is manually integrated
and no longer falls outside the accepted criteria.
Sample caution flags
To display a summary of problems found in the sample, click the caution flag. The summary
does not list compounds that are not found in Unknown sample types.
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Compound Flags
Flags are displayed in these situations:
• When a compound has violated (or is activated by) any of the values set in the method
(See “Editing the QAQC Page” on page 164.)
• For compounds that are not found
• For compounds that are not found in Cal Std or QC Std sample types
• For compounds that are outside the specified ion ratio range
These criteria do not apply to Matrix Blank sample types when the compound is an internal
standard.
The compounds list is sorted first by flag indicators and then by compound names.
Compound flags indicate the following:
• Red flags for compounds that have ion ratio failures or method validation failures
• Orange flags for compounds that are below the LOQ, below the LOD, or between the
LOD and LOQ values specified in the method
• Green flags for compounds that are over the LOR amount specified in the method
• No flag for compounds that have no errors or where no report options are selected
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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 samples list.
All compounds in the selected sample are displayed 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.
3. In the samples list, 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 samples 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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Quan Mode
Use the Quan Mode and the associated Compounds pane to view quantitative information to
complement the textual information for the selected sample. The Quan Mode displays
quantitative peak and confirming ion information for selected compounds that are found in
the processed samples.
Samples list
Quantification Peak pane
Compounds pane
Qualification pane
In addition to the Quan Mode, the Quan Mode view uses the following panes:
• Compounds
• Quantification Peak
• Qualification
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Compounds
The Compounds pane works with the samples list pane to display textual and graphical values
for a unique file and compound combination.
Follow these procedures:
• To sort the compounds list
• To display peaks for a specific compound
• To display specific problems with a compound
• To display the internal standard for a compound
 To sort the compounds list
In the Compounds pane, right-click and choose one of the following sort styles from the
shortcut menu:
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Command
Description
Sort by flag and
alphabetical
Sorts the compounds first by flag and then within each flag
group, sorts the compounds alphabetically.
Sort by flag and
retention time
Sorts the compounds first by flag and then within each flag
group, sorts the compounds by retention time.
Sort by alphabetical
Sorts the compounds alphabetically (1-n followed by a-z).
Sort by retention time
Sorts the compounds from shorter retention time to longer
retention time.
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 To display peaks for a specific compound
1. In the samples list, select the sample.
The Compounds pane lists all compounds specified in the method.
2. In the Compounds pane, select the compound in the sample.
The Quantification Peak pane displays the peaks for the selected compound and its
internal standard.
Sample
Compound peak
Compound
Internal standard
 To display specific problems with a compound
Hold the cursor over the flag to display the problems with the compound.
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 To display the internal standard for a compound
1. Right-click the Quan Peak pane and choose Show Internal Standard from the shortcut
menu.
Note By default, the application does not display the ISTD pane.
The Quantification Peak pane displays an ISTD pane with the internal standard for the
selected sample and compound.
2. To hide the ISTD pane, right-click the Quan Peak or ISTD pane and choose Hide
Internal Standard from the shortcut menu.
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Quantification Peak
The Quantification Peak pane displays the compound selected in the samples list and
Compound pane. 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 method values were originally calculated based on the processing method parameters.
The manual values are a result of what has been edited.
When the sample contains an internal standard, the chromatogram shows both the analyte
and the internal standard in side-by-side panes.
Follow these procedures:
• To zoom in on a peak
• To manually integrate a quantification or qualification ion
• 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
For a description of commands on the shortcut menu, see “Quantification Peak Shortcut
Menu” on page 322.
 To zoom in on a peak
1. In the chromatogram plot, drag your 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.
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 To manually integrate a quantification or qualification ion
1. Place your cursor over one of the two peak delimiter tags in the Quantification 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.
Both the Quantification Peak pane and the Integration mode column in the
Quantification Data pane reflect the change between method and manual modes. The
generated reports for these data identify the manual modifications.
Note Because a Blank Report displays only the quan mass, when you manually
integrate a confirming ion, the manual integration flag in the report is displayed on
the quan mass.
 To manually add a peak
1. Right-click anywhere in the Quantification Peak pane, and choose Add Peak from the
shortcut menu.
If a peak is already detected, the Add Peak command is not enabled.
2. Click to indicate the left and right base points for the peak.
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
base points
 To remove a manually created peak
Right-click the chromatogram plot, and choose Remove Peak from the shortcut menu.
The application removes the manually added peak.
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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.
Note Because a Blank Report displays only the quan mass, when you manually
integrate a confirming ion, the manual integration flag in the report is displayed on
the quan mass.
 To change the displayed information for detected peaks
1. Right-click the quantification chromatogram plot 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 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 quantification peaks, confirming 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 Peak Detection Settings from the
shortcut menu.
The Peak Detection Settings dialog box opens. Use the Peak Detection Settings dialog
box to adjust detection settings that were specified in the method.
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Figure 82. Peak Detection Settings dialog box
2. Edit any of the detection settings.
For detailed descriptions of all detection settings, see “Detection” on page 126.
3. To save your changes to this compound in all samples in this batch, click Apply to ALL.
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Quantification Peak Shortcut Menu
The Quantification Peak shortcut menu includes the following commands:
Table 64. Quantification Peak shortcut menu commands
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Command
Description
Method Integration Settings
Displays method integration settings.
Manual Integration Settings
Displays manual integration settings.
Add Peak
–or–
Remove 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.
Peak Labels
Displays or hides the peak labels (Label Area, Label
Retention Time, Label Height, or Label Signal to Noise).
Show Peak Info
Displays peak information for the selected compound.
For example:
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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Qualification
The Qualification pane displays the compound selected in the Quantification Data pane and
Compounds pane.
The Qualification pane has five pages:
• Calibration Curve
• Spectra
• QED Spectra
• Confirming Ions
• Ion Overlay
Calibration Curve
The Calibration Curve page displays a graphical view of the calibration curve for the selected
compound and key statistical values for evaluating the quality of the calibration.
Follow these procedures:
• To manually exclude a calibration point
• To zoom in on an area
For a description of commands on the shortcut menu, see “Calibration Curve Shortcut
Menu” on page 325.
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 To manually exclude a calibration point
In the samples 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
 To zoom in on an area
1. In the Calibration Curve plot, drag your cursor to delineate a rectangle around an area.
The delineated area expands to fill the view.
2. To restore the method default view, right-click the calibration curve plot and choose
Reset Scaling from the shortcut menu.
Changes to the calibration settings immediately apply to the entire results set, but you
save them only when you save the batch.
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Calibration Curve Shortcut Menu
The Calibration Curve shortcut menu includes the following commands:
Table 65. Calibration Curve shortcut menu commands
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.
Spectra
The Spectra page displays a comparison of the spectra found in the data and the method
reference.
 To zoom in on an area
1. Drag your cursor to delineate a rectangle around an area.
The delineated area expands to fill the view.
2. To restore the method default view, right-click the spectra plot and choose Reset Scaling
from the shortcut menu.
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QED Spectra
The QED spectra display the averaged QED spectra from the raw data file and the datastore
match. If the sample contains no QED data, the page is blank.
 To zoom in on an area
1. Drag your cursor to delineate a rectangle around an area.
The delineated area expands to fill the view.
2. To restore the method default view, right-click the spectra plot and choose Reset Scaling
from the shortcut menu.
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Confirming Ions
The Confirming Ions page displays a graphical view of all qualifying/confirming ions for the
selected sample and compound and displays calculated ion ratios and ion ratio acceptance
windows. A red border indicates that an ion ratio is outside of its window. Depending on the
method option settings, another ion view is available on the Ion Overlay page. See “Ion
Overlay” on page 331.
A red border indicates that an ion ratio is outside of its window.
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Follow these procedures:
• To manually add a peak
• To remove a manually created peak
• To zoom in on a peak
• To change the displayed information for detected peaks
• To display the peak information window
For a description of commands on the shortcut menu, see “Confirming Ions Shortcut Menu”
on page 330.
 To manually add a peak
1. Right-click the chromatogram plot and select Add Peak from the shortcut menu.
If a peak is already detected, the Add Peak command is not enabled.
2. Click to indicate the left and right base points for the peak.
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
base points
 To remove a manually created peak
Right-click the chromatogram plot, and choose Remove Peak from the shortcut menu.
The application removes the manually added peak.
 To zoom in on a peak
1. In the chromatogram plot, drag your cursor to delineate a rectangle around the peak.
The delineated area expands to fill the view.
2. To restore the method default view, right-click the chromatogram plot and choose Reset
Scaling from the shortcut menu.
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 To change the displayed information for detected peaks
1. Right-click the chromatogram plot 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 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 quantification peaks, confirming 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 display the peak information window
1. Right-click the quantification and confirming ion chromatogram plots.
2. Choose Show Peak Info from the shortcut menu.
Information in this window includes the data stream processed for this ion, consisting of
a particular detector, filter (if applicable), and trace. For example, an MS detector might
show a filter of “+ c Full ms [35.00-500.00]” and a Mass Range trace.
This window also shows the peak area and height, along with the retention times of the
peak integration and the peak apex.
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Confirming Ions Shortcut Menu
The Confirming Ions shortcut menu includes the following commands:
Table 66. Confirming Ions shortcut menu commands
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Command
Description
Method Integration Settings
Displays method integration settings.
Manual Integration Settings
Displays manual integration settings.
Add Peak - Remove Peak Cancel Add Peak
Adds a peak, removes a manually added 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
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 signal to noise).
Show Peak Info
Displays peak information for the selected compound. For
example:
Reset Scaling
Resets the original scaling after a zoom operation.
Peak Detection Settings
Opens the Peak Detection Settings dialog box for the
selected compound. See “Peak Detection Settings dialog
box” on page 321.
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Ion Overlay
The Ion Overlay page represents an overlay of the entire ion set—quantification and
qualifying/confirming—for the selected sample and compound. Use this page to graphically
review the peak apex alignment and co-eluting peak profiles.
 To zoom in on a peak
1. Drag your cursor to delineate a rectangle around the peak.
The delineated area expands to fill the view.
2. To restore the method default view, right-click the chromatogram plot and choose Reset
Scaling from the shortcut menu.
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Qual Mode
Use the Qual Mode and the associated peaks pane to view qualitative information that
complements the textual information for the selected Unknown/Qual sample. The Qual
Mode view displays detected peaks for the selected sample. From the Qual Mode view, you
can manually add peaks. The Qual Mode view is available only for Unknown/Qual sample
types.
Samples list
Chromatogram
navigation pane
Qualitative peak pane
Peaks pane
Spectra pane
Ranking pane
Tip To resize the panes, drag the separators that divide the panes.
In addition to the Quan Mode, the Qual Mode view displays data in the following panes:
• Peaks Pane
• Chromatogram Navigation Pane
• Qualitative Peak Pane
• Spectra Pane (Reference and Selected)
• Ranking Pane
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Peaks Pane
The peaks pane works with the samples list to display graphical values for a unique sample
and peak combination. For detailed descriptions of parameters on the peaks pane, see “Peaks
pane” on page 335.
 To display peaks for a specific compound
1. From the samples list, select a sample.
Note If you select a sample type other than Unknown/Qual, the TraceFinder
application returns you to Quan Mode.
The peaks pane lists the retention times for peaks identified in the selected sample, the
values for the best match methods for each peak, and the compound match.
The number of peaks that are listed is specified in the method. You can change the
number of identified peaks in the Method Template Editor. See “Creating a Method
Template” on page 186.
2. From the peaks pane, select a peak in the sample.
The TraceFinder application displays the selected peak in the qualitative peak pane.
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.
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The TraceFinder application displays the Spectra pane with two sections:
• The Qual Data pane shows spectra data for the peak in the raw data file.
• The Qual Library pane shows actual spectra for the identified library compound.
Reference spectra
from the library
Actual spectra for the
compound
The TraceFinder application locates the selected peak in the navigation chromatogram.
 To remove a peak
1. Select a peak in the peaks pane.
2. Right-click and choose Remove Selected Peak from the shortcut menu.
The TraceFinder application removes the selected peak from the peaks list.
Note There is no undo for this action, but you can manually add a peak to redefine a
removed peak. See “Chromatogram Navigation Pane” on page 336.
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Figure 83. Peaks pane
Table 67. Peaks pane parameters
Command
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 (min)
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 method used to search the NIST
library.
MP
Match probability.
Library entry
Library compound that matches the identified peak.
Remove selected peak
Shortcut menu command that removes the selected peak
from the peaks list.
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Chromatogram Navigation Pane
The chromatogram navigation pane displays all peaks in the selected sample. The peak
selected in the peaks pane displays a red marker. See “Chromatogram navigation pane” on
page 337.
For a description of commands on the shortcut menu, see “Chromatogram navigation pane
shortcut menu commands” on page 337.
 To zoom in on a peak
1. In the chromatogram navigation 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 chromatogram navigation pane and choose
Reset Scaling from the shortcut menu.
 To manually add a peak
1. Zoom in to make it easier to identify the peak you want to add to the results set.
2. Right-click the chromatogram navigation pane, and choose Add 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 chromatogram navigation 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 qualitative peak pane.
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Figure 84. Qualitative peak pane with a manually added peak
Manually added
base points
Figure 85. Chromatogram navigation pane
Table 68. Chromatogram navigation pane shortcut menu commands
Thermo Scientific
Command
Description
Add peak
Adds a peak.
Reset scaling
Resets the original scaling after a zoom operation.
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Qualitative Peak Pane
The qualitative peak pane displays the selected peak. See “Qualitative peak pane” on
page 340.
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
For a description of commands on the shortcut menu, see “Qualitative peak pane shortcut
menu commands” on page 340.
 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 qualitative peak pane, and choose Add Peak from the
shortcut menu.
If a peak is already detected, the Add Peak command is not enabled.
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 chromatogram plot, and choose Remove Peak from the shortcut menu.
The TraceFinder application removes the peak displayed in the qualitative peak pane. All
data for this peak are removed from the Qual Mode panes.
 To switch between method and manual integration modes
Right-click the chromatogram view 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 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 chromatogram plot 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 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 qualitative peaks, confirming 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.
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Figure 86. Qualitative peak pane
The qualitative peak pane shortcut menu includes the following commands:
Table 69. Qualitative peak 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 Signal to Noise).
Remove peak
Removes the peak displayed in the Qual pane.
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Spectra Pane (Reference and Selected)
The spectra pane displays the reference spectra and the spectra for the selected sample. The
top pane displays the reference spectra for the identified compound from the library; the
bottom pane displays the spectra for the selected peak.
Figure 87. Spectra pane
Reference
spectrum from
the library
Actual spectrum
for the selected
peak
 To zoom in on a peak
1. In the spectra 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.
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Ranking Pane
The ranking pane displays the three best library matches for the selected peak. Use this pane
to select a different library entry for the peak. See “Ranking pane” on page 343.
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
For a detailed description of ranking pane parameters, see “Ranking pane parameters” on
page 343.
 To change the library entry for a selected peak
In the ranking pane, select the check box for the library entry you want to use to identify
the selected peak.
• In the Spectra pane, the reference spectra change to show the spectra for the selected
library entry.
• In the peaks pane, the SI, RSI, MP, and Library Entry values update to reflect the
selected library entry.
Selected library entry
in the ranking pane
Reference
spectrum
for Acenaphthene
Peaks pane for
Acenaphthene
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Figure 88. Ranking pane
Table 70. Ranking pane parameters
Thermo Scientific
Command
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 method used to search the NIST library.
RSI
Reverse search index method used to search the NIST
library.
MP
Match probability.
Library entry
Library compound that matches the identified peak.
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Working in the Report View
Use the Report View to display or generate reports for the currently selected batch in the
Analysis mode. You must process each sample in the batch before you can view or generate a
sample-level report for that sample.
This section includes the following topics:
• Viewing Reports
• Generating Reports
• Working with Reports
• Working with the Active View
Figure 89. Report View in Analysis mode
• View Only: Displays a PDF or Excel spreadsheet preview of the selected report type for
the batch, sample, or compound. See “Viewing Reports” on page 345.
Preview reports for all Standard report types are always available. You must generate
Custom and Target Screening report types before they are available in this list.
The Report View page displays one of the following report outputs:
• Standard reports as PDF files
• Custom reports in XLSM format
• Target Screening reports as PDF files
• Generate Only: Creates all specified report output formats for the selected sample- or
batch-level report. See “Generating Reports” on page 349.
 To open the Report View
1. Click Analysis in the navigation pane from any mode.
2. In the Analysis navigation pane, click Report View.
The Report View for the currently selected batch opens.
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Viewing Reports
Use the View Only features to view all configured standard reports and any custom or target
screening reports that you have generated. After you generate a report, the application displays
the report in the View Only report list.
Follow these procedures:
• To select a report
• To select a sample
• To select a compound
• To select a sample and a compound
 To select a report
1. Select the View Only option.
2. Click the Select a Report list.
The report list opens, displaying all configured report types.
These reports reflect the Displayed Reports selections in the Configuration mode. To
change the configured reports that are available in this view, see “Specifying the Reports
Configuration” on page 65.
To sort the reports, click the column headers. The application maintains this sort order
each time you open the Report View for this batch.
To help organize your reports, you can filter the list.
3. To limit the types of reports you want to display in the report list, select any combination
of report filter options in the Filter Reports area.
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Table 71. Filter Reports options
Option
Behavior
Only show automated batch
reports
Displays only reports that have an output format
specified in the Automated Batch Reports area in the
Batch View. See “Editing Report Output Formats”
on page 282.
Standard reports
Displays Standard report types.
Custom reports
Displays all generated Custom report types. Custom
reports are not available for viewing until you have
generated the report.
Target Screening reports
Displays all generated Target Screening reports.
Target Screening reports are not available for viewing
until you have generated the report.
Note When you make changes to the method in the Local Method view, to the peaks
in the Data Review view, or to the samples in the Batch View, you must regenerate the
custom or target screening reports before these changes take effect.
4. Double-click the name of the report.
The report list closes.
• When the selected report is a batch-level report, the application displays the report on
the Report View page.
• When the selected report includes separate reports for each sample, you must select a
sample file.
Follow the procedure “To select a sample” on page 347.
• When the selected report includes separate reports for each compound, you must
select a compound.
Follow the procedure “To select a compound” on page 347.
• When the selected report includes separate reports for each sample and each
compound in the sample, you must select both a sample and a compound.
Follow the procedure “To select a sample and a compound” on page 348.
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 To select a sample
1. Click the Sample File list.
The sample list displays all samples in the batch.
2. To show only samples that would be included in the selected report, select the Only
Show Samples Relevant... check box.
For example, if you selected the Check Standard Report, the sample list displays only
QC Std samples.
Note Click the column headers to sort the samples. The application maintains this
sort order each time you open the Report View for this batch.
3. Double-click the name of the sample.
The sample list closes. The Report View page displays the sample-level report.
 To select a compound
1. Click the Compound list.
The compound list displays the names and retention times of all compounds in the
sample.
2. Double-click a single compound or All Compounds.
The compound list closes. The Report View page displays the compound-level report.
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 To select a sample and a compound
1. Click the Sample File list.
The sample list displays all samples in the batch.
2. To show only samples that would be included in the selected report, select the Only
Show Samples Relevant... check box.
For example, if you selected the Check Standard Report, the sample list displays only
QC Std samples.
Tip Click the column headers to sort the samples. The application saves this sort
order in the Report View for this batch.
3. Double-click the name of the sample.
The sample list closes.
4. Click the Compound list.
The compound list displays the names and retention times of all compounds in the
sample.
5. Double-click a single compound or All Compounds.
The compound list closes.
The Report View page displays the compound-level report for the selected sample and
compound.
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Generating Reports
Use the Generate Only features to create sample-level reports. You cannot use the View Only
features to view custom or target screening reports until you generate the report. When you
make changes to the method in the Local Method view or to the peaks in the Data Review
view, you must regenerate the custom or target screening reports to see the effects of those
changes.
Follow these procedures:
• To select a report
• To select a sample
 To select a report
1. Select the Generate Only option.
2. Click the Select a Report list.
The report list opens.
The application displays only configured sample-level report types in the list. You cannot
generate batch-level or compound-level reports from this view. To change the configured
reports that are available in this view, see “Specifying the Reports Configuration” on
page 65.
If you have many reports, you can filter the list.
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3. To limit the types of reports you want to display in the report list, select any combination
of report filter check boxes in the Filter Reports area.
Option
Behavior
Only show automated batch
reports
Displays only sample-level reports that have an
output format specified in the Automated Batch
Reports area in the Batch View. See “Editing Report
Output Formats” on page 282.
If you have only batch-level reports specified in the
Batch View, selecting this option excludes all reports
in the Report Name list.
Standard reports
Displays sample-level Standard report types.
Custom reports
Displays sample-level Custom report types.
Target Screening reports
Displays sample-level Target Screening report types.
Note Click the column headers to sort the samples. The application saves this sort
order in the Report View for this batch.
4. Double-click the name of the report.
The report list closes. You must select a sample file for the selected report.
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 To select a sample
1. Click the Sample File box.
The sample list displays all samples in the batch.
2. To show only samples that would be included in the selected report, select the Only
Show Samples Relevant... check box.
For example, if you selected the QC Standard Report, the sample list displays only QC Std
samples.
Note Click the column headers to sort the samples. The application saves this sort
order in the Report View for this batch.
3. Select the check box for each sample you want to include in the report.
4. Click Generate.
The Report Selection Confirmation dialog box opens.
5. In the What Action Would You Like to Perform area, select the types of reports you want
to create.
Note The application automatically selects required output formats. These options
are not editable.
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6. Click Continue.
The application submits the selected samples to the report queue.
When you have already generated this report in the Batch View or Acquisition mode, the
application time-stamps the new report to differentiate it from the original report.
7. To view the report you generated, follow the instructions in “Viewing Reports” on
page 345.
Note When you make changes to the method in the Local Method view, the peaks in the
Data Review view, or the samples in the Batch View, you must regenerate the custom or
target screening reports before those changes take effect.
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Working with Reports
Use the buttons on the Report View page to view, print, or export a report.
• A PDF report view is available for all Standard and Target Screening report types.
• An Excel Macro-Enabled Workbook report view is available for any Custom report types
that you have generated with the Generate XLSM option selected.
Follow these procedures:
• To print a standard or target screening report
• To export a standard report
• To search for text
• To enlarge the report text
 To print a standard or target screening report
1. Select the report to print from the Select a Report list.
2. (Optional) Select a sample from the Sample File list.
The application displays the report on the Report View page.
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3. Click the Print Report button,
.
The Print dialog box for your default printer opens.
4. Follow the typical procedure to print from your printer.
Landscape reports automatically rotate to fit the paper.
 To export a standard report
1. Select the report you want to print from the Select a Report list.
2. (Optional) Select a sample from the Sample File list.
The application displays the report on the Report View page.
3. Click the Export Report button,
.
The Export Report dialog box opens.
4. Locate the folder where you want to write the report file.
5. Type a file name for the exported report file.
6. Select a file type from the Save as Type list:
7. Click Save.
The TraceFinder application saves the file as the specified file type and writes the report
file to the specified folder.
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 To search for text
1. Select a report from the Select a Report list.
2. (Optional) Select a sample from the Sample File list.
The application displays the report on the Report View page.
3. Click the Find Text button,
.
The Find Text dialog box opens.
4. Enter your text and click Find Next.
When the TraceFinder application locates the text, it encloses the text in a red box.
 To enlarge the report text
1. Select a report from the Select a Report list.
2. (Optional) Select a sample from the Sample File list.
The application displays the report on the Report View page.
3. Click the Zoom button,
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Working with the Active View
Use the Active View page to view quantitative data for each sample in a report. Data in the
Active View are labeled with flag information. These flags are based on a comparison of the
batch data to criteria defined in the master method.
 To display the Active View page
Click the Active View tab.
The Active View page displays quantitative data and QAQC error flags for each sample.
See “Active View page” on page 357.
 To display a report
1. Select a report type from the Select a Report list.
Only the report types created for the current batch are displayed in the list.
2. (Optional) When the report type includes separate reports for each sample, select a
sample file.
 To filter which compounds to display
Click the Showing button to display either all compounds or only compounds that are
flagged for failing a QAQC test.
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Figure 90. Active View page
Table 72. Active View parameters (Sheet 1 of 4)
Parameter
Description
View Only
The Active View pane is available only when View Only is selected.
Select a report
Displays the report types created for the current batch.
Sample file
Used when the report type includes separate reports for each sample.
Total Rows
The number of compound rows currently displayed in the pane.
Showing
Displays all compounds or only the flagged compounds.
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Table 72. Active View parameters (Sheet 2 of 4)
Parameter
Description
Column headings
Many column headings are specific to individual reports. See “Active View Report Contents”
on page 361.
Status
Indicates the status of the reported compound.
• A yellow check mark indicates one of the following conditions:
– The compound was manually integrated.
– Any of the confirming peaks was manually integrated.
– The compound has quan flags.
• A red check mark indicates that the QAQC checks failed.
• A green check mark indicates that none of these conditions exist.
When the compound is an internal standard, warnings are displayed only on the internal
standard report. The Status column is blank for Manual Integration reports.
Compound Name
Alphanumeric name assigned to the compound.
Compound Type
Target Compound or Internal Standard.
QAQC Flags
Indicates that the QAQC check for the sample failed.
Manual Integration reports do not use the QAQC column.
Quan Flags
•
•
•
•
•
Limit of Detection (LOD)
Limit of Quantitation (LOQ)
Limit of Reporting (LOR)
Values between the limit of detection and the limit of quantitation, known as the J flag
Upper Limit of Linearity (ULOL)
Quan flags do not apply to these sample types: Cal Std, QC Std, Matrix Blank, or Solvent.
Manual Integration reports do not use the Quan Flag column.
Manual Flags
Indicates manually integrated peaks.
• M indicates a manually integrated quan peak.
• m indicates a manually integrated confirming peak.
Depending on the selected report, the Active View page contains any or all of the following parameters:
Quan Peak m/z
Mass-to-charge ratio for the selected quantitation peak.
Total Response
The sum of all Quan Peak Response values for the compound.
Quan Peak Response
Response of the quan peak.
Quan peak RT
Retention time for the quan peak.
Theoretical amount
Theoretical amount of the compound. Reports N/A when not applicable.
Concentration
Confirming n Mass
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Table 72. Active View parameters (Sheet 3 of 4)
Parameter
Description
Confirming n
Response
Response of the confirming peak.
Confirming n Manual Indicates a manually integrated confirming peak.
Flag
Confirming n Ion
Ratio Flag
Indicates that the ion ratio is out of range.
Confirming n Ion
Ratio
Actual ratio of the confirming ion response to the quan ion response.
Confirming n Range
Acceptable range for the confirming ion.
Retention Time
The time after injection when the compound elutes. The total time that the compound is
retained on the column.
Quan mass
The mass-to-charge ratio used to determine the peak area and peak height of the compound.
Response
Sum of all Quan Peak Response values for the compound.
Injection
concentration
Calculated amount as the sample was injected, with no conversion applied.
Injection Units
Injection units specified on the Calibration page in Method Development mode. See
“Calibration” on page 156.
Sample Concentration The injected concentration multiplied by the conversion factor.
Sample Units
Sample units specified on the Calibration page in Method Development mode. See
“Calibration” on page 156.
QIon
Mass range for the quan peak.
RT
Retention time. The time after injection when the compound elutes. The total time that the
compound is retained on the column.
Manual Integration reports
m/z
Mass-to-charge ratio for the quan peak.
Method RT
Apex retention time for the method-integrated peak.
Method Peak Height
Height of the method-integrated peak.
Method Peak Area
Area of the method-integrated peak.
Manual RT
Apex retention time for the manually integrated peak.
Manual Peak Height
Height of the manually integrated peak.
Manual Peak Area
Area of the manually integrated peak.
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Table 72. Active View parameters (Sheet 4 of 4)
Parameter
Description
Internal Standard reports
Std Response
Average of the internal standard’s response as found in the calibration file.
Minimum Response
Minimum response time as specified on the ISTD page in Method Development mode. See
“ISTD” on page 169.
Maximum Response
Maximum response time as specified on the ISTD page in Method Development mode. See
“ISTD” on page 169.
Sample Response
Area found in the sample.
Std RT
Average retention time as found in the calibration file.
Min RT
Minimum retention time as specified on the ISTD page in Method Development mode. See
“ISTD” on page 169.
Max RT
Maximum retention time as specified on the ISTD page in Method Development mode. See
“ISTD” on page 169.
Sample RT
Retention time found in the sample.
Graphical data
Quan Peak 1
Calibration curve
Displays a graphical view of the calibration curve for the selected compound and key
statistical values for evaluating the quality of the calibration.
Spectra
Displays a comparison of the spectra found in the data and the method reference.
QED Spectra
Displays the averaged QED spectra from the raw data file and the datastore match. If the
sample contains no QED data, the page is blank.
Confirming Ions
Displays a graphical view of all qualifying/confirming ions for the selected sample and
compound, and displays calculated ion ratios and ion ratio acceptance windows.
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Active View Report Contents
Each standard report that uses the Active View displays values that are common to all reports.
See “Common Active View report columns” on page 362.
In addition to the common values, the following reports display additional active view
features:
• Blank Report Active View columns
• Calibration Report Active View columns
• High Density Sample Report 1 and High Density Sample Report 1 Long Active View
columns
• High Density Sample Report 2 and High Density Sample Report 2 Long Active View
columns
• High Density Sample Report 3 and High Density Sample Report 3 Long Active View
columns
• Internal Standard Summary Report Active View columns
• Ion Ratio Failure Report Active View columns
• Manual Integration Report Active View columns
• Quantitation Report Active View columns
• Solvent Blank Report Active View columns
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Table 73. Common Active View report columns
Column
Description
Status
Indicates the status of the reported compound.
• A yellow caution sign indicates one of the following conditions:
–
The compound was manually integrated.
–
Any of the confirming peaks was manually integrated.
–
The compound has quan flags.
–
The compound has a QAQC failure.
• A green check mark indicates that none of these conditions exists.
When the compound is an internal standard, warning flags are displayed only on the
internal standard report.
Compound name
Alphanumeric name assigned to the compound.
Compound type
Target Compound or Internal Standard.
QAQC flags
Indicates that the QAQC check for the sample failed.
The Method Validation and MDL reports do not use the QAQC column.
Quan flags
•
•
•
•
•
Limit of Detection (LOD)
Limit of Quantitation (LOQ)
Limit of Reporting (LOR)
Values between the limit of detection and the limit of quantitation, known as the J flag
Upper Limit of Linearity (ULOL)
Quan flags do not apply to these sample types: Cal Std, QC Std, Matrix Blank, or Solvent.
The Calibration report does not use the Quan Flags column.
Manual flags
Indicates manually integrated peaks.
• M indicates a manually integrated quan peak.
• m indicates a manually integrated confirming peak.
Table 74. Blank Report Active View columns (Sheet 1 of 2)
Column
Description
Retention Time
Retention time for the quan mass. The time after injection when the compound elutes.
The total time that the compound is retained on the column.
Quan Mass
Mass range for the quan peak.
Response
Sum of all Quan Peak Response values for the compound.
Inj Conc
Calculated amount as the sample was injected, with no conversion applied.
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Table 74. Blank Report Active View columns (Sheet 2 of 2)
Column
Description
Inj Units
Injection units specified on the Calibration page in Method Development mode. See
“Calibration” on page 156.
Sample Conc
Calculated amount multiplied by the conversion factor.
Sample Units
Sample units specified on the Calibration page in Method Development mode. See
“Calibration” on page 156.
Table 75. Calibration Report Active View columns
Column
Description
Curve Type
The type of curve used when calibrating the compound (linear, quadratic, or average
response factor).
Average RF
The average response factor. Applicable if curve type is Average RF.
Average Response
The average response for the internal standard across all calibration points. Applies
only to Internal Standard sample types.
A0
The value with no X. Applies only to linear and quadratic curves.
A1
The X value. Applies only to linear and quadratic curves.
A2
The X^2 value. Applies only to quadratic curves.
R^2
The minimum correlation coefficient (r2) for an acceptable calibration (when in
linear or quadratic mode).
RSD
Relative standard deviation. Applies only to internal standards and targets calibrated
with an average RF curve.
Level
The column specifies the level name; the field value specifies the data point used in
calibration. This field can be Response Factor for external calibration, Response Ratio
for internal linear or quadratic, or Relative Response Factor for Internal Average RF.
There is one column for each level in the curve. If the batch uses an extended
calibration, there might be more columns than calibration standards in the current
batch.
Table 76. High Density Sample Report 1 and High Density Sample Report 1 Long Active View columns
Column
Description
m/z
Mass-to-charge ratio for the quan peak.
Total Response
The sum of all Quan Peak Response values for the compound.
Quan Peak Response
Response of the quan peak.
Quan Peak RT
Retention time for the quan peak.
T Amount
Theoretical amount of the compound. Reports N/A when not applicable.
Conc
Calculated (injected) amount.
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Table 77. High Density Sample Report 2 and High Density Sample Report 2 Long Active View columns
Column
Description
m/z
Mass-to-charge ratio for the quan peak.
Total Response
Sum of all Quan Peak Response values for the compound.
Quan Peak Response
Response of the quan peak.
Quan Peak RT
Retention time for the quan peak.
T Amount
Theoretical amount of the compound. Reports N/A when not applicable.
Conc
Calculated (injected) amount.
Confirming 1 Mass
Mass of the confirming peak.
Confirming 1 Response
Response of the confirming peak.
Confirming 1 Manual Flag
Indicates a manually integrated confirming peak.
Confirming 1 Ion Ratio Flag
Indicates that the ion ratio is out of range.
Confirming 1 Ion Ratio
Actual ratio of the confirming ion response to the quan ion response.
Confirming 1 Range
Acceptable range for the confirming ion.
Table 78. High Density Sample Report 3 and High Density Sample Report 3 Long Active View columns (Sheet 1 of 2)
Column
Description
m/z
Mass-to-charge ratio for the quan peak.
Total Response
Sum of all Quan Peak Response values for the compound.
Quan Peak Response
Response of the quan peak.
Quan Peak RT
Retention time for the quan peak.
T Amount
Theoretical amount of the compound. Reports N/A when not applicable.
Conc
Calculated (injected) amount.
Confirming 1 Mass
Mass of the confirming peak.
Confirming 1 Response
Response of the confirming peak.
Confirming 1 Manual Flag
Indicates a manually integrated confirming peak.
Confirming 1 Ion Ratio Flag
Indicates that the ion ratio is out of range.
Confirming 1 Ion Ratio
Actual ratio of the confirming ion response to the quan ion response.
Confirming 1 Range
Acceptable range for the confirming ion.
Confirming 2 Mass
Mass of the confirming peak.
Confirming 2 Response
Response of the confirming peak.
Confirming 2 Manual Flag
Indicates a manually integrated confirming peak.
Confirming 2 Ion Ratio Flag
Indicates that the ion ratio is out of range.
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Table 78. High Density Sample Report 3 and High Density Sample Report 3 Long Active View columns (Sheet 2 of 2)
Column
Description
Confirming 2 Ion Ratio
Actual ratio of the confirming ion response to the quan ion response.
Confirming 2 Range
Acceptable range for the confirming ion.
Table 79. Internal Standard Summary Report Active View columns
Column
Description
Std Response
Average of the internal standard’s response as found in the calibration file.
Minimum Response
Minimum response time as specified on the ISTD page in Method Development
mode. See “ISTD” on page 169.
Maximum Response
Maximum response time as specified on the ISTD page in Method Development
mode. See “ISTD” on page 169.
Sample Response
Area found in the sample.
Std RT
Average retention time as found in the calibration file.
Min RT
Minimum retention time as specified on the ISTD page in Method Development
mode. See “ISTD” on page 169.
Max RT
Maximum retention time as specified on the ISTD page in Method Development
mode. See “ISTD” on page 169.
Sample RT
Retention time found in the sample.
Table 80. Ion Ratio Failure Report Active View columns
Column
Description
Quan Ion
The ion for quan peak.
Qual Ion
The ion for the confirming peak.
Quan Ion Response
Response of the quantitation ion.
Qual Ion Response
Response of the qualitative ion.
Ratio
The ratio of the confirming ion response to the quan ion response.
Range
The acceptable range.
Table 81. Manual Integration Report Active View columns (Sheet 1 of 2)
Column
Description
m/z
Mass-to-charge ratio for the quan peak.
Method RT
Apex retention time for the method-integrated peak.
Method Peak Height
Height for the method-integrated peak.
Method Peak Area
Area for the method-integrated peak.
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Table 81. Manual Integration Report Active View columns (Sheet 2 of 2)
Column
Description
Manual RT
Apex retention time for the manually integrated peak.
Manual Peak Height
Height of the manually integrated peak.
Manual Peak Area
Area of the manually integrated peak.
Table 82. Manual Integration Report Active View columns
Column
Description
m/z
Mass-to-charge ratio for the quan peak.
Method RT
Apex retention time for the method-integrated peak.
Method Peak Height
Height for the method-integrated peak.
Method Peak Area
Area for the method-integrated peak.
Manual RT
Apex retention time for the manually integrated peak.
Manual Peak Height
Height of the manually integrated peak.
Manual Peak Area
Area of the manually integrated peak.
Table 83. Quantitation Report Active View columns
Column
Description
RT
Retention time for the peak. The time after injection when the compound elutes. The
total time that the compound is retained on the column.
QIon
Mass range for the quan peak.
Response
Sum of all quan peak response values for the compound.
Injected Concentration
Calculated amount as the sample was injected, with no conversion applied.
As each additional sample is processed, calibration data change; therefore, except for
the final sample in a batch, a report in active view or report view shows different
values from a physical (PDF, XML, or printed) report created at the end of
processing. To avoid this discrepancy, do one of the following:
• For the standard Quantitation Report or Quantitation Report - 2, observe the
active or report view for only the last sample in the batch.
• For the custom Quantitation Report, make the report a batch-level report.
Injected units
Injection units specified on the Calibration page in Method Development mode. See
“Calibration” on page 156.
Sample Conc
Calculated injection amount multiplied by the conversion factor. See the Injected
Concentration description.
Sample units
Sample units specified on the Calibration page in Method Development mode. See
“Calibration” on page 156.
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Table 84. Solvent Blank Report Active View columns
Column
Description
RT
Retention time for the quan peak. The time after injection when the compound elutes.
The total time that the compound is retained on the column.
QIon
Mass range for the quan peak.
Response
Sum of all Quan Peak Response values for the compound.
Method
Method of evaluation defined in the method.
Upper Limit
Defined in the method.
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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
BatchName_MasterMethodName.
 To open the Local Method View
1. Do one of the following:
From the dashboard, click Analysis.
–Or–
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 method parameters, see “Working with Master Methods” on
page 94.
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 91. Local Method View
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Working in the Batch Template Editor
Working in the Batch Template Editor
In the Batch Template Editor, you can create a batch template that contains the basic settings
for your batches. Batches are created as a routine operation and, because the nature and types
of batches are often similar (in some cases specified by laboratory operating procedure), you
can define a batch template that supplies the basic structure of a batch.
To create a batch using a batch template, choose File > New > Batch Using Wizard from the
application menu. See “Creating a Batch Using the Batch Wizard” on page 290.
Follow these procedures:
• To create a new batch template
• To specify active compounds
• To specify template method information
• To specify active compounds
• To insert a sample into the list
• To copy a sample
• To remove samples from the list
• To edit sample values
• To add multiple samples of the same type
• To specify report options
• To specify active compounds
 To create a new batch template
1. Choose File > New > Batch Template from the application menu.
The Open Method dialog box opens where you can select a master method to use for
your template.
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2. Select a master method and click Open.
The Batch Template Editor opens. For detailed descriptions of all parameters, see “Batch
Template Editor” on page 376.
The editor uses the selected master method for the template.
 To open a batch template
1. Choose File > Open > Batch Template from the application menu.
The Open Batch Template dialog box opens.
2. Select a batch template and click Open.
The Batch Template Editor opens with the settings from the selected template. To view
the editor and for detailed descriptions of the parameters, see “Batch Template Editor” on
page 376.
 To specify template method information
1. From the Project list, select a project name.
2. From the Subproject list, select a subproject name.
Tip If there are no projects or subprojects to select, go to the Project Administration
view of the Configuration mode and create a new subproject. See “Project
Administration” on page 46.
3. To change the current method, click Select Method and select a new method.
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 To add a sample to the batch
Right-click and choose Add Sample from the shortcut menu, or click the add sample
icon,
.
The application adds a new, Unknown sample to the end of the sample list.
 To insert a sample into the list
1. Select the sample above which you will insert a new, Unknown sample.
2. Right-click and choose Insert Sample from the shortcut menu.
The application inserts a new, Unknown sample above the selected sample.
Inserted
sample
 To copy a sample
1. Select the sample you want to copy.
2. Right-click and choose Insert Copy Sample from the shortcut menu.
The application inserts the copy above the selected sample.
 To remove samples from the list
1. Select the sample you want to remove.
Use the SHIFT or CTRL keys to select multiple samples.
2. Right-click and choose Remove Selected Samples from the shortcut menu, or click the
Remove Sample icon,
.
The application removes the selected samples from the list.
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 To edit sample values
1. For each sample, click the Sample Type column and select a sample type from the list.
Available sample types
Matrix Blank
Solvent
Unknown
Cal Std
QC Std
Unknown/Qual
2. For each Cal Std or QC Std sample, click the Level cell and select a level from the list.
The calibration and QC levels were defined in the master method. If there is nothing to
select in the Level list, do the following:
a. Close the Batch Template Editor.
b. Return to the Method Development mode.
c. Open the master method.
d. Click the Compounds tab.
e. Click the Calibration Levels tab.
f.
Add the levels.
g. Save the method.
h. Return to the Analysis mode, and begin this batch template again.
You must close your original batch template without saving it and start a new template.
For detailed instructions, see “Editing a Master Method” on page 110.
3. (Optional) Type a sample ID, sample name, or comment.
These values can be any text string.
 To add multiple samples of the same type
In the Repeat Sample Count column, type the number of samples you want to create for
each sample type.
When you use this template to create a batch, the batch will contain this number of
individual samples of the specified type. In the batch, you can change any of the column
values for the individual samples.
 To specify report options
1. To specify the type of report output to create for each report type, select the check box in
the appropriate column.
By default, all report output types are cleared.
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2. To duplicate the output type for all reports below the selected report, 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.
You can duplicate the output type only for reports that have this output format available.
3. To duplicate the selected report output formats for all samples in the batch, right-click the
cell and choose Apply Selection to All Samples from the shortcut menu.
Example:
Copying selected output formats from the first sample
Duplicates the selected output formats to all samples in the batch
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 To specify active compounds
1. In the sample table, click anywhere in the sample row to select the sample for which you
want to specify active compounds.
Compound selections are specific to a sample. You can select different compounds for
each of the samples even if they are the same sample type.
2. In the Compound Active Status area, select the Active check box for each compound you
want to identify in the selected sample.
If you created compound groups, you can make the entire group active or inactive.
Right-click and choose the group from the list.
Inactive groups
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Figure 92. Batch Template Editor
Table 85. Batch Template Editor parameters (Sheet 1 of 2)
Parameter
Description
Template Method Information
Project
The top-level project for the batch.
Subproject
The lower-level project for the batch.
Method
The master method to use for the batch. The Select Method button opens the Open
Method dialog box where you can select a different master method for the batch template.
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, an
assay type of PAH might be used for the analysis of Polynuclear Aromatic Hydrocarbons).
The application uses this assay type in the batch template. You can also select an
appropriate combination of method and batch template.
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Table 85. Batch Template Editor parameters (Sheet 2 of 2)
Parameter
Description
Column values
Sample type
Defines how the application processes the sample data. Each sample is classified as one of
the following sample types: Matrix Blank, Solvent, Cal Std, QC Std, Unknown, or
Unknown/Qual
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.
Comment
A user-defined comment for the sample.
Repeat sample count
Number of samples to create for this sample type.
Level / Batch Level
Report Name
The name of a report.
Type
Standard, Custom, or Target Screening
Print
Sends reports to the printer.
Create PDF
Saves reports as PDF files.
Available only for standard and target screening reports.
Create XML
Exports reports in XML format.
Available only for standard reports.
Create XLSM
Exports reports in Excel Macro-Enabled Workbook (.xlsm) format.
Available only for custom reports.
Compound Active Status
Compound name
List of all compounds for the method.
Active
Compounds to identify in the selected sample.
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Reports
This appendix contains information about standard and custom reports.
Contents
• Specifying Reports
• Report Flags
• Sample Standard Reports
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 reports listed in this appendix meet the requirements of various methods and
worldwide regulatory agencies and are designed to help track the performance of the system
and method. The TraceFinder application can produce both standard reports and custom
reports.
Specifying Reports
As a user in the ITAdmin or LabDirector role, you can configure a list of reports that are
available for the Method Development or Acquisition mode.
For detailed information about configuring reports in the Configuration mode, see
“Specifying the Reports Configuration” on page 65.
For detailed information about specifying reports when you create a method in the Method
Development mode, see “Editing the Reports Page” on page 173.
For detailed information about viewing batch reports in the Acquisition mode, see “Selecting
and Reviewing Reports” on page 234.
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Specifying Reports
Standard Reports
For each standard report you generate, you can create a version in hardcopy print, as a PDF
(.pdf ) file, or in an XML (.xml) output format. In addition to the report type, you can specify
a report description for each of your reports. The default report description is the report
name.
The TraceFinder application can generate the following types of standard reports:
• Batch Report
• BatchReportRevision1
• Blank Report
• Calibration Report
• Chromatogram Report
• Compound Calibration Report
• Compound Calibration Report - Alternate
• Confirmation Report
• High Density Calibration Report
• High Density Internal Standard Report Long
• Internal Standard Summary Report
• Ion Ratio Failure Report
• Manual Integration Report
• Method Report
• QC Standard Report
• Qualitative Peak Report
• Qualitative Summary Report
• Quantitation Report
• Quantitation Report - 2
• Solvent Blank Report
To view an example of each type of standard report, see “Sample Standard Reports” on
page 383.
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Specifying Reports
Custom Reports
For each custom report you generate, you can create a hardcopy printout or an Excel
Macro-Enabled Workbook (.xlsm) output file. The default report description is the report
name.
A user in the ITAdmin or LabDirector role can configure custom reports to generate a single
report for an entire batch or to create separate reports for each sample. Rather than creating
separate reports for each sample, this method uses data from only the last sample to create a
single report for the entire batch.
The TraceFinder application includes the following custom reports:
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
AltCalibrationReport
Alternate BatchReport
Alternate CalibrationReport
Alternate ConfirmationReport
Alternate MatrixSpikeReport
Alternate SampleReport
Alternate SummaryReport
BatchReport
BlankReport
CalibrationDensityReport
CalibrationReport
CheckStandardReport
CompoundCalibrationReport
ConfirmationReport2
HighDensitySampleReport1Long
HighDensitySampleReport2Long
HighDensitySampleReport3Long
HighDensitySampleReport4
HighDensitySampleReport5
QuantitationReport
Target Screening Reports
• Target Screening Long Report
• Target Screening Summary Report
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Report Flags
Report Flags
When generating or viewing a report, you might see one of the following quantification or
calibration flags listed on the page.
Table 86. Quantification flags
Flag
Definition
b
Compound was observed at a concentration in a Matrix Blank sample above the
specified limit.
s
Compound was observed at a response in a solvent blank sample above the specified
limit.
J
Compound was observed at a concentration above the limit of detection, but below
the limit of quantitation.
I or * Confirming/qualifying ion ratio for a compound was observed outside the target
ratio range or the coelution between quantification and confirming/qualifying ion
was larger than acceptable limit.
C
Compound was observed at a concentration above the specified carryover limit.
?
Compound was observed at a concentration above the specified linearity limit.
D
Compound was observed at a concentration below the specified limit of detection.
Q
Compound was observed at a concentration below the specified limit of
quantitation.
POS
Compound was observed at a concentration above the specified cutoff.
Table 87. Calibration flags
Flag
Definition
D
Calibration for this compound exceeded the specified maximum percent relative
standard deviation (%RSD).
F
Response factor for this compound was below the specified minimum response
factor (Min RF).
R
Calibration for this compound was below the specified minimum correlation
coefficient (r2).
A
Back calculation of the calibration points for this compound exceeded the
specified maximum percent difference (Max %D).
X
Calibration point for this compound was excluded from the overall calibration
by manual selection.
X(ISNF)
Calibration point for this compound was excluded from the overall calibration
because its associated internal standard was not found.
A flags failure is identified by an asterisk (*), a shaded row, or the word Fail.
Values on a report that are the result of a manual integration use an uppercase M to signify a
manually integrated quantification ion and a lowercase m to signify a manually integrated
qualifying/confirming ion. On alternate reports, manual integration uses a black box around
the value.
382
TraceFinder User Guide
Thermo Scientific
A Reports
Sample Standard Reports
Sample Standard Reports
This section shows samples of the following standard report types:
• Batch Report
• Batch Report Rev 1
• Blank 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
High Density Internal Standard Report Long
High Density Sample Report 1
High Density Sample Report 1 Long
High Density Sample Report 2
High Density Sample Report 2 Long
High Density Sample Report 3
High Density Sample Report 3 Long
Internal Standard Summary Report
• Ion Ratio Failure Report
• LCSLCSD Report
•
•
•
•
•
Manual Integration Report
Method Detection Limit Report
Method Report
Method Validation Report
MSMSD Report
• QC Standard Report
• Quantitation Report
• Quantitation Report - 2
• Solvent Blank Report
• Surrogate Recovery Report
• TIC Report
• TIC Summary Report
Tip To easily view reports in landscape format, choose View > Rotate View > Clockwise
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Thermo Scientific
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383
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Thermo Scientific
A Reports
Sample Standard Reports
LCSLCSD Report
IMPORTANT When the Sample ID is the same for an unknown sample and an LCS or LCSD sample, the unknown
sample is included in the LCSLCSD report. The report information for the unknown sample displays as zeros.
LCSLCSD Report
Lab name:
Instrument:
User:
Batch:
Thermo Fisher Laboratory
Thermo Scientific Instrument
AMER\jamie.humphries
Preview2
Pos
Tray1:16
Tray1:9
Tray1:3
Tray1:15
Tray1:8
Sample ID
SampleID002
SampleID002
SampleID002
SampleID008
SampleID008
Page 1 of 1
Preview2_EPA536-Triazines
EPA536-Triazines
Cali File: Preview2.calx
Method:
Filename
5ppb-002
500ppt-002
Cal002
5ppb-001
500ppt-001
Level
N/A
QC
c2
N/A
QC
Sample Name
D008
D002
D002
D008
D008
File Date
6/27/2007 1:25:44 AM
6/26/2007 9:47:43 PM
6/26/2007 6:09:47 PM
6/27/2007 12:54:35 AM
6/26/2007 9:16:35 PM
Comment
New Dilutions 6/26/2007 H
New Dilutions 6/26/2007 H
New Dilutions 6/26/2007 H
New Dilutions 6/26/2007 H
New Dilutions 6/26/2007 H
SampleID002
50.00
Max Rec
RPD Fails
0
50.00
DEA
0.500
50.00
150.00
5.065
0.00
50.00
50.00
0
Cyanazine
0.500
50.00
150.00
5.127
0.00
50.00
50.00
0
0
Simazine
0.500
50.00
150.00
4.862
0.00
50.00
50.00
0
0
Atrazine
0.500
50.00
150.00
5.184
0.00
50.00
50.00
0
0
Propazine
0.500
50.00
150.00
3.829
0.00
50.00
50.00
0
0
LCSD
Conc % Rec
4.712
0.00
RPD
RPD
Fails
0
Compound
DIA
Lower
Upper
Limit % Limit %
50.00
150.00
Spike Amt
0.500
LCSD
Conc % Rec
4.712
0.00
RPD
RPD
Fails
0
0
SampleID008
0.500
4.754
0.00
Max Rec
RPD Fails
0
50.00
DEA
0.500
4.960
0.00
50.00
150.00
5.065
0.00
0.00
50.00
0
0
Cyanazine
0.500
5.218
0.00
50.00
150.00
5.127
0.00
0.00
50.00
0
0
Simazine
0.500
4.839
0.00
50.00
150.00
4.862
0.00
0.00
50.00
0
0
Atrazine
0.500
5.178
0.00
50.00
150.00
5.184
0.00
0.00
50.00
0
0
Propazine
0.500
3.829
0.00
50.00
150.00
3.829
0.00
0.00
50.00
0
0
Compound
DIA
Spike Amt LCS Conc
Lower
Upper
% Rec Limit % Limit %
50.00
150.00
0.00
Manually integrated
Thermo Scientific
TraceFinder User Guide
411
A
Reports
Sample Standard Reports
Manual Integration Report
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Method Detection Limit Report
Lab name:
Instrument:
User:
Batch:
Thermo Fisher Laboratory
Thermo Scientific Instrument
AMER\jamie.humphries
Preview2
Page 1 of 3
Preview2_EPA536-Triazines
EPA536-Triazines
Cali File: Preview2.calx
Method:
Method Detection Limit Summary
Compound
DIA D-5
DIA
DEA D-7
DEA
Cyanazine D-5
Cyanazine
Simazine D-10
Simazine
Atrazine D-5
Atrazine
Propazine
Propazine D-14
Avg Conc
290218
Std Dev
0
t-stat
% RSD
0.00
MDL
0.095
0.000
0.000
0.00
0.000
<<<
0.000
<<<
0.000
<<<
0.000
<<<
1704578
0
0.065
0.000
2204710
0
0.062
0.000
513521
0
0.168
0.000
IS
0.00
0.000
0.00
IS
0.00
0.000
0.00
IS
0.00
0.000
0.00
IS
2292164
0
0.023
0.000
0.000
0.00
0.00
0.000
<<<
-1069.216
0.000
0.000
0.00
0.000
<<<
826
0
0.00
IS
IS
Manually integrated
Thermo Scientific
TraceFinder User Guide
413
A
Reports
Sample Standard Reports
Method Detection Limit Report
Lab name:
Instrument:
User:
Batch:
Thermo Fisher Laboratory
Thermo Scientific Instrument
AMER\jamie.humphries
Preview2
Method Validation Report Data
Compound
DIA D-5
DIA
Page 2 of 3
Preview2_EPA536-Triazines
EPA536-Triazines
Cali File: Preview2.calx
Method:
1
290218
0.095
DEA D-7
DEA
1704578
0.065
Cyanazine D-5
Cyanazine
Simazine D-10
Simazine
Atrazine D-5
Atrazine
Propazine
Propazine D-14
2204710
0.062
513521
0.168
2292164
0.023
-1069.216
826
Manually integrated
414
TraceFinder User Guide
Thermo Scientific
A Reports
Sample Standard Reports
Method Detection Limit Report
Lab name:
Instrument:
User:
Batch:
Pos
Tray1:1
Thermo Fisher Laboratory
Thermo Scientific Instrument
AMER\jamie.humphries
Preview2
Sample ID
SampleID007
Filename
Cal007
Page 3 of 3
Preview2_EPA536-Triazines
EPA536-Triazines
Cali File: Preview2.calx
Method:
Level
N/A
Sample Name
D007
File Date
6/26/2007 8:45:28 PM
Comment
New Dilutions 6/26/2007 H
Manually integrated
Thermo Scientific
TraceFinder User Guide
415
A
Reports
Sample Standard Reports
Method Report
416
TraceFinder User Guide
Thermo Scientific
A Reports
Sample Standard Reports
Thermo Scientific
TraceFinder User Guide
417
A
Reports
Sample Standard Reports
418
TraceFinder User Guide
Thermo Scientific
A Reports
Sample Standard Reports
Method Validation Report
Method Validation Report
Lab name:
Instrument:
User:
Batch:
Thermo Fisher Laboratory
Thermo Scientific Instrument
AMER\jamie.humphries
Preview2
Page 1 of 3
Preview2_EPA536-Triazines
EPA536-Triazines
Cali File: Preview2.calx
Method:
Method Validation Summary
Compound
DIA D-5
DIA
DEA D-7
Avg Conc
295652
Theo Conc
% Diff
Min Conc
Max Conc
0.358
0.500
-28.34
0.250
0.750
1778658
0.602
DEA
Cyanazine D-5
Cyanazine
Simazine D-10
Simazine
Atrazine D-5
Atrazine
Propazine
Propazine D-14
Manually integrated
Thermo Scientific
0.500
20.45
0.250
0.750
20.00
0.00
IS
20.00
0.00
0.500
12.90
0.250
0.750
505462
0.607
0.00
0.00
2224244
0.565
% RSD Max % RSD
0.00
IS
0.00
IS
20.00
0.00
IS
0.500
21.49
0.250
0.750
0.00
0.512
0.500
2.46
0.250
0.750
0.00
20.00
0.757
0.500
51.41
0.250
0.750
0.00
20.00 <<<
2334865
272050
20.00
0.00
IS
0.00
IS
<<< = Failure
TraceFinder User Guide
419
A
Reports
Sample Standard Reports
Method Validation Report
Lab name:
Instrument:
User:
Batch:
Thermo Fisher Laboratory
Thermo Scientific Instrument
AMER\jamie.humphries
Preview2
Method Validation Report Data
Compound
DIA D-5
DIA
1
295652
0.358
DEA D-7
DEA
1778658
0.602
Cyanazine D-5
Cyanazine
Simazine D-10
Simazine
Atrazine D-5
2224244
0.565
505462
0.607
2334865
Atrazine
0.512
Propazine
0.757
Propazine D-14
Manually integrated
420
Page 2 of 3
Preview2_EPA536-Triazines
EPA536-Triazines
Cali File: Preview2.calx
Method:
TraceFinder User Guide
272050
<<< = Failure
Thermo Scientific
A Reports
Sample Standard Reports
Method Validation Report
Lab name:
Instrument:
User:
Batch:
Thermo Fisher Laboratory
Thermo Scientific Instrument
AMER\jamie.humphries
Preview2
Pos
Tray1:10
Sample ID
SampleID003
Manually integrated
Thermo Scientific
Filename
500ppt-003
Page 3 of 3
Preview2_EPA536-Triazines
EPA536-Triazines
Cali File: Preview2.calx
Method:
Level
N/A
Sample Name
D003
File Date
6/26/2007 10:18:49 PM
Comment
New Dilutions 6/26/2007 H
<<< = Failure
TraceFinder User Guide
421
A
Reports
Sample Standard Reports
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Thermo Scientific
TraceFinder User Guide
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TraceFinder User Guide
, %
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.
.
Thermo Scientific
B
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, and Comment 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 non selected 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.
Thermo Scientific
TraceFinder User Guide
433
B
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 non selected 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.
434
TraceFinder User Guide
Thermo Scientific
B
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.
Thermo Scientific
TraceFinder User Guide
435
C
Using Filter Criteria
The filter criteria tool is available from the compound datastore in the Configuration mode
and the acquisition list in the Method Development mode.
 To filter the compound list
1. To display only a filtered list of compounds, click the funnel button,
header.
, in the column
For each column, a list of filterable criteria is displayed. In all columns, your filter choices
are All, Blanks, and NonBlanks. Other filter criteria are specific to the individual
columns.
2. To create a custom filter based on compound values in a specific column, choose Custom
from the column list.
The Enter Filter Criteria dialog box opens. See “Enter Filter Criteria dialog box” on
page 438.
3. From the Operator list, select an operator.
4. From the Operand list, select an operand.
5. When all conditions are defined, click OK.
The complete filter string is displayed at the bottom of the dialog box, for example,
chemical formula = Blanks.
Thermo Scientific
TraceFinder User Guide
437
C
Using Filter Criteria
Note The Enter Filter Criteria dialog box is specifically named for the column on which
you are filtering. In this example, the selected column is the Compound Name column.
Figure 93. Enter Filter Criteria dialog box
Table 88. Enter Filter Criteria dialog box parameters
438
TraceFinder User Guide
Parameter
Description
And
conditions
Requires meeting all filter criteria.
Or
conditions
Requires meeting any of the specified filter criteria.
Add a
condition
Adds a new, empty condition to the filter criteria.
Delete
condition
Deletes the selected condition. Click the box at the left of the row to select
the condition.
Operator
The mathematical function applied to the operand.
Operand
The arguments to which the operator is applied.
Thermo Scientific
I
Index
Symbols
.csv, defined 2
.meth, defined 2
.pmd, defined 2
.raw, defined 2
.xml, defined 2
# background scans parameter 76, 143
% Test parameter 160
A
Account number parameter 41
Acquire a new raw data file parameter 102
Acquisition command 33
Acquisition List page, Master Method View 120
Active parameter 125
Active View page 356
Add a condition parameter 438
Add a mass as new confirming ion command 153
Add command 81
Add compound command 60
Add Confirming Ion command 62
Add Group command 172
Add Quan Peak command 61
Add this mass to existing quan mass ranges command 153
Add to CDS command 104
Add user parameter 42
Amount parameter 156
And conditions parameter 438
Apply command 81
Area noise factor parameter 78, 145
Area scan window parameter 79, 146
Area tail extension parameter 79, 146
Area Threshold, event type 82
Assay type parameter
Batch Wizard 292
Master Method View 117
Associate a Raw Data File dialog box 105
Associate a Raw Data File parameter 105
Thermo Scientific
automated background subtraction options 114
Automatically create the master method parameter 102
Available Methods parameter 292
Available Templates parameter 292
Avalon detection algorithm 72
Avalon Event List dialog box 81
B
background subtraction options 114
Background subtraction range option parameter 118
Baseline window parameter 78, 145
Batch Level parameter 65, 175
Batch view 267
Batch/Template Selection view 220
batches
Acquisition mode 216
calibration 239
Data Review mode 267
development batch 204
Best match method parameter 193
Bunch Factor, event type 82
C
cal1-caln parameter 158
Calibration Curve page 323
Calibration Levels page, Master Method View 157
Calibration method parameter 193
Calibration page, Master Method View 156
Calibration page, QAQC page, Master Method View 166
calibration standard (Cal Std) sample type, defined 262
Cancel changes parameter 42
Cancel command 81
Carryover limit parameter 165
CAS No parameter 125
Category parameter
Acquisition List 122
Compound Datastore 56
caution flags 310
TraceFinder User Guide
439
Index: C
Change command 81
Chemical Formula parameter
Acquisition List 122
Compound Datastore 56
Chk Std page, Master Method View 167
Collision Energy parameter
Acquisition List
confirming ion 123
quan peak 123
Compound Datastore
quan peak 57
compound datastore
confirming ion 58
commands
Acquisition 33
Add 81
Add a mass as new confirming ion 153
Add compound 60
Add Confirming Ion 62
Add Group 172
Add Quan Peak 61
Add this mass to existing quan mass ranges 153
Add to CDS 104
Apply 81
Cancel 81
Change 81
Configuration 34
Continue to Method 104
Copy down 433
Data Review 33
Delete 81
Enable Target Screening 85
Exit TraceFinder 12
Fill down 433
Help, dashboard 33
Hide Internal Standard 317
Import Compounds 59
Import Published Method 195
Load Compound Datastore 54
Log Off 33
Methods 34
Modify Columns
Batch View 277
Data Review View 308
New Compound Datastore 54
Real Time Status 33
Reset scaling 153
Save As Compound Datastore 55
Save Compound Datastore 54
Set this mass as a new quan peak 153
Set this mass as quan mass 153
Show Internal Standard 317
Update confirming ion ratios with this spectrum 153
440
TraceFinder User Guide
comma-separated values, defined 2
Compound Datastore Name parameter, Save Compound
Datastore 55
Compound Datastore view 56
Compound Datastore, administration 52
Compound Name parameter
Acquisition List 122
Compound Datastore 56
Compound parameter
Calibration 156
Calibration levels 158
Calibration page 166
Chk Std page 167
Identification 125
ISTD page 169
Limits page 165
Matrix Blank page 168
QC levels page 160
Solvent Blank page 170
Compound type parameter
Calibration 156
Identification 125
compound types
internal standards 124, 127
quan 124, 127
target 124, 127
Compounds page, Master Method View 120
compounds, importing to compound datastore 59
Configuration command 34
Configuration navigation pane 36
Confirming Ions page 327
Confirming n Ion Ratio Flag parameter 359
Confirming n Ion Ratio parameter 359
Confirming n Manual Flag parameter 359
Confirming n Mass parameter 358
Confirming n Range parameter 359
Confirming n Response parameter 359
Constrain peak width parameter
Genesis
application configuration parameters 75
method development 142
ICIS
application configuration 78
method development 145
Continue to Method command 104
Copy down command 433
Create Master Method dialog box 95
Create method parameter 92
Create PDF parameter 174
Create PDF parameter, standard reports 377
Create XLSM parameter 175, 377
Thermo Scientific
Index: D
Create XML parameter 174
Create XML parameter, standard reports 377
Curve type parameter
Calibration 156
Method Template Editor 193
custom reports
listed 6
custom reports, listed 6
CV Test (%) parameter 169
D
dashboard parameters 33
Data Review command 33
Data Review view 303
Decimal places to be reported parameter 178
Delay Calibration Calculation option 86
Delete command 81
Delete condition parameter 438
Detection method parameter
Avalon
application configuration 80
method development 147
Genesis
application configuration 74
method development 142
ICIS
application configuration 77
method development 145
Detection page, Master Method View 126
Detector parameter, Detection 138
Development Batch view 204
dialog boxes
Add Library 15
Associate a Raw Data File 105
Avalon Event List 81
Create Master Method 95
Edit Compound Dependent Parameters 104
Import an Xcalibur Method 103
Invalid Compound Datastore not saved 54
Open Chromatograph Reference Sample 115
Open Compound Datastore 54
Save Compound Datastore 55
Select Compounds to Add 108
Thermo Library Manager 15
Thermo Xcalibur Instrument Setup 113
Thermo Xcalibur Roadmap 14
Disable Cluster Off, event type 83
Disable Cluster On, event type 83
Display compounds above set limit parameter 178
Display Quan flags and legend parameter 178
Displayed Reports parameter
Thermo Scientific
General Quantitation 69
E
Edit Compound Dependent Parameters dialog box 104
Edit user parameter 42
Email address parameter 41
Enable peak threshold parameter 193
Enable Target Screening command 85
Enable valley detection parameter
application configuration 75
method development 142
Enabled parameter 41
End Threshold, event type 82
Energy Ramp parameter
application configuration 57
method development 123
Event parameter 81
Event types 82
Example parameter 174
Exclude matching quan peaks parameter 194
Exit TraceFinder command 12
Expected RT parameter, Detection 136
Expected width parameter
application configuration 75
method development 142
Experiment Type parameter
Acquisition List 122
Compound Datastore 56
experiment types 63
Export SRM data parameter 93
Extend Calibrations parameter 302
Extracted Ion Chromatogram 63
F
feature summary 4
file types, supported 2
Fill down command 433
Filter parameter, Detection 138
Finish view 238
Flag values above Carryover parameter 179
Flag values above LOR parameter 179
Flag values above ULOL parameter 179
Flag values below LOD parameter 179
Flag values below LOQ parameter 179
Flag values between LOD and LOQ parameter 179
Force Cluster Off, event type 83
Force Cluster On, event type 83
Full name parameter 41
TraceFinder User Guide
441
Index: G
G
General page
Background subtraction range option 118
editing 112
Injection volume parameter 118
Instrument method parameter 118
Ion range calc method parameter 118
Number of scans to subtract parameter 118
Qualitative peak processing template parameter 118
Set chromatogram reference sample parameter 118
Set Reference sample parameter 118
Stepoff value parameter 118
General page, Master Method View 112
Genesis detection algorithm 72
Groups page, Master Method View 171
H
Help command, dashboard 33
Hide Internal Standard command 317
I
ICIS detection algorithm 72
Identification page, Master Method View 124
Import an Xcalibur Method dialog box 103
Import Compounds command 59
Import parameter
General Quantitation 69
Import Published Method command 195
Import Xcalibur Processing Method parameter 103
Include compound peak spectrum as reference spectrum
parameter 193
Include confirming ions parameter 193
Injection amount parameter 102
Injection concentration parameter 359
Injection Units parameter 359
Injection volume parameter 118
Installed Reports parameter
General Quantitation 69
installing
NIST and QED libraries 14
installing TraceFinder 10
Instrument method parameter
General page 118
Method Forge 102
Instrument view 197
instruments, supported ix
Invalid Compound Datastore not saved dialog box 54
Ion Overlay page 331
Ion range calc method parameter 118
Ionization parameter
442
TraceFinder User Guide
Acquisition List 122
Compound Datastore 56
ISTD page, Master Method View 169
ISTD parameter 156
IT Administrator role 43
L
Lab name parameter 117
Lens parameter
application configuration 57
method development 123
Level parameter 160
licenses, types of x
Limit library hits parameter 193
Limit the retention time range parameter 193
Limits page, Master Method View 165
Load Compound Datastore command 54
Local Method view 368
LOD (Detection limit) parameter 165
Log Off command 33
Login parameter 12
login screen 12
LOQ (Quantitation limit) parameter 165
LOR (Reporting limit) parameter 165
M
Manual Flags parameter 358
Manual injection parameter 102
Mass parameter
confirming ion
Acquisition List 123
Compound Datastore 58
quan peak 57, 122
Master Method View
Acquisition List page 120
Calibration Levels page 157
Calibration page 156
Chk Std page 167
Compounds page 120
Detection page 126
General page 112
Groups page 171
Identification page 124
ISTD page 169
Limits page 165
Matrix Blank page 168
QAQC page, Calibration page 166
QC Check page 167
QC Levels page 159
Ratios page 154
Real Time Viewer page 161
Thermo Scientific
Index: N
Reports page 173
Solvent Blank page 170
Spectrum page 149
Master Method View, QAQC page 164
Matrix Blank page, Master Method View 168
Matrix Blank sample type, defined 262
Max Amt Diff (%) parameter 166
Max Conc parameter 168
Max recovery (%) parameter
ISTD page 169
Max RF Diff (%) parameter 167
Max RSD (%) parameter
Calibration page 166
Max RT (+min) parameter, ISTD page 169
Method parameter
Matrix Blank page 168
Solvent Blank page 170
Method Template Editor 192
Method view 95
methods
importing Xcalibur 103
instrument 197
local 368
master 94
Method Template Editor 192
update TSQ method 238
Methods command 34
Min peak height (S/N) parameter
Genesis 75, 143
ICIS 78, 146
Min peak width parameter 79, 146
Min recovery (%) parameter
ISTD page 169
Min RF parameter 167
Min RT (-min) parameter 169
modes
choosing 30
defined 33
Modify Calibrations or Active Compounds by Group
parameter 299
Modify Columns command
Batch View 277
Data Review View 308
Multiplet resolution parameter 79, 146
N
Name the master method parameter 102
Negative Peaks, event type 82
New Compound Datastore command 54
New instrument method parameter 93
New sample list parameter 93
Thermo Scientific
NIST library, installing 14
Noise method parameter 78, 146
Number of Scans to Subtract parameter 114
Number of scans to subtract parameter 118
O
Only select top peaks parameter 193
Open Chromatograph Reference Sample dialog box 115
Open Compound Datastore dialog box 54
Open instrument method parameter 93
Open method parameter 92
Open Qual Browser parameter 93
Operand parameter 438
Operator parameter 438
Or conditions parameter 438
Origin parameter
Calibration 156
Method Template Editor 194
Overwrite parameter
Method Forge dialog box 102
Save Compound Datastore dialog box 55
P
parameters
# background scans 76, 143
% Test 160
Account number 41
Acquire a new raw data file 102
Active 125
Add a condition 438
Add user 42
Amount 156
And conditions 438
Area noise factor 78, 145
Area scan window 79, 146
Area tail extension 79, 146
Assay type
Batch Wizard 292
Master Method View 117
Associate a Raw Data File 105
Automatically create the master method 102
Available Methods 292
Available Templates 292
Background subtraction range option 118
Baseline window 78, 145
Batch Level 65, 175
Best match method 193
cal1-caln 158
Calibration method 193
Cancel changes 42
Carryover limit 165
TraceFinder User Guide
443
Index: P
CAS No 125
Category
Acquisition List 122
Compound Datastore 56
Chemical Formula
Acquisition List 122
Compound Datastore 56
Collision Energy
Acquisition List
confirming ion 123
quan peak 123
compound datastore
confirming ion 58
quan peak
Compound Datastore 57
Compound
Calibration 156
Calibration levels 158
Calibration page 166
Chk Std page 167
Identification 125
ISTD page 169
Limits page 165
Matrix Blank page 168
QC levels page 160
Solvent Blank page 170
Compound Name
Acquisition List 122
Compound Datastore 56
Compound type
Calibration 156
Identification 125
Confirming n Ion Ratio 359
Confirming n Ion Ratio Flag 359
Confirming n Manual Flag 359
Confirming n Mass 358
Confirming n Range 359
Confirming n Response 359
Constrain peak width
Genesis 142
ICIS 78, 145
Create method 92
Create PDF 174
Create PDF, standard reports 377
Create XLSM 175, 377
Create XML 174
Create XML, standard reports 377
Curve type
Calibration 156
Method Template Editor 193
CV Test (%) 169
dashboard 33
Decimal places to be reported 178
Delete condition 438
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TraceFinder User Guide
Detection method
Avalon 80, 147
Genesis 74, 142
ICIS 77, 145
Detector 138
Display compounds above set limit 178
Display Quan flags and legend 178
Displayed Reports
General Quantitation 69
Edit user 42
Email address 41
Enable peak threshold 193
Enable valley detection
application configuration 75
method development 142
Enabled 41
Energy Ramp
application configuration 57
method development 123
Event 81
Example 174
Exclude matching quan peaks 194
Expected RT, Detection 136
Expected width
application configuration 75
method development 142
Experiment Type
Acquisition List 122
Compound Datastore 56
Export SRM data 93
Extend Calibrations 302
Filter, Detection 138
Flag values above Carryover 179
Flag values above LOR 179
Flag values above ULOL 179
Flag values below LOD 179
Flag values below LOQ 179
Flag values between LOD and LOQ 179
Full name 41
Import
General Quantitation 69
Import Xcalibur Processing Method 103
Include compound peak spectrum as reference spectrum
193
Include confirming ions 193
Injection amount 102
Injection concentration 359
Injection Units 359
Injection volume 118
Installed Reports
General Quantitation 69
Instrument method
General page 118
Method Forge 102
Thermo Scientific
Index: P
Ion range calc method 118
Ionization
Acquisition List 122
Compound Datastore 56
ISTD 156
Lab name 117
Lens
application configuration 57
method development 123
Level 160
Limit library hits 193
Limit the retention time range 193
LOD (Detection limit) 165
Login 12
LOQ (Quantitation limit) 165
LOR (Reporting limit) 165
Manual Flags 358
Manual injection 102
Mass
confirming ion
Acquisition List 123
Compound Datastore 58
quan peak 57, 122
Max Amt Diff (%) 166
Max Conc 168
Max recovery (%)
ISTD page 169
Max RF Diff (%) 167
Max RSD (%)
Calibration page 166
Max RT (+min), ISTD page 169
Method
Matrix Blank page 168
Solvent Blank page 170
Min peak height (S/N)
Genesis 75, 143
ICIS 78, 146
Min peak width 79, 146
Min recovery (%)
ISTD page 169
Min RF 167
Min RT (-min) 169
Modify Calibrations or Active Compounds by Group
299
Multiplet resolution 79, 146
Name the master method 102
New instrument method 93
New sample list 93
Noise method 78, 146
Number of Scans to Subtract 114
Number of scans to subtract 118
Only select top peaks 193
Open instrument method 93
Open method 92
Thermo Scientific
Open Qual Browser 93
Operand 438
Operator 438
Or conditions 438
Origin
Calibration 156
Method Template Editor 194
Overwrite
Method Forge dialog box 102
Save Compound Datastore dialog box 55
Password
login screen 12
user administration 41
Path 102
Peak height (%)
Genesis 75, 142
ICIS 78, 145
Peak noise factor 78, 145
Peak S/N cutoff 76, 143
Percentage 168
Phone number 41
Polarity
Acquisition List 123
Compound Datastore 57
Precursor Mass
Acquisition List 122–123
Compound Datastore 57–58
Print 174
Print, standard reports 377
Product Mass
Acquisition List 122–123
Compound Datastore 57–58
QAQC Flags 358
QC1-QCn 160
QIon 359
Qualitative peak processing template 118
Quan Flags 358
Quan mass 359
Quan peak m/z 358
Quan peak response 358
Quan peak RT 358
Quick mode 292
R^2 threshold 166
Ranges, compound detection 139
Raw filename 102
Recent Files (master methods) 93
Reference compound 125
Remove user 42
Report concentration 178
Report Description 174
Report Name 174
Report noise as 76, 143
Report Type 174
Response 359
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Index: P
Response via
Calibration 156
Method Template Editor 194
Retention Time 359
RMS 79, 146
Role 41
RT
Acquisition List 123
Calibration 156
Calibration levels 158
Calibration page 166
Chk Std page 167
Compound Datastore 57
Identification 125
ISTD page 169
Limits page 165
Matrix Blank page 168
QC levels page 160
Solvent Blank page 170
S/N threshold 75, 142
Sample comment 102
Sample Concentration 359
Sample file 357
Sample Units 359
Save changes 42
Select a custom template 102
Select a report 357
Select batch location 93
Select Compounds from CDS 108
Sensitivity
Avalon 80
Genesis 74, 142
ICIS 77, 145, 147
sensitivity 193
Separate ion overlay display 178
Set Chromatogram Reference Sample 115
Set chromatogram reference sample 118
Set Reference sample 118
Shade row when sample is outside of evaluation criteria
178
Show chromatogram on Quantitation Report 178
Showing 357
Smoothing
Avalon 80
Genesis 74, 142
ICIS 77, 145, 148
Specify default ion ratio ranges 193
Standard type 156
Starting vial number 292
Status 358
Stepoff value 118
Tailing factor
Genesis 75, 143
ICIS 78, 145
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Template Layout 292
Theoretical amount 358
Time 81
Total batch rows 292
Total response 358
Total rows 357
Trace, Detection 138
ULOL (Linearity limit) 165
Units 156
Upper Limit 170
Use alternate calibration report format 178
Use an existing raw data file 102
Use as RT Reference 125
Use autosampler 102
Use data dependent scans 194
Use Genesis algorithm for qual processing 194
Use Method Forge 96, 99
Use the default template 102
Use these libraries 193
User Security 85
Username 12, 41
Valley rise (%) 76, 143
Valley S/N 76, 143
Value 81
Vial position 102
View width, Detection 73, 136
Weighting
Calibration 156
Method Template Editor 194
Window
Acquisition List 123
Compound Datastore 57
Detection 73, 136
Password parameter
login screen 12
user administration 41
password, administrator 11
Path parameter 102
Peak height (%) parameter
Genesis 75, 142
ICIS 78, 145
Peak noise factor parameter 78, 145
Peak S/N cutoff parameter 76, 143
Percentage parameter 168
Phone number parameter 41
Polarity parameter
Acquisition List 123
Compound Datastore 57
P-P Threshold, event type 82
Precursor Mass parameter
Acquisition List 122–123
Compound Datastore 57–58
Print parameter 174
Thermo Scientific
Index: P
Print parameter, standard reports 377
procedures
acquisition mode
access real-time display 249
add samples to the samples list 225
assign a specific channel to a sample 231
create a batch template 224
export reports to a folder 235
import samples into the sample list 228
insert samples into the samples list 226
pause all batches in a queue 256
preview a standard report 234
re-inject a sample from 230
remove a batch from a queue 258
remove a pending batch from a queue 258
remove a pending sample from a queued batch 259
remove a single batch from a queue 257
remove all batches in a queue 257
remove all pending batches in a queue 257
remove pending samples from a queued batch 258
remove samples from the samples list 230
save a to-be-run batch 241
select a previously acquired batch 223
select a ready-to-acquire batch 222
specify a calibration batch 239
specify device states 240
specify startup or shutdown methods 238
start a new batch 220
start an acquisition 241
update TSRM data 238
view output files 244
configuration mode
access the Configuration mode 35
add a compound to the datastore 60
add a confirming ion to a quan peak 62
add a quan peak to a compound 61
add a user 37
change the default drive 47
choose a drive 47
copy the folder hierarchy from another drive 50
create a new compound datastore 54
create projects or subprojects 49
delete projects or subprojects 50
edit user information 38
enable user security 85
hide a drive from display 48
import compounds 59
import new report types 66
open a compound datastore 54
open the Application Configuration view 64
open the Compound Datastore editor 53
open the Defaults page 70
open the Project Administration view 46
open the User Administration view 37
Thermo Scientific
refresh the drives display 48
remove a compound 60
remove a confirming ion 62
remove a user 40
remove all empty folders 50
save a datastore 54
save a datastore to a new name 55
specify common detection parameters 72
specify default laboratory and instrument names 71
specify default mass precision and intensity scale 71
data review mode
access the Data Review mode 264
add samples to the samples list 272
change the displayed information for a detected
peaks 329
change the displayed information for detected peaks
320, 339
change the library entry for a selected peak 342
copy a sample in the samples list 274
create a new batch 271
customize the column display 277, 308
display peaks for a specific compound 316, 333
display specific problems with a compound 316
display the internal standard for a compound 317
display the peak information window 329
edit samples in a batch 280
edit the batch-level output formats 283
edit the sample-level output formats 282
enlarge the report text 355
exclude a calibration point 313
export a report 354
insert samples in the samples list 273
make a compound active or inactive 312
manually add a peak
chromatogram pane 336
confirming ions 328
qual peak pane 338
quantification peak 319
manually exclude a calibration point 324
manually integrate a quan or qual ion 319
modify the peak detection settings 320
open a recent batch 280
open a saved batch 279
open the Data Review mode 303
open the Local Method View 368
open the Report View 344
print a report 353
reinject a sample 275
reinject a sample from a previously acquired batch
280
remove a manually created peak
confirming ions 328
quantification peak 319
remove a peak from the peaks pane 334
TraceFinder User Guide
447
Index: P
remove a peak from the qual peak pane 339
remove samples from the samples list 274
scroll the samples list 308
search for text 355
select a compound 347
select a report
generating reports 349
viewing reports 345
select a sample
generating reports 351
viewing reports 347
sort the compounds list 315
submit all samples in the batch 286
submit selected samples 287
switch between method and manual integration
qual mode 339
quan mode 320
zoom in on a peak
chromatogram navigation 336
confirming ions 328
ion overlay 331
qual peak 338
quantification peak 318
spectra pane 341
zoom in on an area
calibration curve 324
QED spectra 326
spectra 325
getting started
choose a node 30
display a log of instrument errors 31
install the NIST library 14
install the QED library 14
log on to the TraceFinder application 11
monitor the instrument status 31
start the TraceFinder application 11
watch the real-time display from the dashboard 32
method development mode 157
access the Method Development mode 91
acquire selected samples 209
acquire the batch 209
add a compound to the list 121
add a mass as a new compound 131
add a mass as a new confirming ion 133
add a mass to the existing quan mass ranges 130
add a quan peak 131
add a quan peak to an existing compound 151
add compounds to the method 106, 127
add confirming ions to an existing compound 152
add ions to get an accumulated signal 151
add sample to the development batch 205
apply current peak detection settings
to all peaks in method 140
to all peaks that use the same detection mode 140
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TraceFinder User Guide
associate a raw data file with the method 105
automatically select compounds to create a new
method 96
calculate and report semi-quantitative results 181
calibrate the compounds 189
change the compound reference spectrum 130
change the quantitation mass used for a quan peak
149
copy a sample 206
create a group 171
create a new instrument method 198
create a new multiplexing instrument method 200
delete a compound from the list 121
edit the instrument method parameters 113
enter a note for the method 191
enter column values 207
export SRM data to an XML file 196
filter the displayed compounds 124, 127
identify the peaks 188
import a master method 195
import an instrument method 203
import an Xcalibur method 103
insert samples into the development batch 206
manually select compounds to create a new method
99
open a saved master method 110
open an instrument method 202
open the Development Batch view 204
open the Instrument View 197
open the Qual Browser 210
remove all samples from the samples list 208
remove selected samples from the samples list 208
replace a confirming ion 133
replace a quan mass 130
resize or reorganize the columns 208
save the method template 191
save the new method 133
select compounds from the datastore 108
set automated background subtraction options 114
specify a chromatogram reference sample 115
specify a location for development batch data 205
specify general information for a master method 112
specify ion ratio criteria 154
specify mass tolerance 116
specify peak criteria 187
specify QC levels and concentrations 159
specify qualitative peak processing 190
specify quantitation flag options 177
specify quantitation limits 176
specify ranges of ions for detection and integration
137
specify standard report types and output formats 173
specify the default parameters 180
specify the exact mass window 182
Thermo Scientific
Index: Q
specify the Exactive parameters 182
specify the ion ratio calculation method 182
specify the maximum concentration as a percentage
168
specify user interface options 177
update confirming ion ratios 149
zoom in the chromatogram or spectrum displays 152
Product Mass parameter
Acquisition List 122–123
Compound Datastore 57–58
Project Administration view 46
projects and subprojects, creating 46
Q
QAQC Flags parameter 358
QAQC page, Master Method View 164
QAQC role 45
QC Check page, Master Method View 167
QC Levels page, Master Method View 159
QC1-QCn parameter 160
QED library, installing 14
QED Spectra page 326
QIon parameter 359
Qual Mode 303
Qualitative peak processing template parameter 118
quality check standard (QC Std) sample type, defined 262
Quan Flags parameter 358
Quan mass parameter 359
Quan Mode 303
Quan peak m/z parameter 358
Quan peak response parameter 358
Quan peak RT parameter 358
quan report settings, specifying 176, 180
Quick mode parameter 292
R
R^2 threshold parameter 166
Ranges parameter, compound detection 139
Ratios page, Master Method View 154
Raw filename parameter 102
Real Time Status command 33
Real Time Viewer page, Master Method View 161
real-time display 249
Recent Files parameter (master methods) 93
Reference compound parameter 125
reference spectra 341
Remove user parameter 42
Report concentration parameter 178
Report Description parameter 174
Thermo Scientific
report formats, specifying 173
Report Name parameter 174
Report noise as parameter 76, 143
Report selection view 234
Report Type parameter 174
Report View 344
reports
Acquisition mode 234
configuring 65
Data Review mode 344
flags defined 382
listed 6
sample PDFs 383
viewing landscape in PDF 383
Reports page, Master Method View 173
Reset scaling command 153
Response parameter 359
Response via parameter
Calibration 156
Method Template Editor 194
Retention Time parameter 359
RMS parameter 79, 146
Role parameter 41
RT parameter
Acquisition List 123
Calibration 156
Calibration levels 158
Calibration page 166
Chk Std page 167
Compound Datastore 57
Identification 125
ISTD page 169
Limits page 165
Matrix Blank page 168
QC levels page 160
Solvent Blank page 170
S
S/N threshold parameter 75, 142
Sample comment parameter 102
Sample Concentration parameter 359
Sample definition view 225
Sample file parameter 357
sample types, defined 262
Sample Units parameter 359
Save As Compound Datastore command 55
Save changes parameter 42
Save Compound Datastore command 54
Save Compound Datastore dialog box 55
Select a custom template parameter 102
Select a report parameter 357
TraceFinder User Guide
449
Index: T
Select batch location parameter 93
Select Compounds from CDS parameter 108
Select Compounds to Add dialog box 108
Selected Reaction Monitoring 63
Sensitivity parameter
Avalon 80
Genesis 74, 142
ICIS 77, 145, 147
sensitivity parameter 193
Separate ion overlay display parameter 178
Set Chromatogram Reference Sample parameter 115
Set chromatogram reference sample parameter 118
Set Reference sample parameter 118
Set this mass as a new quan peak command 153
Set this mass as quan mass command 153
Shade row when sample is outside of evaluation criteria
parameter 178
Shoulders On, event type 83
Show chromatogram on Quantitation Report parameter 178
Show Internal Standard command 317
Showing parameter 357
SIM experiment type 63
Single Ion Monitoring 63
Smoothing parameter
Avalon 80
Genesis 74, 142
ICIS 77, 145, 148
Solvent Blank page, Master Method View 170
Solvent sample type, defined 262
Specify default ion ratio ranges parameter 193
Spectra page 325
Spectrum page, Master Method View 149
SRM data, exporting 196
SRM experiment type 63
standard reports, listed 6
Standard type parameter 156
Start Threshold, event type 82–83
Starting vial number parameter 292
Status parameter 358
Stepoff value parameter 118
Supervisor role 44
supported file types, defined 2
supported software and hardware ix
system requirements ix
T
Tailing factor parameter
Genesis 75, 143
ICIS 78, 145
Tangent Skim, event type 83
450
TraceFinder User Guide
target screening reports, listed 7
Technician role 44
Template Layout parameter 292
templates
batch 224
method 186
Tension, event type 83
Theoretical amount parameter 358
Thermo Xcalibur Instrument Setup dialog box 113
Time parameter 81
Total batch rows parameter 292
Total response parameter 358
Total rows parameter 357
Trace parameter, Detection 138
U
ULOL (Linearity limit) parameter 165
Units parameter 156
Unknown sample type, defined 262
Unknown/Qual sample type, defined 262
Update confirming ion ratios with this spectrum command
153
Upper Limit parameter 170
Use alternate calibration report format parameter 178
Use an existing raw data file parameter 102
Use as RT Reference parameter 125
Use autosampler parameter 102
Use data dependent scans parameter 194
Use Genesis algorithm for qual processing parameter 194
Use Method Forge parameter 96, 99
Use the default template parameter 102
Use these libraries parameter 193
user accounts, creating 37
User Administration view 37
user roles and permissions 43
user roles, defined 43
User Security parameter 85
user security, enabling 85
Username parameter 12, 41
V
Valley rise (%) parameter 76, 143
Valley S/N parameter 76, 143
Value parameter 81
Vial position parameter 102
View width parameter, Detection 73, 136
views
Batch 267
Batch/Template Selection 220
Thermo Scientific
Index: W
Compound Datastore 56
Data Review 303
Development Batch 204
Finish 238
Instrument 197
Local Method 368
Method 95
Project Administration 46
Report selection 234
Report View 344
Sample definition 225
User Administration 37
W
Weighting parameter
Calibration 156
Method Template Editor 194
Window parameter
Acquisition List 123
Compound Datastore 57
Detection 73, 136
workflow
acquisition mode 218
general 5
X
XIC experiment type 63
Thermo Scientific
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