TraceFinder 3.0 User Guide Optimized for Forensic Toxicology

TraceFinder 3.0 User Guide Optimized for Forensic Toxicology
Thermo
TraceFinder
Version 3.0
User Guide
Optimized for Forensic Toxicology
XCALI-97504 Revision A
October 2012
© 2012 Thermo Fisher Scientific Inc. All rights reserved.
Aria, Exactive, FOCUS, LCquan, ToxID, and TriPlus are trademarks, and Accela, Dionex, Thermo Scientific,
Trace GC Ultra, TSQ Quantum, and Xcalibur are registered trademarks of Thermo Fisher Scientific Inc. in the
United States.
NIST is a registered trademark of the National Institute of Standards and Technology in the United States.
Windows, Excel, and Microsoft are registered trademarks of Microsoft Corporation in the United States and
other countries. Adobe, Acrobat, and Reader are registered trademarks of Adobe Systems Inc. in the United
States and other countries.
Agilent is a registered trademark of Agilent Technologies Inc.
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, March 2012
Software version: Thermo Foundation 2.0 SP1; Thermo Xcalibur 2.2 SP1; Microsoft Windows XP
Professional SP3 or Windows 7 Professional; Thermo LC Devices 2.5 SP2; Thermo GC Devices 2.2
For Research Use Only. Not for use in diagnostic procedures.
C
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .viii
System Activation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi
Thermo Scientific
Chapter 1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
About the TraceFinder Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
TraceFinder Summary of Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
TraceFinder Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Reporting Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Standard Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Custom Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Target Screening Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
ToxID Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Chapter 2
Getting Started. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Installing the TraceFinder Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Installing the Power Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Installing the NIST and QED Libraries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Launching the NIST Library Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Launching the Qual Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Converting Legacy Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Converting Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Converting Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Converting Method Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Converting Batch Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Choosing a Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Chapter 3
Using the Application Configuration Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37
Specifying the Reports Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Specifying Application Defaults. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Specifying Default Peak Detection Parameters . . . . . . . . . . . . . . . . . . . . . . . . . 46
Specifying Adducts Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
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Contents
Activating Optional Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
User Security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
ToxID . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Delay Calibration Calculation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Batch Wizard Style . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Multiplexing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Intelligent Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Acquisition Submission Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Screening Library. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Managing User Administration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Editing User Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Choosing User Roles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
iv
Chapter 4
Using the Method Development Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .79
Working with Master Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Creating a New Master Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Editing a Quantitation Master Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
Editing a Target Screening Master Method . . . . . . . . . . . . . . . . . . . . . . . . . 202
Creating a Method Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224
Importing Published Master Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235
Exporting SRM Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 236
Working with the Compound Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239
Opening and Saving a Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240
Compound Database Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243
Editing Compounds in the Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251
Choosing Experiment Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 258
Exporting and Importing Compounds . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261
Working with Instrument Methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 269
Working with Development Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
Creating a Development Batch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
Editing Samples in a Development Batch . . . . . . . . . . . . . . . . . . . . . . . . . . 277
Acquiring Samples in a Development Batch . . . . . . . . . . . . . . . . . . . . . . . . 280
Viewing Raw Data Files in the Qual Browser . . . . . . . . . . . . . . . . . . . . . . . 281
Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283
Chapter 5
Using the Acquisition Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .285
Working with Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 286
Opening and Navigating the Acquisition Mode . . . . . . . . . . . . . . . . . . . . . 286
Creating and Submitting Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 288
Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321
TraceFinder User Guide
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Contents
Real Time Status Pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323
Acquisition Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 324
Instrument Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 325
Devices Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 326
Queues Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 330
Real-Time Trace Display. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335
Sample Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337
Chapter 6
Using the Analysis Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .339
Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 341
Working in the Batch View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 343
Samples Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 344
Auto Samples Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 376
Reference Samples Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 378
Creating a Batch Using the Batch Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . 379
Working in Data Review for Quantitation Methods . . . . . . . . . . . . . . . . . . . . 393
Sample View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 394
Compound View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 406
Qualitative View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 416
Features Common to All Data Review Pages . . . . . . . . . . . . . . . . . . . . . . . . 432
Working in Data Review for Target Screening Methods . . . . . . . . . . . . . . . . . 454
Samples Pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 457
Compounds Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 458
Chromatogram Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 461
Spectrum Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 462
Working in the Report View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 468
Viewing Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 469
Generating Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 473
Working with Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 477
Working with the Active View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 480
Working in the Project Administration View . . . . . . . . . . . . . . . . . . . . . . . . . 492
Working with Drives. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 493
Working with Projects. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 495
Working in the Local Method View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 498
Working in the Batch Template Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 500
Appendix A Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .509
Specifying Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 509
Standard Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 510
Custom Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 511
Target Screening Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 511
ToxID Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 511
Report Flags . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 512
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Sample Standard Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 513
Batch Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 514
Batch Report Rev 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 515
Calibration Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 516
Calibration Density Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 519
Chromatogram Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 520
Compound Calibration Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 521
Compound Calibration Report - Alternate . . . . . . . . . . . . . . . . . . . . . . . . . 523
Confirmation Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 525
Confirmation Report 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 526
High Density Calibration Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 527
High Density Internal Standard Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . 528
High Density Internal Standard Report Long . . . . . . . . . . . . . . . . . . . . . . . 529
High Density Sample Report 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 530
High Density Sample Report 1 Long. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 531
High Density Sample Report 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 532
High Density Sample Report 2 Long. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 533
High Density Sample Report 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 534
High Density Sample Report 3 Long. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 535
Internal Standard Summary Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 536
Ion Ratio Failure Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 537
Manual Integration Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 538
Method Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 539
Method Validation Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 542
MSMSD Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 545
Quality Control Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 546
Quantitation Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 547
Quantitation Report - 2. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 548
Solvent Blank Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 550
Appendix B Using Copy Down and Fill Down . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .551
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .555
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P
Preface
Thermo TraceFinder™ 3.0 is the newest application in the Thermo Scientific™ series of
GC/MS and LC/MS analytical software.
Contents
• Related Documentation
• Special Notices
• System Activation
• Contacting Us
 To suggest changes to documentation or to Help
Complete a brief survey about this document by clicking the button below.
Thank you in advance for your help.
Related Documentation
TraceFinder includes Help and these manuals as PDF files:
• 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 view TraceFinder documents using the Start menu
Choose Start > All Programs > Thermo TraceFinder > Manuals.
 To open TraceFinder Help and access related documents from the application
1. Open the TraceFinder application and choose Help > TraceFinder Help.
• To find a particular topic, use the Contents, Index, or Search panes.
• To create your own bookmarks, use the Favorites pane.
2. To view the user guide or one of the quick reference guides, choose Help > Manuals >
TraceFinder User Guide or TraceFinder * Quick Reference Guide.
The PDF of the selected guide 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.
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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: Th[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.
Note The barcode might already be filled in for you.
3. When you finish entering all the information, click Copy.
The application copies this XML text to the Clipboard.
If you have not completed all the information, a pop-up box identifies the missing
information.
4. Paste this XML text in the body of an e-mail and send the e-mail to
[email protected]
You will receive an e-mail response containing the activation key.
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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.
Note The License Activation window for power modules automatically opens when
you try to enable the power module features in the Application Configuration mode.
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
Find software updates and utilities to download at mssupport.thermo.com.
 To contact Customer Service for ordering information
Phone
800-532-4752
Fax
561-688-8731
E-mail
[email protected]
Web site
www.thermo.com/ms
 To get local contact information for sales or service
Go to www.thermoscientific.com/wps/portal/ts/contactus.
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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 forensic toxicology market. It supports a focused
quantification workflow for specific nonbioanalytical laboratory use, instrument control, and
method development functionality. TraceFinder is the primary application for the TSQ
Quantum™ XLS triple quadrupole mass spectrometers.
The TraceFinder application can export SRM data in .xml format so that other applications,
including TSQ and Q Exactive™, can import the files into their databases.
The TraceFinder application can import the following file types:
• Sample lists in .csv or .xml format
See “Defining the Sample List” on page 298.
• Processing (.pmd) and instrument (.meth) method files from the Xcalibur data system
For detailed information about creating processing methods, see “Working with Master
Methods” on page 83.
For detailed information about creating instrument methods, see “Working with
Instrument Methods” on page 269.
• Compounds from files that use the database (.xml or .cdb) format
See “Editing Compounds in the Database” on page 251.
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About the TraceFinder Application
• Batches, methods, or templates from the following applications:
–
TraceFinder 1.0, 1.1, 2.0, or 2.1
–
QuanLab Forms or ToxLab Forms 2.5 or 3.0
See “Converting Legacy Data” on page 21.
The TraceFinder application checks the accuracy and precision of data against systems that
have previously been certified against a standard processing program, such as the Statistical
Analysis System (SAS).
Supported File Types
The TraceFinder application supports the following file types:
• Comma-separated values (.csv): A set of file formats used to store tabular data in which
numbers and text are stored in plain textual form that can be read in a text editor. Lines in
the text file represent rows of a table, and commas in a line separate fields in the tables
row.
• Extensible Markup Language (.xml): A generic framework for storing any amount of text
or any data whose structure can be represented as a tree. The only indispensable
syntactical requirement is that the document has exactly one root element (also called the
document element). This means that the text must be enclosed between a root start-tag
and a corresponding end-tag.
• Instrument method (.meth): A proprietary file format for the Xcalibur software suite with
specific instructions that enable scientific instruments to perform data acquisition.
• Processing method (.pmd): A proprietary file format for the Xcalibur software suite with
specific instructions on processing data that was acquired through the instruments
attached to the system.
• Raw data (.raw): The file type for acquired samples on the system.
• Compound database (.cdb): The file type for TraceFinder or ExactFinder compound
database data.
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TraceFinder Summary of Features
TraceFinder Directory Structure
The TraceFinder application creates folders for projects/subprojects/batches and templates in
the C:\Thermo\TraceFinder\3.0\Forensic 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.
Example batch directory structure
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 forensic toxicology applications. The
application has a fully automated acquisition mode and a manual data analysis mode. You can
use the data acquisition system to create and submit batches and monitor real-time review of
results.
The TraceFinder application uses a comprehensive processing method to provide improved
handling of ion ratio calculations, reviewing, and reporting. In addition, it can compare the
mass spectra and integrate the processes of data review and reporting.
Key features include the following:
• Role-based authorization for LabDirector, ITAdmin, Supervisor, Technician, and QAQC
(quality assurance) roles
• Configuration mode for report configuration, detection defaults, and application
administration
• Method Development mode for editing instrument methods, setting processing and error
flag parameters, and setting report options
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TraceFinder Workflow
• Choice of acquisition wizards:
–
Acquisition batch mode that guides you in creating batches and running samples
–
Batch template wizard similar to the interface used in the ToxLab Forms application
• Analysis mode with project administration, batch views, data review, local method views,
and report views
• Database-capable method development
• Quantification workflows, supporting capabilities present in the LCquan™ and ToxLab
Forms applications
• Target screening workflows
• 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
TraceFinder Workflow
The TraceFinder application is structured with a typical laboratory workflow in mind. You
create a batch, and the system injects samples into the instrument, runs the samples, analyzes
the data, and generates a report. You can set up a master method for specific compound
groups or assays that you expect to run in your laboratory. When you are ready to run a
particular type of sample, select the appropriate method and begin.
When using the TraceFinder application, follow these basic steps:
1. Create and save a master method in the Method Development mode.
A master method combines the instrument method and processing method that define
the following:
• How the raw data is acquired and processed
• How the error checking information evaluates the results
• How the results appear in reports
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Reporting Features
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 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.
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 four groups: Standard, Custom, Target Screening, and
ToxID.
For additional information about standard, custom, target screening, or ToxID reports and
examples of each standard report type, see “Reports” on page 509.
Examples of standard reports (as PDF files) are also located in the following folder:
C:\Thermo\TraceFinder\3.0\Forensic\ExampleReports
Standard Report Types
•
•
•
•
•
•
•
•
•
•
•
•
Thermo Scientific
Batch Report
Batch Summary Report
Batch Report Rev 1
Calibration Report
Calibration Curve Report
Chromatogram Report
Compound Calibration Report
Compound Calibration Report - Alternate
Confirmation Report
High Density Calibration Report
High Density Internal Standard Report
High Density Internal Standard Report Long
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Reporting Features
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
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
Intelligent Sequencing Report
Internal Standard Summary Report
Ion Ratio Failure Report
Manual Integration Report
Method Report
Negative Report
Qualitative Peak Report
Qualitative Summary Report
Quality Control Report
Quantitation Report
Quantitation Report - 2
Sample Report
Sample Report Long
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
CalibrationDensityReport
CalibrationReport
CheckStandardReport
CompoundCalibrationReport
ConfirmationReport
ConfirmationReport2
HighDensitySampleReport1Long
HighDensitySampleReport2Long
HighDensitySampleReport3Long
HighDensitySampleReport4
HighDensitySampleReport5
QuantitationReport
SteroidAnalysisReport
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1 Introduction
Reporting Features
Target Screening Report Types
• Target Screening High Density Sample Report
• Target Screening Summary Report
ToxID Report Types
• 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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Installing the TraceFinder Application
Installing the TraceFinder Application
To initially install the TraceFinder 3.0 application, follow the instructions in the TraceFinder
Installation Guide. Later, you might need to reinstall the TraceFinder application or other
features on the InstallShield Wizard, such as the power modules.
Follow these instructions to reinstall, start, and log in to the TraceFinder application.
 To reinstall the TraceFinder application
1. From the Thermo Foundation Instrument Configuration window, remove all
instruments.
2. From the Windows™ Control Panel, uninstall the TraceFinder application and then
uninstall all Thermo instrument drivers.
3. Insert the TraceFinder CD, and install both the TraceFinder 3.0 application and the
NIST library as follows:
a. Open the TraceFinder launcher and click Next.
The InstallShield Wizard opens.
b. Click TraceFinder 3.0, and follow the instructions in the InstallShield Wizard.
c. At the prompt, click Yes to completely remove any previously installed TraceFinder
applications.
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Installing the TraceFinder Application
d. Open the TraceFinder launcher again and click Next.
e. Click TraceFinder 3.0, and follow the instructions in the InstallShield Wizard.
IMPORTANT For the TraceFinder application to properly install, you might be
prompted to uninstall Thermo Foundation™. Do the following:
1. Click Yes, and then when prompted to restart your computer, click OK.
The wizard continues the TraceFinder installation.
2. When prompted to install Thermo Foundation, click Yes, and then when
prompted to restart your computer, click OK.
The wizard continues the installation.
f.
When prompted, choose to install either the GC or LC version of the software.
g. When the installation completes, open the TraceFinder launcher again and click
Next.
h. (Required for ToxID) If you have not previously installed the NIST library, click
NIST Library and follow the instructions to install the library.
3. (Optional) Click Example Data, and follow the instructions to install an example project
that contains example batch data.
4. Install the appropriate device drivers, and configure the instruments in the Thermo
Foundation Instrument Configuration window.
Follow these instructions to start the TraceFinder application.
 To start the TraceFinder application
1. Configure your instruments.
You must close the TraceFinder application before you can configure your instruments.
2. Double-click the TraceFinder icon on your desktop, or choose Start > All Programs >
Thermo TraceFinder > TraceFinder Forensic Toxicology.
By default, user security is not activated and the application does not require a password.
To activate user security, see “User Security” on page 64.
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Getting Started
Installing the TraceFinder Application
 To log in to the TraceFinder application (when user security is activated)
Note Before you can log in to the TraceFinder application when user security is
activated, a system administrator must set up a user account for you. The
administrator assigns you a user name and password and gives you permission to
access specific modes.
1. Enter your assigned user name in the TraceFinder login window.
IMPORTANT If you are the administrator logging in for the first time with user
security activated, 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 login window opens.
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2 Getting Started
Installing the TraceFinder Application
Figure 2.
Main window with user security activated
User name and Log Off button available
only when user security is activated
Figure 3.
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TraceFinder login window
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Installing the TraceFinder Application
Table 1. Login window parameters
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Parameter
Description
Login text box
The user’s assigned user name.
Password
The assigned password for the user name.
Login button
Verifies the user name and password, and opens the TraceFinder
application.
Cancel
Closes the TraceFinder login window.
Thermo Scientific
2 Getting Started
Installing the Power Modules
Installing the Power Modules
Follow these instructions to install and activate the TraceFinder power modules for
multiplexing and intelligent sequencing.
 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 TraceFinder Power Modules, and follow the instructions to install the
multiplexing and intelligent sequencing modules.
4. License the power modules.
To license the power modules, follow the same procedures for licensing the TraceFinder
application. See “System Activation” on page ix.
The features associated with these power modules are mutually exclusive and are not
automatically activated.
5. To activate these power modules, see “Activating Optional Features” on page 63.
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Installing the NIST and QED Libraries
Installing the NIST and QED Libraries
When you are using triple quadrupole instruments, such as the TSQ Quantum XLS, follow
these instructions to install the NIST and QED libraries.
 To install the NIST library
1. Open the TraceFinder launcher, and click Next.
2. Click NIST Library.
The NIST 08 MS Search and AMDIS Setup wizard opens.
3. Follow the instructions in the setup wizard.
4. When the wizard prompts you to select a destination folder, select
C:\Program Files\NISTMS.
 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 Libraries list.
3. Click Add.
The Add Library dialog box opens.
4. Click Browse, and locate your QED library in the C:\Thermo folder.
5. Click OK.
The Xcalibur application reports that it has added the library to the NIST application.
6. Click Dismiss to close the message box.
The Xcalibur application adds the QED library to the NIST Libraries list in the Library
Manager dialog box.
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Installing the NIST and QED Libraries
7. Click Exit in the Thermo Library Manager dialog box.
8. To confirm the library installation, do the following:
a. Start the TraceFinder application.
b. Click Method Development in the navigation pane.
c. Click Method View in the Method Development navigation pane.
d. Choose File > New > Method Template from the main menu.
The Method Template Editor displays the QED NIST Library in the Use These
Libraries list.
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Launching the NIST Library Browser
Launching the NIST Library Browser
Use the NIST MS Search tool to search the NIST library.
 To open the NIST library browser
Choose Go > Launch Library Browser from the TraceFinder main menu.
The NIST MS Search window opens.
For detailed instructions about using the library browser, refer to the Help in the NIST MS
Search window.
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Launching the Qual Browser
Launching the Qual Browser
Use the Xcalibur application’s 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 TraceFinder main menu.
The Thermo Xcalibur Qual Browser opens.
For detailed instructions about using the Qual Browser, refer to the Help in the Qual Browser
window.
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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 the source versions to compatible TraceFinder 3.0 target
configurations. See Version compatibility.
• You can convert legacy data from TraceFinder versions 1.0.1, 1.1, 2.0, or 2.1.
• You can convert data from EnviroLab Forms, QuanLab Forms, or ToxLab Forms.
• You can convert data from TraceFinder 3.0 for general quantitation to another installed
configuration of TraceFinder 3.0.
 To open the TraceFinder Legacy Data Converter
Choose Go > Launch Legacy Data Converter from the TraceFinder main menu.
The TraceFinder Legacy Data Converter window opens.
This section includes the following topics:
• Converting Methods
• Converting Batches
• Converting Method Templates
• Converting Batch Templates
Table 2. Version compatibility (Sheet 1 of 2)
Source
TraceFinder 3.0 target
EFS
Clinical
Research






TraceFinder 2.1 Clinical Research


TraceFinder 2.1 Forensic Toxicology




General
TraceFinder 3.0 General
TraceFinder 2.1 General

TraceFinder 2.1 EFS
TraceFinder 2.0 General
TraceFinder 2.0 EFS
Thermo Scientific
Forensic
Toxicology




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Converting Legacy Data
Table 2. Version compatibility (Sheet 2 of 2)
Source
TraceFinder 3.0 target
General
EFS
TraceFinder 2.0 Clinical Research
TraceFinder 1.1 General


TraceFinder 1.1 EFS

TraceFinder 1.0.1

EnviroLab Forms 3.1

QuanLab Forms 3.1


ToxLab Forms 3.1
ToxLab Forms 2.5.2
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Forensic
Toxicology













EnviroLab Forms 2.5.2
QuanLab Forms 2.5.2
Clinical
Research


Thermo Scientific
2 Getting Started
Converting Legacy Data
Converting Methods
Use the data converter to convert legacy methods to TraceFinder 3.0 methods.
 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 that you will convert.
The Methods to be Converted table displays the methods in the Methods folder for the
selected source version. The application verifies that the method file is in the .mmx file
format.
3. To convert a method that is not in the default list, do the following:
a. Click the Change Default 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 table.
When you select a folder that contains multiple method folders, the application displays
all the methods.
4. In the Target Version list, select the version that you are converting to.
The list displays only TraceFinder configurations with compatible data. See “Version
compatibility” on page 21.
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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 table, the application checks each
method to see if a method with this name exists in the target folder.
• If the method name already exists in the target folder, the default new name is the
original name with “_1” appended.
• If the method name does not exist in the target folder, the application keeps the
original method name.
IMPORTANT The conversion cannot overwrite an existing file name. If the new name
is identical to an existing method file, the conversion will not work. When you
manually enter a new name, you must verify that the name does not already exist.
7. Select the check box for each method that you will convert,
and click
.
The application confirms that all methods to be converted use the .mmx file format.
When the conversion process begins, the application displays a status bar and a Cancel
button. You can cancel pending conversions, but not the method that is currently
converting.
When the Status column reports that a method is successfully converted, the application
writes the converted file to the C:\Thermo\TargetVersion\Methods folder.
Note If a method conversion is unsuccessful, 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 Microsoft Notepad text
editor window.
Figure 4.
24
Sample log file for converting a method
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2 Getting Started
Converting Legacy Data
Converting Batches
Use the data converter to convert legacy batches to TraceFinder 3.0 batches.
 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 that you will convert.
The Batches to be Converted table 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.
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Converting Legacy Data
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 table.
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 that you are converting to.
The list displays only TraceFinder configurations with compatible data. See “Version
compatibility” on page 21.
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 table, the application checks each batch
to see if a batch with this name exists in the target folder.
• If the batch name already exists in the target folder, the default new name is the
original name with “_1” appended.
• If the batch name does not exist in the target folder, the application keeps the original
batch name.
IMPORTANT The conversion cannot overwrite an existing file name. If the new name
is identical to an existing batch folder, the conversion will not work. When you
manually enter a new name, you must verify that the name does not already exist.
8. Select the check box for each batch that you will convert,
and click
.
The application confirms that all batches to be converted use the .btx file format.
When the conversion process begins, the application displays a status bar and a Cancel
button. You can cancel pending conversions, but not the batch that is currently
converting.
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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 and uses either
the original project and subproject names or the new names that you entered.
Note If a batch conversion is unsuccessful, the Status column displays 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 5.
Sample log file for converting a batch
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Converting Legacy Data
Converting Method Templates
Use the data converter to convert legacy method templates to TraceFinder 3.0 method
templates.
 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 that you will convert.
The Method Templates to be Converted table displays the method templates in the
Templates folder for the selected source version. The application verifies that the method
template file is in the .pmtx file format.
3. To convert a method template that is not in the default list, do the following:
a. Click 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
table.
When you select a folder that contains multiple method template folders, the application
displays all the method templates.
4. In the Target Version list, select the version that you are converting to.
The list displays only TraceFinder configurations with compatible data. See “Version
compatibility” on page 21.
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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 table, the application checks
each method template to see if a method template with this name exists in the target
folder.
• If the method template name already exists in the target folder, the default new name
is the original name with “_1” appended.
• If the method template name does not exist in the target folder, the application keeps
the original method template name.
IMPORTANT The conversion cannot overwrite an existing file name. If the new name
is identical to an existing method template file, the conversion will fail. When you
manually enter a new name, you must verify that the name does not already exist.
7. Select the check box for each method template that you will convert,
and click
.
The application confirms that all method templates to be converted use the .pmtx file
format.
When the conversion process begins, the application displays a status bar and a Cancel
button. You can cancel pending conversions, but not the template that is currently
converting.
When the Status column reports that the template is successfully converted, the
application writes the converted template to the following folder:
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 6.
Sample log file for converting a method template
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Getting Started
Converting Legacy Data
Converting Batch Templates
Use the data converter to convert legacy batch templates to TraceFinder 3.0 batch templates.
 To convert a batch template
1. In the Data Type list, select Batch Template.
You can choose either LabForms batch templates or TraceFinder batch templates.
The TraceFinder Legacy Data Converter displays the interface for converting batch
templates.
2. In the Source Version list, select the version of the batch template that you will convert.
The Batch Templates to be Converted table 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 table.
When you select a folder that contains multiple batch template folders, the application
displays all the batch templates.
4. In the Target Version list, select the version that you are converting to.
The list displays only TraceFinder configurations with compatible data. See “Version
compatibility” on page 21.
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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 batch
template that you want converted.
When you populate the Batch Templates to be Converted table, the application checks
each batch template to see if a batch template with this name exists in the target folder.
• If the batch template name already exists in the target folder, the default new name is
the original name with “_1” appended.
• If the batch template name does not exist in the target folder, the application keeps
the original batch template name.
IMPORTANT The conversion cannot overwrite an existing file name. If the new name
is identical to an existing batch template file, the conversion will fail. When you
manually enter a new name, you must verify that the name does not already exist.
7. Select the check box for each batch template that you will convert,
and click
.
The application confirms that all batch templates to be converted use the .btx file format.
When the conversion process begins, the application displays a status bar and a Cancel
button. You can cancel pending conversions, but not the template that is currently
converting.
When the Status column reports that the template is successfully converted,
the application writes the converted template folder to the
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.
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 7.
Sample log file for converting a batch template
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Getting Started
Choosing a Mode
Choosing a Mode
When user security is activated, the navigation pane displays the modes available to the
current user’s assigned role. The following table shows the available modes for each user role.
Table 3. User roles and mode access
User role
Method
Development
Acquisition
Analysis
Application
Configuration




LabDirector

ITAdmin
Supervisor

Technician




QAQC

Note When user security is not activated, 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 acquisition and processing in real time
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Getting Started
Choosing a Mode
 To choose a mode
Do one of the following:
• To access a mode from the navigation pane, click the mode where you want to work.
The navigation pane shows only the modes that you have permission to use.
Mode
Description
Acquisition
Opens the Acquisition mode where you can create and review
batches, batch data, reports, and local methods. See
Chapter 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 65.
Analysis
Opens the Analysis mode where you can review batches, batch
data, reports, and local methods. See Chapter 6, “Using the
Analysis Mode.”
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.”
–or–
• Click the Application Configuration icon,
TraceFinder window.
, in the upper right corner of the
When user security is activated, only users in the LabDirector or ITAdmin role have
permission to use the Application Configuration mode.
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Getting Started
Choosing a Mode
 To display a log of instrument errors
1. Click the status light in the upper right corner of the TraceFinder window.
Status light
The Instrument Log dialog box opens.
The Instrument Log displays all instrument errors that have occurred since the
TraceFinder application started or since the last time that you cleared the message log.
2. Do any of the following:
• Click Refresh to display errors that occur after you open the Instrument Log dialog
box.
• Click Clear Messages to remove messages from the Instrument Log display.
The application clears messages only from the Instrument Log display. These
messages remain in the following log file:
C:\Thermo\TraceFinder\3.0\Forensic\Logs\TraceFinder.log
• Click OK to dismiss the Instrument Log dialog box.
 To monitor instrument status
Look at the status light in the upper right corner of the TraceFinder window.
Green indicates that the instrument is ready.
Yellow indicates that the instrument is in standby mode.
Red indicates that the instrument is turned off or no device is configured.
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Getting Started
Choosing a Mode
 To watch acquisition and processing in real time
Click Real Time Status in the upper right corner of the TraceFinder window.
The application displays the Real Time Status pane at the bottom of the window.
For descriptions of all the features of the Real Time Status pane, see “Real Time Status
Pane” on page 323.
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Getting Started
Choosing a Mode
TraceFinder Window Features
A TraceFinder window with user security for a user in the LabDirector role has these
functions.
Table 4. TraceFinder window parameters
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Parameter
Description
Real Time Status
Opens the Real Time Status pane for the current acquisition. The
acquisition progress is displayed within the current mode window.
CurrentUserName
Displays the name of the current user. This is displayed only when user
security is activated. See “User Security” on page 64.
Log Off
Logs off the current user and displays the login screen. This function is
available only when user security is activated. See “User Security” on
page 64.
Help
Opens the TraceFinder Help.
Application
Configuration
Opens the Application Configuration mode where you can configure
several options for using the TraceFinder application. See Chapter 3,
“Using the Application Configuration Mode.”
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3
Using the Application Configuration Mode
This chapter discusses the configuration tasks assigned to the ITAdmin and LabDirector roles
when user security is activated. When user security is not activated, all users have access to all
features in the Application Configuration mode except the User Administration tasks.
When user security is activated, in either the LabDirector or ITAdmin role, you can activate
features such as available reports, user security, 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.
Contents
• Specifying the Reports Configuration
• Specifying Application Defaults
• Specifying Default Peak Detection Parameters
• Specifying Adducts Configuration
• Activating Optional Features
• Managing User Administration
 To access the Application Configuration mode
Click the Application Configuration icon,
window.
, in the upper right corner of any
The navigation pane for this mode opens with the following functions (see Navigation
pane functions in the Application Configuration mode).
Available only to users in the LabDirector
or ITAdmin role
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Table 5.
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Navigation pane functions in the Application Configuration mode
Function
Description
Reports
From the Reports view, you can configure standard, custom,
ToxID, or target screening reports. See “Specifying the Reports
Configuration” on page 39.
Defaults
From the Defaults view, you can specify the default laboratory
and instrument names, the displayed mass precision, and the
intensity scale to use for reporting. See “Specifying Application
Defaults” on page 44.
Peak Detection Defaults
Use the Peak Detection Defaults view to specify a peak
detection algorithm and its options and to determine the area
under a curve. See “Specifying Default Peak Detection
Parameters” on page 46.
Adducts
Use the Adducts Configuration view to specify the adducts
that will be available for you to use in method development.
See “Specifying Adducts Configuration” on page 60.
Optional Features
See “Activating Optional Features” on page 63.
User Administration
With user security activated, in either the LabDirector or
ITAdmin role, you can add, remove, or edit user accounts and
permissions. See “Managing User Administration” on page 69.
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Using the Application Configuration Mode
Specifying the Reports Configuration
Specifying the Reports Configuration
When user security is activated, as a user in either the LabDirector or ITAdmin role, you can
configure a list of reports that are available to all users when they generate reports from the
Method Development, Analysis, or Acquisition modes. From the Reports view, you can
configure standard, custom, ToxID, or target screening reports.
When you first open the report configuration, all reports are included in the Displayed
Reports pane and are available for use in any method you create. By default, the Intelligent
Sequencing Report is not included in the Displayed Reports pane.
Note The Intelligent Sequencing Report is available only when you install the Intelligent
Sequencing power module and enable the Intelligent Sequencing features. See “Installing
the Power Modules” on page 15 and “Intelligent Sequencing” on page 66.
Note ToxID reports are available only when you activate the ToxID features. See “ToxID”
on page 64.
Example PDF files of report formats are located in the following folder:
C:\Thermo\TraceFinder\3.0\Forensic\ExampleReports
Follow these procedures:
• To open the Reports Configuration
• To specify which reports are available
• To import new reports
 To open the Reports Configuration
In the Application Configuration mode, click Reports.
The Reports view of the Application Configuration mode opens. For a list of all reports
for the forensic toxicology market, see “Reports” on page 41.
 To specify which reports are available
1. Use the directional arrows to move reports between the Installed Reports pane and 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 a separate report 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. The application
adds a B to the beginning of all batch-level report names to differentiate them.
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Specifying the Reports Configuration
Note Only reports that can aggregate data at the batch level have the Batch Level
check box activated. By default, the application selects the Batch Level feature for all
these reports.
3. 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 in the Reports
view, click No.
If you want to return the report selections to their original state (when you first opened
this view), click Undo Changes.
 To import new reports
1. Click Import.
The Open dialog box opens.
2. In the Open dialog box, locate a Crystal Reports .dll file or a Custom Reports .xltm file
and open it.
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, target screening, and ToxID reports. For
descriptions of the parameters in the Reports view, see “Reports view parameters” on page 43.
Figure 8.
Reports view showing standard reports
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Specifying the Reports Configuration
Figure 9.
Reports view showing custom reports
Figure 10. Reports view showing target screening reports
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Using the Application Configuration Mode
Specifying the Reports Configuration
Figure 11. Reports view showing ToxID reports
Note ToxID reports are available only when you install the ToxID™ software and activate
the ToxID features. For a detailed procedure for activating ToxID features, see “ToxID” on
page 64.
Table 6.
Thermo Scientific
Reports view parameters
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.
Cancel
Returns the report selections to their original state (when you
first opened this view).
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
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3 Using the Application Configuration Mode
Specifying Application Defaults
Specifying Application Defaults
Use the Application Defaults view of the Application Configuration mode to specify the
default laboratory and instrument names, the displayed mass precision, and the
chromatogram intensity scale to use for reporting. When user security is activated, you can
access these features only in the LabDirector or ITAdmin role.
Follow these procedures:
• To open the Application Defaults view
• To specify a default laboratory name and instrument name
• To specify default mass precision and the intensity scale
 To open the Application Defaults view
In the navigation pane for the Application Configuration mode, click Defaults.
The Application Defaults view of the Application Configuration mode opens.
 To specify a default laboratory name and instrument name
1. Type the name of your laboratory in the Lab Name box.
When you create a method, the application uses this default laboratory name for the
Laboratory Name value on the General page of the Method View. The application uses
this laboratory name in the report headings.
The application does not apply this default laboratory name to previously created
methods. By default, the laboratory name is Default Laboratory.
2. Type the name of your instrument in the Instrument Name box.
When you create a batch, the application uses this default instrument name for the
Instrument Name value. The application uses this instrument name in the report
headings.
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3. In the Application Configuration mode, 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. When asked if you want to restart the application, click Restart Now.
 To specify default mass precision and the intensity scale
1. In the Display Mass Precision box, set the decimal value for the mass precision to an
integer from 2 to 6, inclusive.
The default number of digits to display is 2. The TraceFinder application uses this mass
precision value to display mass values in the following locations:
• Reports:
– Blank Report
– Confirmation Report (data spectra, library spectra, quantitation ion display, and
qualitative ion display)
– All High Density reports (m/z values)
– Ion Ratio Failure Report (quantitation ion and qualitative ion)
– Manual Integration Report (m/z value)
– 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
IMPORTANT When you create a method using a raw data file, the application reads
the filter precision value from the raw data file to create scan filters; however, the
Tracefinder application uses the Display Mass Precision value when showing masses
that are not embedded within filter strings and masses that are displayed on spectral
plots.
2. Select 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 mode, click Apply.
4. When asked if you want to restart the application, click Restart Now.
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3 Using the Application Configuration Mode
Specifying Default Peak Detection Parameters
Specifying Default Peak Detection Parameters
When user security is activated, as a user in either the LabDirector or ITAdmin role, you can
specify default peak detection parameters for the Genesis, ICIS, or Avalon detection
algorithms. Use the Peak Detection Defaults view to specify a peak detection algorithm and
its options and to determine the area under a curve. These parameters are available for
quantitation methods only.
This section includes procedures for specifying common peak detection parameters (see
“Common peak detection areas” on page 48) and the parameters used for each of the
following detection algorithms:
• Genesis Detection Method
• ICIS Detection Method
• Avalon Detection Method
 To open the Peak Detection Defaults view
In the navigation pane for the Application Configuration mode, click Peak Detection
Defaults.
The Peak Detection Defaults view opens.
• For detailed descriptions of detection parameters used for all detection algorithms,
see “Common peak detection parameters” on page 48.
• For detailed descriptions of detection parameters used for the Genesis detection
algorithm, see “Genesis peak detection parameters” on page 50.
• For detailed descriptions of detection parameters used for the ICIS detection
algorithm, see “ICIS peak detection parameters” on page 53.
• For detailed descriptions of detection parameters used for the Avalon detection
algorithm, see “Avalon peak detection parameters” on page 56.
 To specify common detection parameters
1. In the Detector Type list, select a detector type.
For detailed descriptions of the available detector types, see “Common peak detection
parameters” on page 48.
2. In the Mass Tolerance area, do the following:
a. Select the unit of measure that you want to use (MMU or PPM).
b. In the Value box, specify the number of millimass units or parts per million to use as
the upper limit.
The application applies this mass tolerance to the extracted chromatograms. The default
is 500 MMU.
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3. In the Retention Time area, do the following:
a. In the Window box, specify the width of the window (in seconds) to indicate how far
around the expected retention time the system will look for a peak apex.
b. In the View Width box, specify the viewable size (in minutes) of the ion
chromatogram display.
4. In the Ion Ratio Parameters area, do the following:
a. In the Window Type list, select Absolute or Relative as the calculation approach for
determining the acceptable ion ratio range.
b. In the Window box, select the acceptable ion ratio range.
c. In the Ion Coelution box, select the maximum difference in retention time between a
confirming ion peak and the quantification ion peak.
5. In the Peak Detection Parameters area, select one of the detection algorithms: Genesis,
ICIS, or Avalon.
6. Specify the parameters for the selected detection algorithm.
For detailed parameter descriptions, see one of the following:
• Genesis Detection Method
• ICIS Detection Method
• Avalon Detection Method
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Figure 12. Common peak detection areas
Table 7. Common peak detection parameters (Sheet 1 of 2)
Parameter
Description
Detector Type
MS: Mass spectrometer that ionizes sample molecules and then separates the ions according
to their mass-to-charge ratio (m/z).
PDA: Photodiode array detector providing a linear array of discrete photodiodes on an
integrated circuit chip. It is placed at the image plane of a spectrometer so that a range of
wavelengths can be simultaneously detected.
Analog: Supplemental detectors (for example, FID, ECD). When you select this detector,
any reports that display a QIon value show the value as Analog and any reports that display
spectra show the spectra as Not Available.
A/D card: If your detector is not under data system control, you can capture the analog
signal and convert it to digital using an interface box (for example, SS420X) for storage in
the raw data file.
UV: A UV spectrophotometer (for variable-wavelength detection) or photometer (for
single-wavelength detection) equipped with a low-volume flow cell. This detector detects
analytes that readily absorb light at a selected wavelength.
Mass Tolerance
Units
• (Default) MMU (millimass units)
MMU is a static calculation to the extracted mass.
• PPM (parts per million)
PPM is a variable calculation dependent on the actual mass. The smaller the mass, the
narrower the tolerance range. The larger the mass, the wider the tolerance range.
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Table 7. Common peak detection parameters (Sheet 2 of 2)
Parameter
Description
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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Genesis Detection Method
The TraceFinder application provides the Genesis peak detection algorithm for backward
compatibility with Xcalibur 1.0 studies.
Figure 13. Genesis peak detection
Table 8. Genesis peak detection 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
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Determines the degree of data smoothing to be performed on the active component peak
prior to peak detection and integration. The ICIS peak detection algorithm uses this value.
Default: 1
Range: Any odd integer from 1 through 15 points
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Specifying Default Peak Detection Parameters
Table 8. Genesis peak detection 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
threshold and a tailing factor. Selecting the Constrain Peak Width check box activates the
Peak Height (%) and Tailing Factor options.
Peak Height (%)
A signal must be above the baseline percentage of the total peak height (100%) before
integration is turned on or off. This text box is active only when you select the Constrain
Peak Width check box.
Range: 0.0 to 100.0%
Tailing Factor
A factor that controls how the TraceFinder application integrates the tail of a peak. This
factor is the maximum ratio of the trailing edge to the leading side of a constrained peak.
This text box is active only when you select the Constrain the Peak Width check box.
Range: 0.5 through 9.0
Min Peak Height (S/N) For the valley detection approximation method to use the Nearest RT Peak Identification
criteria, this peak signal-to-noise value must be equaled or exceeded. For component
identification purposes, the TraceFinder application ignores all chromatogram peaks that
have signal-to-noise values that are less than the S/N Threshold value.
Range: 0.0 (all peaks) through 999.0
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Table 8. Genesis peak detection 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.
Default: 2.0
Range: 1.0 to 100.0
# Background Scans
Number of background scans performed by the TraceFinder application.
Report Noise As
Determines if the noise used in calculating S/N values is calculated using an RMS
calculation or peak-to-peak resolution threshold. Options are RMS or Peak To Peak.
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ICIS Detection Method
The ICIS peak detection algorithm is designed for MS data and has superior peak detection
efficiency at low MS signal levels.
Figure 14. ICIS peak detection
Table 9. ICIS peak detection 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.
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Table 9. ICIS peak detection parameters (Sheet 2 of 3)
Parameter
Description
Smoothing
Determines the degree of data smoothing to be performed on the active component peak
prior to peak detection and integration. The ICIS peak detection algorithm uses this value.
Range: Any odd integer from 1 through 15 points
Default: 1
Area Noise Factor
The noise level multiplier used to determine the peak edge after the location of the possible
peak. The ICIS peak detection algorithm uses this value.
Range: 1 through 500
Default: 5
Peak Noise Factor
The noise level multiplier used to determine the potential peak signal threshold. The ICIS
peak detection algorithm uses this value.
Range: 1 through 1000
Default: 10
Baseline Window
The TraceFinder application looks for a local minima over this number of scans. The ICIS
peak detection algorithm uses this value.
Range: 1 through 500
Default: 40
Constrain Peak Width
Constrains the peak width of a component during peak integration of a chromatogram. You
can then set values that control when peak integration is turned on and off by specifying a
peak height threshold and a tailing factor. Selecting the Constrain Peak Width check box
activates the Peak Height (%) and Tailing Factor options.
Peak Height (%)
A signal must be above the baseline percentage of the total peak height (100%) before
integration is turned on or off. This text box is active only when you select the Constrain
Peak Width check box.
Range: 0.0 to 100.0%
Tailing Factor
A factor that controls how the TraceFinder application integrates the tail of a peak. This
factor is the maximum ratio of the trailing edge to the leading side of a constrained peak.
This text box is active only when you select the Constrain the Peak Width check box.
Range: 0.5 through 9.0
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 9. ICIS peak detection parameters (Sheet 3 of 3)
Parameter
Description
Noise Method
The options are INCOS or Repetitive.
INCOS: Uses a single pass algorithm to determine the noise level. The ICIS peak detection
algorithm uses this value.
Repetitive: Uses a multiple pass algorithm to determine the noise level. The ICIS peak
detection algorithm uses this value. In general, this algorithm is more accurate in analyzing
the noise than the INCOS Noise algorithm, but the analysis takes longer.
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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Specifying Default Peak Detection Parameters
Avalon Detection Method
The Avalon peak detection algorithm is designed for UV data. The Avalon peak detection
algorithm also supports negative peaks. You can edit the Event values from the “Avalon Event
List.”
Figure 15. Avalon peak detection
Table 10. Avalon peak detection 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.
Default: 1
Range: Any odd integer from 1 through 15 points
Time/Event/Value
Displays the events specified in the Avalon Event List dialog box. Initially displays only the
default events that cannot be edited or deleted.
Edit
Opens the Avalon Event List dialog box where you can edit the Time/Event/Value
parameters. See “Avalon Event List.”
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Avalon Event List
The event list includes both user-defined and noneditable default events. The application
displays the default events when you choose Avalon sensitivity. You cannot delete these events
or change their time or values. For a detailed list of events and value ranges, see Event types.
Figure 16. Avalon Event List dialog box
Table 11. Avalon Event List dialog box parameters
Thermo Scientific
Parameter
Description
Time (Min)
Specifies the start time of the event.
Event
Specifies the type of event. For a detailed list of events and value
ranges, see “Event types.”
Value
Specifies the value of the event.
Add
Adds a new event to the list with the current Time/Event/Value
parameters.
Delete
Removes the selected Time/Event/Value parameter from the event
list.
Change
Applies the current parameter values.
Cancel
Closes the dialog box without making any changes. Any additions,
deletions, or changes revert to their original state.
Apply
Closes the dialog box.
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Figure 17. Event types
Table 12. Event type descriptions (Sheet 1 of 2)
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Event type
Description
Start Threshold
Specifies the threshold at the start of a peak. The Start Threshold is
directly related to the RMS noise in the chromatogram.
Range: 0 to 999 999 999
End Threshold
Specifies the threshold at the end of a peak. The End Threshold is
directly related to the RMS noise in the chromatogram.
Range: 0 to 999 999 999
Area Threshold
Controls the area cutoff. Any peaks with a final area less than the area
threshold will not be detected. This control is in units of area for the
data.
Range: 0 to 999 999 999
P-P Threshold
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 12. Event type descriptions (Sheet 2 of 2)
Thermo Scientific
Event type
Description
Tension
Controls how closely the baseline should follow the overall shape of
the chromatogram. A lower tension traces the baseline to more
closely follow changes in the chromatogram. A high baseline tension
follows the baseline less closely, over longer time intervals.
Range: 0 to 999.99 minutes
Tangent Skim
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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Specifying Adducts Configuration
An adduct ion is formed from a precursor ion and contains all of the constituent atoms of that
ion and additional atoms or molecules. Adduct ions are often formed in the mass
spectrometer ion source. Adducts can be either positive or negative.
Use the Adducts Configuration page to specify the adducts that will be available for you to use
in method development.
Follow these procedures:
• To open the Adducts Configuration view
• To add an adduct
• To remove an adduct
 To open the Adducts Configuration view
In the navigation pane for the Application Configuration mode, click Adducts.
The Adducts Configuration view opens, displaying the default positive and negative
adducts.
 To add an adduct
1. In the Positive Adducts or Negative Adducts pane, click the Add New Adduct icon,
.
The application adds an empty row in the Adducts list.
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2. Type the formula for the new adduct ion.
The formula syntax is alphanumeric and case sensitive. It can include parentheses and
brackets.
The formula specifies the difference between the neutral molecule and the charged ion
that you expect to see in the results.
For example, a sodium adduct has [M+Na]+ as the expected charged ion (where M is the
neutral molecule), so you would type “Na” for the formula. A water adduct has
[M+H+H2O]+ as the expected charged ion, so you would type “H3O” for the formula.
IMPORTANT When you create an adduct formula, you can type both uppercase and
lowercase letters; however, the TraceFinder application interprets all uppercase input
as single-letter elements and all lowercase input as two-letter elements.
For example, it interprets the string “inau” as In Au and “COSI” as C O S I.
3. In the Gain/Loss column, select Gain or Loss.
This indicates if the adduct is a loss or gain to the calculated neutral mass.
The application calculates the neutral mass value for the adduct.
These adducts are available for you to select in the Compound Database view of the
Method Development mode when you specify parameter values for target peaks. See
“Editing Compounds in the Database” on page 251.
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 To remove an adduct
1. In the Positive Adducts or Negative Adducts pane, select the adduct that you want to
remove.
2. Click the Delete Selected Adduct icon,
.
You can delete only adducts that you added to the adducts list. You cannot delete default
adducts defined by the TraceFinder installation.
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Activating Optional Features
In the Optional Features view of the Application Configuration mode, you can activate the
following features:
• User Security
• ToxID
• Quick Acquisition
• Delay Calibration Calculation
• Batch Wizard Style
• Multiplexing
• Intelligent Sequencing
• Acquisition Submission Options
• Screening Library
 To open the Optional Features view
In the Application Configuration mode, click Optional Features.
The Optional Features view opens.
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Activating Optional Features
User Security
When user security is activated, you must log in to the TraceFinder application, which gives
you access to only those modes assigned to your user role. See “Choosing User Roles” on
page 75.
 To turn on user security
1. Select the User Security check box.
You must now log in to the TraceFinder application to access the modes assigned to your
user role. See “Choosing User Roles” on page 75. When user security is activated, only
users in the LabDirector or ITAdmin roles can access the Application Configuration
mode.
When this check box is cleared, you are not required to log in to the TraceFinder
application. All modes are available to all users when the application starts; however, you
cannot see the User Administration view in the Application Configuration mode unless
you are assigned the LabDirector or ITAdmin role.
IMPORTANT If you are the administrator logging in with user security activated, you
can use Administrator/Password as the username/password.
2. Click Apply.
3. When prompted to restart the application, click Restart Now.
ToxID
You must activate the ToxID option before you can generate ToxID reports.
 To activate ToxID
1. Select the ToxID check box.
2. Click Apply.
3. When prompted to restart the application, click Restart Now.
For a list of available ToxID reports, see “Reports” on page 41.
Quick Acquisition
The quick acquisition option activates the Quick Acquisition feature in the Acquisition,
Analysis, or Method Development mode.
Note The Quick Acquisition feature is not available when you activate Multiplexing. See
“Multiplexing” on page 66.
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 To activate quick acquisition
1. Select the Quick Acquisition (EnviroLab/ToxLab/QuanLab Forms) check box.
2. Click Apply.
3. When prompted to restart the application, click Restart Now.
For a description of the Quick Acquisition features, see “Working with Master Methods” on
page 83.
Delay Calibration Calculation
You can determine when the application calculates the calibration curve, using the Delay
Calibration Calculation... option. Delaying the recalibration until the application processes
the last calibration sample in a batch is faster but less responsive than recalibration after each
calibration sample.
 To delay calculation of a calibration curve
1. Select the Delay Calibration Calculation... check box.
2. Click Apply.
3. When prompted to restart the application, click Restart Now.
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 activate multiplexing, the application automatically activates 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 379.
Note The Batch Template Wizard is not available when you activate
Multiplexing. See Multiplexing.
2. Click Apply.
3. When prompted to restart the application, click Restart Now.
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Multiplexing
The Multiplexing options are available only when you install the Multiplexing Power Module.
See “Installing the Power Modules” on page 15.
Note Multiplexing is not available when you activate Intelligent Sequencing. See
Intelligent Sequencing.
 To specify multiplexing features
1. Select the Multiplexing check box.
2. Select 2 Channels or 4 Channels:
• For 2 channels, select a 1- or 2-arm Autosampler Arm Configuration.
The 1 arm configuration activates channels 1 and 3; the 2 arm configuration
activates channels 2 and 4.
• For 4-channels, autosampler 1 uses channels 1 and 3 and autosampler 2 uses channels
2 and 4.
3. Click Apply.
4. When prompted to restart the application, click Restart Now.
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 298) or monitor an
acquisition (see “Devices Page” on page 326).
Note When you activate multiplexing, the following optional features are not available:
• Quick Acquisition
• Batch Template Wizard
• Single Sample Submission (Intelligent Sequencing)
Intelligent Sequencing
The Intelligent Sequencing option is available only when you install the Intelligent
Sequencing Power Module. See “Installing the Power Modules” on page 15.
Use Intelligent Sequencing for single-sample submission. When you submit a batch, the
autosampler begins preparing for one sample injection at a time. Higher priority batches can
interrupt the sample sequence in the currently acquiring batch.
 To activate the intelligent sequencing feature
1. Select the Intelligent Sequencing check box.
Note Intelligent Sequencing is not available when you activate Multiplexing. See
“Multiplexing” on page 66.
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The Acquisition Submission Options default to Single Sample Submission. The Full
Sequence Submission option is not available when you select the Intelligent Sequencing
option.
2. Click Apply.
3. When prompted to restart the application, click Restart Now.
Acquisition Submission Options
To control acquisitions, you can activate 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 use Full Sequence Submission, priority batches always run immediately after
the currently acquiring batch is completed.
• When you use Single Sample Submission, priority batches always run immediately after
the currently acquiring sample is completed.
 To specify acquisition submission features
1. Select either the Full Sequence Submission or the Single Sample Submission option:
• Full Sequence Submission: Supports look-ahead features of the autosampler. When
the instrument method specifies the look-ahead feature, the Tracefinder application
functions like a multiplex driver and feeds the autosampler the next vial position.
When you submit a batch, the autosampler begins preparing for all sample injections
when the pre-run condition begins. All samples in the batch must be completed
before other batches (even higher priority batches) can begin.
Note The Full Sequence Submission feature is not available when you activate
Intelligent Sequencing.
• Single Sample Submission: Supports intelligent-sequencing features. When you
submit a batch, the autosampler begins preparing for one sample injection at a time.
Higher priority batches can interrupt the sample sequence in the currently acquiring
batch.
Note The Single Sample Submission feature is not available when you activate
Multiplexing. See “Multiplexing” on page 66.
2. Click Apply.
3. When prompted to restart the application, click Restart Now.
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Activating Optional Features
Screening Library
Use the screening library specified here for identification and confirmation when you specify
Library Manager as the Library Search Type for a method. See “Editing the General Page” on
page 107.
The application searches the screening library to identify or confirm a sample compound,
matches the fragment ion spectrum in the library to the compound’s ion spectrum, and
returns the highest score (best match).
The application performs either a forward library search or a reverse library search. A forward
search compares the mass spectrum of an unknown compound to a mass spectral library
entry, while a reverse search compares a library entry to an unknown compound.
In a target screening master method, you can specify the library search to either identify or
confirm library matches and set a score threshold to minimize poor matches. See “To specify
identification and confirmation settings” on page 216.
• Identify or Confirm: The application identifies or confirms the sample compound by
searching the specified search library and returning the highest score (as a percentage
value) for the fragment ion spectrum in that library that matches the compound’s ion
spectrum.
• Score Threshold: The resulting score from a library search match must be higher than the
threshold value to identify or confirm the presence of a compound.
IMPORTANT To use a library search for identification or confirmation, the application
requires meeting these conditions:
• The raw data file contains HCD (higher energy collision-induced dissociation), source
CID (source collision-induced dissociation), or AIF (all ions fragmentation) ion spectra.
• The spectra exist at a time point within the compound’s elution time range.
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Managing User Administration
In the User Administration view of the Application Configuration mode (when user security
is activated), in either the LabDirector or ITAdmin role, you 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 75.
 To open the User Administration view
1. Click the Application Configuration icon,
window.
, in the upper right corner of any
The Application Configuration navigation pane opens.
Available only to users in the LabDirector
or ITAdmin role
Note The User Administration option is available only when you activate user
security. Follow the instructions “To turn on user security” on page 64.
2. Click User Administration.
The User Administration view opens. See “User Administration view” on page 73.
This section includes instructions for the following tasks:
• Editing User Information
• Choosing User Roles
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Editing User Information
When user security is activated, in either the LabDirector or ITAdmin role, you can assign
each user to one of the defined roles.
Follow these procedures:
• To add a user
• To edit user information
• To change a user password
• To remove a user
For a list of all parameters in the User Administration view, see “User Administration view
parameters” on page 74.
 To add a user
1. Click the Add User icon,
.
The application activates the parameters in the User area at the bottom of the view.
2. Type a unique name in the Username box.
The user name is case insensitive.
3. Select a role from the Role list.
For detailed information about the permissions allowed for each role, see “Choosing User
Roles” on page 75.
4. Type the user’s password and type it again to confirm it.
The password is case sensitive.
Note 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 activate 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 71.
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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 of the User
Administration view.
2. Click the Edit User icon,
.
The application activates the parameter fields in the User area.
3. Edit any of the parameter values.
IMPORTANT You must have an ITAdmin or LabDirector role to access the user
administration features. If you are the only user in the ITAdmin or LabDirector role,
you cannot remove your user name, clear the Enabled check box, or change your role
to anything other than ITAdmin or LabDirector. At least one activated user must be
assigned to the ITAdmin or LabDirector role so that there is a least one user who can
access the User Administration page.
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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 application activates the fields in the User area.
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.
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 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 in to the TraceFinder application, the user’s current session
is not affected.
4. Click OK.
Note Rather than completely removing the user, you can make the user login unavailable
without removing all the user information from the system. Follow the instructions “To
edit user information” on page 71.
Figure 18. User Administration view
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Table 13. User Administration view parameters
Parameter
Description
Security Groups
All permission levels defined in the TraceFinder application. For detailed descriptions of
user permissions, see “Choosing User Roles” on page 75.
User Listing
Username
User login name.
Role
Security group that defines user permissions.
Account Number
User account number.
Phone Number
User telephone number.
Email Address
User e-mail address.
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.
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 in, 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
Activates 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
Activates 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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Choosing User Roles
This section describes the responsibilities for five different user roles when user security is
activated: LabDirector, ITAdmin, Supervisor, Technician, and QAQC.
IMPORTANT User roles are in effect only when user security is activated. When user
security is not activated, all users have access to all modes.
TraceFinder Mode Access
A user in either the LabDirector or ITAdmin role assigns you to a role that gives you access to
specific modes of the TraceFinder application. When you log in, the navigation pane displays
links to only the modes that you can access.
Table 14. User roles and mode access
User role
Method
Development
Acquisition
Analysis
Application
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 their 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
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• Creating local users and network groups
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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Managing 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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This chapter includes method development tasks assigned to the Supervisor or LabDirector
role when user security is activated.
Contents
• Working with Master Methods
• Working with the Compound Database
• Working with Instrument Methods
• Working with Development Batches
• Using Quick Acquisition
From the Method Development mode, you can create a quantitative or screening 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 in the navigation pane.
The Method Development navigation pane opens.
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For descriptions of all the features on the Method Development navigation pane for a
quantitation method, see “Method Development navigation pane for quantitation
methods.”
For descriptions of all the features on the Method Development navigation pane for a
screening method, see “Method Development navigation pane for screening methods” on
page 82.
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Figure 19. Method Development navigation pane for quantitation methods
Available only when you select the Acquisition Batch Wizard
as your wizard style in the Application Configuration mode.
Table 15. Method Development navigation pane commands for quantitation methods
Command
Description
Method View
Displays the Method View for the master method. See “Working with Master Methods” on
page 83.
General
Displays the General page of the Method View. See “Editing the General Page” on page 107.
Compounds
Displays the Compounds page of the Method View. See “Editing the Compounds Page” on
page 114.
QAQC
Displays the QAQC page of the Method View. See “Editing the QAQC Page” on page 174.
Groups
Displays the Groups page of the Method View. See “Editing the Groups Page” on page 183.
Intel Seq
Displays the Intelligent Sequencing page of the Method View. See “Editing the Intelligent
Sequencing Page” on page 185.
Reports
Displays the Reports page of the Method View. See “Editing the Reports Page” on page 189.
Compound
Database
See “Working with the Compound Database” on page 239.
Instrument View
See “Working with Instrument Methods” on page 269.
Development Batch
See “Working with Development Batches” on page 275.
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Figure 20. Method Development navigation pane for screening methods
Available only when you select the Acquisition Batch Wizard
as your wizard style in the Application Configuration mode.
Table 16. Method Development navigation pane commands for screening methods
Command
Description
Method View
Displays the Method View for the master method. See “Working with Master Methods” on
page 83.
General
Displays the General page of the Method View. See “Editing the General Page” on
page 107.
Reports
Displays the Reports page of the Method View. See “Editing the Reports Page” on page 189.
Screening
Displays the Screening page of the Method View. See “Editing the Screening Page” on
page 212
Peak Detection
Displays the Peak Detection page of the Method View. See “Editing the Peak Detection
Page” on page 221
Compound Database
See “Working with the Compound Database” on page 239.
Instrument View
See “Working with Instrument Methods” on page 269.
Development Batch
See “Working with Development Batches” on page 275.
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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 quantitation master method contains a list of compounds and settings for detecting,
processing, and reporting those compounds.
A target screening master method contains compound databases, identification and
confirmation criteria used in detecting and processing, and settings for reporting 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 scans.
This section includes instructions for the following tasks:
• Creating a New Master Method
• Editing a Quantitation Master Method
• Editing a Target Screening Master Method
• Creating a Method Template
• Importing Published Master Methods
• Exporting SRM Data
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Creating a New Master Method
Use any of the following procedures to start a method in the specific way indicated. Then, use
the common features of the Method View to complete and save it as a master method.
Choose File > New > Master Method from the main menu.
The Create Master Method dialog box opens.
Select from five different procedures (or techniques) in the Create Master Method dialog box:
• Creating a New Method with Method Forge
• Importing an Xcalibur Master Method
• Creating a Blank Quantitation Method
• Selecting Compounds from the Compound Database
• Creating a Screening Method
Figure 21. Create Master Method dialog box
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Creating a New Method with Method Forge
With Method Forge, you can create a new master method by manually selecting peaks,
selecting multiple compounds, renaming peaks, or comparing mass spectra from the library
searches. You can also choose to let the TraceFinder application automatically create a master
method for you. For detailed descriptions of all the Method Forge parameters, see “Method
Forge dialog box parameters” on page 93.
When the TraceFinder application automatically creates a master method for you, it performs
the following functions:
• Reviews your raw data file and identifies compounds that are present in your sample.
• Uses your mass spectral reference libraries to assign compound names and CAS numbers.
• Uses mass spectral information to select potential quantification and confirming ions and
a reference mass spectrum for the compound.
Note When the identified peak is from an analog trace, the application does not perform
a library search and does not identify any confirming ions.
Follow these procedures:
• To automatically select compounds to create a new method
• To manually select compounds to create a new method
 To automatically select compounds to create a new method
1. From the File menu, choose New > Master Method.
The Create Master Method dialog box opens. To view all available ways to create a master
method, see “Create Master Method dialog box” on page 84.
2. Select the Use Method Forge option and click OK.
The Method Forge dialog box opens. For detailed descriptions of all the features on the
Method Forge dialog box, see “Method Forge dialog box” on page 93.
Use Method Forge to create a master method from an existing raw data file or to create a
new raw data file to use for the master method.
Each method requires a processing method template. The application displays all saved
method templates in the template list.
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3. To select a processing method template, do one of the following:
• Click Open Method Template Editor to create and save a new method template.
See “Creating a Method Template” on page 224.
• Select a method template from the template list, and click Open Method Template
Editor to edit and save the method template.
• Select a method template from the template list.
The selected template is now selected by default each time you open the Method Forge
dialog box until you restart the TraceFinder application. To view the parameters for each
available method template, hold your cursor over the template name.
Figure 22. Example method template parameters
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4. Select the Name the Master Method check box and type a name for your master method.
You can enter a new method name, or you can enter an existing method name to
overwrite when you create the method. If you do not select this option, the method is
named for the raw data file used to create the method.
IMPORTANT When the Name the Master Method check box is selected, you must
enter a method name. To let the application name the method with the raw data file
name, clear the Name the Master Method check box.
5. 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. To acquire a new raw data file, do one of the following:
Select Manual Injection.
–or–
Specify the autosampler settings:
a. Select Use Autosampler.
b. In the Vial Position box, type a vial position.
c. In the Injection Volume box, type an injection volume.
Range: 0.1 to 2000 μL
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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 bars:
• For analog peaks, the Method Forge displays the detected peak as [email protected](RT)Analog.
The Method Forge does not perform a library search for peaks found in analog traces.
• For mass spectral peaks, the Method Forge process searches the associated libraries
and displays the identified compound names instead of the peak times.
When the acquisition is completed, Method Forge performs peak detection, library
searching (except for analog peaks), and identification of characteristic ion and reference
spectra. Method Forge then loads this information into a new master method. This
process occurs immediately if you selected a previously acquired raw data file.
9. From the Instrument Method list, select an instrument method.
10. From the Qualitative Peak Processing Template list, select a method template for
performing peak detection on quantitative samples following target compound analysis.
11. 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.
12. To save the new method, choose File > Save from the main menu.
For a detailed description of how to modify all the parameters in a master method, see
“Editing a Quantitation Master Method” on page 106.
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 To manually select compounds to create a new method
1. From the File menu, choose New > Master Method.
The Create Master Method dialog box opens. See “Create Master Method dialog box” on
page 84.
2. Select the Use Method Forge option and click OK.
The Method Forge dialog box opens. For detailed descriptions of all the features on the
Method Forge dialog box, see “Importing an Xcalibur Master Method” on page 95.
Each method requires a qualitative peak processing template. The application displays all
saved method templates in the template list.
3. To select a qualitative peak processing template, do one of the following:
• Click Open Method Template Editor to create and save a new method template.
See “Creating a Method Template” on page 224.
• Select a method template from the template list, and click Open Method Template
Editor to edit and save the method template. The application saves the methods to
the following folder:
C:\Thermo\TraceFinder\3.0\Forensic\Templates\Methods
• Select a method template from the template list.
The selected template is now selected by default each time you open the Method Forge
dialog box until you restart the TraceFinder application.
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To view the parameters for each available method template, hold your cursor over the
template name. For example:
4. Select the Name the Master Method check box and type a name for your master method.
You can enter a new method name, or you can enter an existing method name and
overwrite it when you create the method. If you do not select this option, the method is
named for the raw data file used to create the method.
IMPORTANT When the Name the Master Method check box is selected, you must
enter a method name. To let the application name the method with the raw data file
name, clear the Name the Master Method check box.
5. Ensure that the Automatically Create the Master Method check box is cleared.
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6. To select a raw data file, browse to the file location.
7. To manually create the master method, click OK (or Overwrite).
The method forge results view opens, listing all peaks found in the raw data file.
For each peak listed in the RT column, the application displays a list of possible matches
in the Libraries pane. The TraceFinder application selects the best match, displays the
name in the Compound Name list, and displays the peak spectrum for that compound in
the first Libraries pane.
Best match compound spectra
Peaks found in raw data file
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8. (Optional) To use a library compound other than the compound chosen by the
TraceFinder application, do the following:
a. Select the peak in the RT column.
b. In the Libraries pane, scroll to the spectrum for the compound that you want to use.
c. Select the check box in the header of the spectrum pane.
Selected
compound
d. Repeat these steps for each peak that you want to replace.
9. In the Compound Name list, use the CTRL or SHIFT keys to select each compound that
you want to include in the method compound.
Note When you select multiple compounds, the method forge results view does not
display any spectrum panes.
10. (Optional) To exit the method forge results view without creating a method, click
Cancel.
The method forge results view closes and the application returns to the Method View
without creating a method.
Note To return to the method forge results view to create a method from the same
results, choose Method View > View Method Forge Results from the main menu.
11. Click Create.
The TraceFinder application uses all selected compounds to create the method and
displays the General page of the Method View. For detailed descriptions of all the features
on the General page, see “General page for a quantitation method” on page 111.
Note To return to the method forge results view, choose Method View > View
Method Forge Results from the main menu.
12. From the Instrument Method list, select an instrument method.
13. To save the new method, choose File > Save from the main menu.
For a detailed description of how to modify a master method, see “Editing a Quantitation
Master Method” on page 106.
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Figure 23. Method Forge dialog box
Table 17. Method Forge dialog box parameters (Sheet 1 of 2)
Parameter
Description
Method template selection
Open Method
Template Editor
Opens the Method Template Editor, where you can edit the currently selected method
template. See “Creating a Method Template” on page 224.
Template
Method template to use to create this master method. All methods require a method
template. To view the parameters of each template, hold your cursor over the method name.
See “Example method template parameters” on page 86.
Name the Master
Method
The name for the new master method. If you do not specify a method name, the application
uses the raw data file name for the method.
Automatically Create
the Master Method
When the acquisition is completed, Method Forge performs peak detection, library
searching, and identification of characteristic ion and reference spectra. This information is
loaded into a new master method. This process occurs immediately when you specify an
existing raw data file.
Raw file selection
Use an Existing Raw
Data File
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Activates the Raw Filename box where you can select a raw data file used in creating the
master method.
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Table 17. Method Forge dialog box parameters (Sheet 2 of 2)
Parameter
Description
Acquire a New Raw
Data File
Activates functions to acquire data to create a raw data file used in creating the master
method.
Instrument
Method
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) A 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.
Check Instruments
Opens the Submit to Acquisition dialog box that prompts you to prepare the instrument
before you acquire the sample used to create a method. Available only when you select the
Acquire a New Raw Data File option.
Function button
Overwrite
Overwrites the specified master method name. This function is activated only when the
specified master method name already exists.
OK
Creates a master method using the data and parameters that you specified.
Cancel
Closes Method Forge and does not create a master method.
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Importing an Xcalibur Master Method
You can create a new master method from an existing Xcalibur processing method.
 To import an Xcalibur master method
1. Choose File > New > Master Method from the main menu.
The Create Master Method dialog box opens. To view all available ways to create a master
method, see “Create Master Method dialog box” on page 84.
2. Select the Import Xcalibur Processing Method option and click OK.
The Import an Xcalibur Method dialog box opens.
3. For the Xcalibur Method to Import box, browse to the location of the Xcalibur processing
method file, and open the file.
The TraceFinder application imports the compound information from the Xcalibur
method file.
4. (Optional) For the Raw Data File to Associate box, browse to the location of a raw data
file to associate with the method (or select from the list of previously associated raw data
files), and open the file.
To assure that this raw data file is always available to the method (for example, if you
move the method to another system), the application saves the raw data file in the method
folder:
C:\Thermo\TraceFinder\3.0\Forensic\Methods\MethodName
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5. (Optional) Change the number of decimal places in the Filter Precision box.
You can set the number of filter precision decimal places to any integer between 2 and 5,
inclusive.
Note When you select a raw data file to associate, the application reads the filter
precision from the file and this feature is not available.
6. (Optional) Change the number of decimal places in the Mass Precision box.
You can set the number of mass precision decimal places to any integer between 2 and 6,
inclusive.
Note When you associate a raw data file, the application reads the filter precision
from the associated file so that you cannot change the Filter Precision value.
7. Click OK.
The TraceFinder application adds all compounds found in the imported Xcalibur method
and displays the General page of the Method View. For detailed descriptions of the
features on the General page, see “General page for a quantitation method” on page 111.
8. From the Instrument Method list, select an instrument method.
9. To save the new method, choose File > Save from the main menu.
For a detailed description of how to modify a master method, see “Editing a Quantitation
Master Method” on page 106.
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Creating a Blank Quantitation Method
You can use the compounds in a previously acquired raw data file to create a new quantitation
master method.
 To create a blank quantitation method
1. From the File menu, choose New > Master Method.
The Create Master Method dialog box opens. To view all available ways to create a master
method, see “Create Master Method dialog box” on page 84.
2. Select the Create Blank Quantitation Method option and click OK.
The Method View for a new, unnamed method opens. This method has no associated
data. You can use the compounds in a previously acquired raw data file to create a new
quantitation master method.
3. From the Method View menu, choose Associate a Raw Data File.
The Associate a Raw Data File dialog box opens.
Browse to a data file
Select a previously associated data file
4. Browse to a raw data file to associate with the method (or select from the list of previously
associated raw data files) and open the file.
To assure that this raw data file is always available to the method (for example, if you
move the method to another system), the application saves the raw data file in the method
folder:
C:\Thermo\TraceFinder\3.0\Forensic\Methods
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5. Select the update options to use for creating your method:
• Update Instrument/Trace Selections: Reads the Detector and Trace options from
the associated raw data file. On the Detection page, only detector types and traces
that are defined in the raw data file are available. For detailed descriptions of the
available Detector and Trace values, see “Signal” on page 135.
• Update Target Ion Ratio Values: Reads the ion ratio values from the associated raw
data file.
• Update Scan Filters for All Peaks: Updates all peaks with scan filters from the
associated raw data file.
• Automatically Set Reference Spectrum: Reads a reference spectrum from the
associated raw data file.
When you also select Yes, with Background Subtraction, the application uses the
background subtraction range specified on the General page. See “Editing the
General Page” on page 107.
Options that are set to No use the standard values in the method.
6. Click OK.
The TraceFinder application displays the General page of the Method View.
7. Select a qualitative peak processing template from the list.
The application uses the libraries in this template to identify compounds for the method.
If there is no library selected in the method template, found peaks are identified as
[email protected] on the Compounds page.
To specify the libraries in the qualitative peak processing template, open the template in
the Method Template Editor, and then follow the instructions “To identify the peaks” on
page 226.
8. Click Compounds in the navigation pane.
The method must include at least one compound.
9. Click the Detection tab.
The Detection page shows an empty Compound list and displays the chromatographic
data for the compounds in the raw data file.
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10. Select a filter from the Filter list.
11. Select the peak in the chromatogram that represents the compound that you want to add
to the method.
12. Right-click and choose Add This Peak as New Compound from the shortcut menu.
The TraceFinder application performs a library search for the selected compound. The
application uses the first match it finds as the compound name, the base peak of the mass
spectrum as the quantitative peak, and the second and third largest ions as the confirming
ion peaks.
Note When the peak is from an analog trace, the application does not perform a
library search and does not identify any confirming ions.
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If the name of the first match is already in the library, the Add New Compound dialog
box opens.
13. (Optional) Do the following:
a. To use a compound other than the compound already in the library, scroll to the
spectrum for that compound and select the compound name in the title bar of the
spectrum pane.
Selected
compound
b. In the Type of Compound To Add list, select a compound type.
c. Click OK.
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14. Repeat this procedure for each compound that you want to add to the method.
For detailed descriptions of all the features on the Detection page, see “Editing the
Compounds Page” on page 114.
15. Click General in the navigation pane.
The General page for the method opens. For detailed descriptions of all the features on
the General page, see “General page for a quantitation method” on page 111.
16. From the Instrument Method list, select an instrument method.
17. To save the new method, choose File > Save from the main menu and name the method.
For a detailed description of how to modify the parameters in a master method, see
“Editing a Quantitation Master Method” on page 106.
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Selecting Compounds from the Compound Database
You can select compounds from the compound database to create a new master method.
 To select compounds form the compound database
1. Choose File > New > Master Method from the main menu.
The Create Master Method dialog box opens. To view all available ways to create a master
method, see “Create Master Method dialog box” on page 84.
2. Select the Select Compounds from CDB option and click OK.
The Select Compounds from Database dialog box opens, listing all the compounds
defined in the compound database.
3. Select the check box for each of the compounds that you want to add to the method.
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4. To select all compounds in the database, select the Compound check box at the top of
the list.
5. Click Apply.
The TraceFinder application adds the selected compounds to the method.
6. Click General in the navigation pane.
The General page for the method opens. For detailed descriptions of all the features on
the General page, see “General page for a quantitation method” on page 111.
7. From the Instrument Method list, select an instrument method.
8. To save the new method, choose File > Save from the main menu and name the method.
For a detailed description of how to modify a master method, see “Editing a Quantitation
Master Method” on page 106.
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Creating a Screening Method
You can create a new master method specifically for target screening.
 To create a target screening method
1. Choose File > New > Master Method from the main menu.
The Create Master Method dialog box opens. To view all available ways to create a master
method, see “Create Master Method dialog box” on page 84.
2. Select the Create Screening Method option and click OK.
The Method View for a target screening method includes General, Reports, Screening,
and Peak Detection pages.
These instructions demonstrate the minimum parameters you must define to create and
save a screening master method. For a detailed description of how to modify all
parameters in a screening master method, see “Editing a Target Screening Master
Method” on page 202.
The General page for the screening method opens.
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3. From the Instrument Method list, select an instrument method.
4. Click Screening in the Method View navigation pane.
The Screening page for the screening method opens.
The Target Screening Settings pane displays the compound databases stored in the
following folder:
C:\Thermo\TraceFinder\3.0\Forensic\Databases
5. Select the Enabled check box for at least one compound database.
You must select at least one compound database before you can save the method.
6. To save the new method, choose File > Save from the main menu.
7. In the Save Master Method dialog box, type a name for the method and click OK.
For a detailed description of how to modify a master method, see “Editing a Target
Screening Master Method” on page 202.
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Editing a Quantitation 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 Quantitation Master Method
• Editing the General Page
• Editing the Compounds Page
• Editing the QAQC Page
• Editing the Groups Page
• Editing the Intelligent Sequencing Page
• Editing the Reports Page
Opening a Quantitation Master Method
Use the TraceFinder application to open a master method that was created and saved in the
current TraceFinder application or converted from these legacy applications: previous versions
of TraceFinder, EnviroLab Forms, QuanLab Forms, or ToxLab Forms. To convert legacy
methods, see “Converting Legacy Data” on page 21.
 To open a saved master method
1. Click Method Development from the navigation pane.
2. Choose File > Open > Master Method from the main menu.
The Open Master Method dialog box opens, displaying all available methods.
Tip You can also open one of your most recently used master method files. Choose
Files > Recent Files > MethodName.
3. Select a master method and click Open.
The General page for the selected method opens. For detailed descriptions of all the
features on the General page, see “General page parameters” on page 111.
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Editing the General Page
The General page defines basic information about the master method. For detailed
descriptions of all the features, see “General page parameters” on page 111.
Follow these procedures:
• To open the General page
• To specify general information for a master method
• To edit an instrument method
• To select a qualitative peak processing template
• To set automated background subtraction options
• To specify mass tolerance
• To include data-dependent filters
• To enter a note for the method
 To open the General page
Click General in the Method View navigation pane.
Available only when you activate
Intelligent Sequencing in
the Application Configuration mode.
 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 an injection volume (between 0.1 and 2000 μL) to
be used for sample injection.
Use the up/down arrows to change the volume in increments/decrements of 1 μL, or use
the keyboard to enter non-integer injection volumes.
IMPORTANT The TraceFinder application uses this injection volume in the master
method, not the injection volume from the instrument method.
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4. From the Mass Precision box, select a precision value (between 2 and 6 inclusive) as the
number of decimal places to be used in reports and in peak and spectrum displays.
5. From the Ion Range Calc Method list, select a method for calculating the ion ratio range
windows.
When you select Level, the TraceFinder application displays a Use Level list where you
can choose a calibration level. To define the available calibration levels on the
Compounds page, see “Editing the Compounds Page” on page 114.
 To edit an instrument method
1. From the Instrument Method list on the General page, select an instrument method.
2. To edit the selected instrument method, click Edit.
The Thermo Xcalibur Instrument Setup dialog box opens. This example of an
instrument setup showing multiple configured instruments.
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3. Edit the values on the instrument page for your instrument.
4. From the main menu in the Thermo Xcalibur Instrument Setup dialog box,
choose File > Save and then choose File > Exit.
The TraceFinder application returns you to the General page. See “General page for a
quantitation method” on page 111.
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 that you want to use
to perform peak detection on quantitative samples after compound analysis is complete.
The application lists all method templates (.pmtx files) in the following folder:
C:\Thermo\TraceFinder\3.0\Forensic\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:
• None: Subtracts no scans.
• Before Peak: Averages and subtracts a specified number of scans before the apex of
the peak.
• After Peak: Subtracts a specified number of scans after the apex of the peak.
• Both Sides of Peak: Subtracts a specified number of scans from each side of the apex
of the peak.
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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 selected the Both Sides of Peak option, the application
subtracts this number of scans from each side of the peak.
3. In the Stepoff Value box, enter a number.
The TraceFinder application uses this offset value to average and subtract scans that are
not adjacent to the apex of the peak. For example:
If you entered 3 in the Number of Scans To Subtract box and the stepoff value is 5, the
TraceFinder application ignores the first 5 scans to the left of the peak and applies the
averaging and subtraction to the 6th, 7th, and 8th scans to the left of the peak.
 To specify mass tolerance
1. Select the units of measure that you want to use.
2. Specify the number of millimass units or parts per million to use as the m/z ± tolerance
value.
The application applies this mass tolerance to the extracted chromatograms.
 To include data-dependent filters
Select the Include Data Dependent Filters option.
The application includes data-dependent filters when you specify filters in the method.
See “Signal” on page 135.
Data-dependent filters are indicated with a “d”.
Data-dependent filter
When you process a sample using a data-dependent filter, the application uses the TIC
trace to find all data-dependent full scans, lists them, and performs a library search against
the data-dependent MS/MS or MSn scan.
 To 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 explain what makes this method unique.
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Figure 24. General page for a quantitation method
Table 18. 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 Application Defaults” on page 44.
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 18. 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 to 2000 μL
Mass Precision
Number of decimal places used in reports and in peak and spectrum displays.
Valid values: Integers from 2 to 6, inclusive.
Ion Range Calc
Method
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 114.
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.
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Table 18. 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.
Include Data
Dependent Filters
Available only for quantitation methods.
Notes
Optional notes about the method.
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Editing the Compounds Page
Use the Compounds page to set all parameters used to identify, detect, and quantify the target
compound list.
 To open the Compounds page
Click Compounds in the Method View navigation pane.
Available only when you activate
Intelligent Sequencing in
the Application Configuration mode.
From the Compounds page of the Method View, you can access the following pages:
Acquisition List
See also Acquisition List.
Identification
See also “Identification page parameters” on page 117.
Detection
See also “Detection page panes” on page 132.
Calibration
See also “Calibration page parameters” on page 165.
Calibration Levels
See also “Calibration levels page parameters” on page 167.
QC Levels
See also “QC levels page parameters” on page 169.
Real Time Viewer
See also “Real Time Viewer page parameters” on page 170.
Each page on the Compounds page (except the Acquisition List and Real Time Viewer pages)
uses a right-click shortcut menu. See “Using the Shortcut Menu Commands” on page 172.
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Acquisition List
The Acquisition List page displays all compounds defined for the current method in a display
similar to the Compound Database view. From the Acquisition List page, you can add
additional compounds from the Compound Database or delete compounds from the method.
For detailed descriptions of all the features on the Compound Database view, see “Compound
Database view parameters” on page 246.
 To remove a compound from the method
1. Select the compound in the Compound list.
2. Click the Remove Compound icon,
.
3. If you are sure you want to delete the selected compound, at the prompt, click OK.
The application removes the selected compound and all its peak information.
4. To remove multiple compounds, use the CTRL or SHIFT keys.
The application confirms that you want to remove the selected compounds.
 To add a compound to the method
1. Click the Add Compound from Compound Database icon,
.
The Select Compounds from Database dialog box opens, listing all the compounds
defined in the compound database. This dialog box is identical to the Compound
Database with the exception that you cannot edit the compound data from here; you can
only choose which compounds you want to include in your method.
Figure 25. Select Compounds from Database dialog box
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2. Select the compounds to add to the method.
You can use the SHIFT or CTRL keys to select multiple compounds.
3. Click Add Selected Compounds to Method.
The TraceFinder application adds the selected compounds to the acquisition list for the
method.
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Identification
The Identification page lists the compounds that are targeted for analysis, reporting, and other
compound-specific values. For descriptions of all values on the Identification page, see
“Identification page.”
 To filter the displayed compounds
From the Show list, select the type of compounds that you want to display in the
compounds list.
Compound type
Description
Quan Compounds
Displays only quantitation compounds, such as target
compounds and internal standards.
Target Compounds
Displays only target compounds.
Internal Standards
Displays only internal standard compounds.
Figure 26. Identification page
Table 19. Identification page parameters (Sheet 1 of 2)
Parameter
Description
RT
Retention time. The time after injection when the compound elutes. The total time that the
compound is retained on the column.
The TraceFinder application uses the RT and Window values to determine the start and
stop time for the acquisition.
Range: 0.00 to 999.00
Start time = RT – (Window/2)
Stop time = RT + (Window/2)
Start and stop range: 0.00 to 999.00
Compound
A list of identified compounds. To customize the compound names, click the cell and type a
new name. To display a filtered list of compounds, use the Show list.
Compound Type
Compound types are Target Compound and Internal Standard. The TraceFinder
application uses target compounds and internal standards in quantitative analysis.
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Table 19. Identification page parameters (Sheet 2 of 2)
Parameter
Description
Active
Identifies each compound to be included in data review and reporting. By default, all added
compounds are set to active. This active or inactive setting populates the Batch View and
Data Review view in the Analysis mode.
CAS No
The Chemical Abstract Service (CAS) number that the TraceFinder application matched
with each compound. To change or add a number, click the CAS No cell and enter a new
number.
Use as RT Reference
When performing peak detection with retention time standards, the TraceFinder
application first identifies those compounds identified as retention time standards and then
uses their observed retention times to adjust any associated target compound.
Reference Compound
To be used for retention time adjustment for a compound. This list includes all compounds
that are selected in the Use as RT Reference column.
Shortcut menu
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The Identification page uses a right-click shortcut menu. See “Using the Shortcut Menu
Commands” on page 172.
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Detection
Use the Detection page to customize peak detection and integration for any ions that define
peaks and compounds.
From the Detection page, you can access the following pages:
Times
See also “Times page parameters” on page 133.
Signal
See also “Signal page parameters” on page 141.
Detect
See also “Detect page parameters for Genesis” on page 146.
See also “Detect page parameters for ICIS” on page 150.
See also “Detect page parameters for Avalon” on page 152.
Suitability
See also “System Suitability dialog box” on page 156.
Spectrum
See also “Spectrum page shortcut menu commands” on page 161.
Ratios
See also “Ratios page parameters” on page 163.
On the Detection page (see “Detection page” on page 131), you can configure how
characteristic ions for targeted compounds are detected and integrated. You can also edit the
list of characteristic ions for a specific compound. Refining these parameters in the master
method for each compound and its ions can reduce the degree of manual integration that
would otherwise be required.
You can change the parameters used to identify a quantitative peak, mass range, or confirming
ion peak. The TraceFinder application automatically uses the first match it finds as the
compound name, the base peak of the mass spectrum as the quantitative peak, and the second
and third largest ions as the confirming ion peaks.
Follow these procedures:
• To filter the displayed compounds
• To change the displayed information for detected peaks
• To add compounds to the method
• To change the compound reference spectrum
• To replace a quantitation mass
• To add a mass to the existing quantitation mass ranges
• To add a quantitative peak
• To add a spectral peak as a new compound
• To replace a quantitative peak with a confirming ion peak
• To set a confirming ion peak as an additional quantitative peak
• To add a trace to the Real Time Status pane
• To replace a confirming ion peak
• To add a mass as a new confirming ion peak
• To use the cut-and-paste feature on confirming ion peaks
• To save the new method
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 To filter the displayed compounds
From the Show list, select the type of compounds that you want to display in the
compounds list.
Compound type
Description
Quan Compounds
Displays only quantitation compounds, such as target
compounds, internal standards, and surrogates.
Target Compounds
Displays only target compounds.
Internal Standards
Displays only internal standard compounds.
 To change the displayed information for detected peaks
1. Right-click the chromatogram plot for any of the quan or confirming peaks and hold the
cursor over Peak Labels.
2. Choose to display labels for the peak area, peak retention time, peak height, or signal to
noise.
3. To remove a label, select the label type again and clear it.
The application globally applies these label settings to all quantitative peaks, confirming
peaks, and internal standard peaks in the method.
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 To add compounds to the method
Tip You can add compounds from the current raw data file (begin at step 7), or you
can associate another raw data file and add compounds from that file (begin at step 1).
1. From the main menu, choose Method View > Associate a Raw Data File.
The Associate a Raw Data File dialog box opens.
Browse to a data file.
Select a previously associated data file.
2. Browse to a raw data file to associate with the method (or click the arrow and select from
the list of previously associated raw data files) and open the file.
To assure that this raw data file is always available to the method (for example, if you
move the method to another system), the application saves the raw data file in the method
folder:
C:\Thermo\TraceFinder\3.0\Forensic\Methods
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 Method View. See “Editing the General Page” on page 107.
6. Click OK.
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The TraceFinder application displays the chromatographic and spectrum data for the
compounds in the associated raw data file.
IMPORTANT While the spectra pane displays the associated raw data file, you cannot
display peak information for an original compound in the Compound list. You can
display peak information only for compounds in the associated raw data file. To
return the display functionality for all compounds in the method, save the method.
7. Select a filter from the Filter list.
8. Click to select the peak in the chromatogram that represents the compound that you
want to add to the method.
9. Right-click and choose Add This Peak as New Compound from the shortcut menu.
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The TraceFinder application performs a library search for the selected compound. The
application uses the first match it finds as the compound name, the base peak of the mass
spectrum as the quantitative peak, and the second and third largest ions as the confirming
ion peaks.
• When the name of the first match does not exist in the method, the application adds this
compound to the method and displays the name in the Compound list. You can now
view and edit the parameters for this compound.
• When the name of the first match is already in the method, the Add New Compound
dialog box opens. You cannot overwrite a compound name in the method. If the selected
peak already exists in the method, you must give it a new name to add it to the method.
Or, you can select a different compound to add to the method, following step 10 through
12.
Figure 27. Add New Compound dialog box
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10. Do one of the following:
• Type a new name for the first matched compound.
The application displays a red warning when the selected compound name already
exists in the method. You cannot overwrite the compound name, and you cannot
create a duplicate name in the method. You must type a unique name.
–or–
• To use a compound other than the first matched compound, scroll to the spectrum
for that compound and select its corresponding check box in the title bar of the
spectrum pane.
Selected
compound
11. In the Type of Compound To Add list, select a compound type.
12. Click OK.
 To change the compound reference spectrum
1. In the chromatogram pane, click a peak.
The TraceFinder application displays the spectrum for the selected peak in the spectrum
pane.
2. In the spectrum pane, right-click and choose Use This Spectrum for Compound
Reference Spectrum from the shortcut menu.
The TraceFinder application replaces the spectrum on the Spectrum page of the
quantitative peak pane with this spectrum.
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 To replace a quantitation mass
1. Click the data pane for the quantitation mass that you want to replace.
2. In the spectrum pane, hold the cursor over a peak.
The red box indicates the selected peak.
3. Right-click and choose Set This Spectral Peak as Quan Value from the shortcut menu.
4. Choose either Don’t Update Ion Ratios or Update Ion Ratios Using This Spectrum.
You can see the updated ion ratios on the Ratios page for the confirming ion peaks. See
“Ratios” on page 162.
 To add a mass to the existing quantitation mass ranges
1. In the spectrum pane, hold the cursor over a peak.
The red box indicates the selected peak.
2. Right-click and choose Add This Spectral Peak to Existing Quan Ranges from the
shortcut menu.
3. Choose either Don’t Update Ion Ratios or Update Ion Ratios Using This Spectrum.
The TraceFinder application adds the selected mass to the existing quantitation mass
ranges to increase the signal.
If you chose to update the ion ratios, you can see the updated ion ratios on the Ratios
page for the confirming ion peaks. See “Ratios” on page 162.
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 To add a quantitative peak
1. In the spectrum pane, hold the cursor over a peak.
The red box indicates the selected peak.
2. Right-click and choose Add This Spectral Peak as New Quan Peak from the shortcut
menu.
The application adds a new quantitative peak to the compound.
You can use the shortcut menu in the spectrum pane for this new quantitative peak to
perform any of the tasks that you would perform on the original quantitative peak.
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 To add a spectral peak as a new compound
1. In the raw data file spectrum pane, hold the cursor over a peak.
The red box indicates the selected peak.
2. Right-click and choose Add This Spectral Peak as New Compound from the shortcut
menu.
The TraceFinder application performs a library search for the selected compound. The
application uses the first match it finds as the compound name, the base peak of the mass
spectrum as the quantitative peak, and the second and third largest ions as the confirming
ion peaks.
When there are multiple matches, the Add New Compound dialog box opens. If the
name of the first match is already in the library, the dialog box opens with the matching
compound selected.
Figure 28. Add New Compound dialog box
3. (Optional) Make any of the following changes:
• Change the name for the compound in the Name of New Compound box.
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• Use a compound other than the compound chosen by the TraceFinder application by
scrolling to the spectrum for that compound and selecting the compound name in
the title bar of the spectrum pane.
Selected
compound
• In the Type of Compound To Add list, select a compound type.
4. Click OK.
 To replace a quantitative peak with a confirming ion peak
1. When you have multiple quantitative peaks, select the quantitative peak that you want to
replace.
2. Right-click the header bar for the confirming ion peak that you want to use as the
quantitative peak, and choose Swap with Quan Peak from the shortcut menu.
The application swaps the quantitative peak and the confirming ion peak. The
application replaces all information for the quantitative peak with information for the
confirming ion. This includes the expected retention time that the confirming ion
inherited from the original quantitative peak. The original quantitative peak replaces the
confirming ion peak. The application recalculates the ratios for all confirming ion peaks.
 To set a confirming ion peak as an additional quantitative peak
Right-click the header bar for the confirming ion peak and choose Promote to Separate
Quan Peak from the shortcut menu.
The application creates a new quantitative peak, using information from the confirming
ion peak. This includes the expected retention time that the confirming ion peak
inherited from the original quantitative peak. The application removes all references to
the confirming ion peak from the method.
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 To add a trace to the Real Time Status pane
Right-click the header bar for the quantitative peak or confirming ion peak that you want
to add to the Real Time Status pane and choose Display in Real Time Viewer from the
shortcut menu.
The application moves the peak to the Traces To Display in Real Time Viewer pane on
the Real Time Viewer page. See “Real Time Viewer” on page 170.
Trace m/z 465.36 added
to Real Time Viewer
When you acquire samples with this method, the application displays the m/z 311.09
trace in addition to the TIC in the Real Time Status pane.
Trace m/z 311.09 added to
Real Time Status display
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 To replace a confirming ion peak
1. Click the pane for the confirming ion peak that you want to replace.
2. In the raw data file spectrum pane, hold the cursor over a peak.
The red box indicates the selected peak.
3. Right-click and choose Set This Spectral Peak as Confirming from the shortcut menu.
The TraceFinder application replaces the confirming ion peak with the selected mass.
 To add a mass as a new confirming ion peak
1. In the spectrum pane, hold the cursor over a peak.
The red box indicates the selected peak.
2. Right-click and choose Add This Spectral Peak as New Confirming from the shortcut
menu.
The TraceFinder application adds the confirming ion peak to the quantitative peak.
You can use the shortcut menu in the spectrum pane for this new confirming ion peak to
perform any of the tasks that you would perform on the original confirming ion peaks.
 To use the cut-and-paste feature on confirming ion peaks
1. Right-click the header bar for the confirming ion peak that you want to remove and
choose Cut Confirming Peak from the shortcut menu.
2. Right-click the header bar for the confirming ion peak that you want to replace and
choose Paste Confirming Peak from the shortcut menu.
The application pastes the confirming ion peak that you removed. You can paste a deleted
peak back to the quantitative peak from which it was removed, or you can paste the
confirming ion peak that was deleted to another quantitative peak for this compound.
 To save the new method
1. Choose File > Save.
The Save Master Method dialog box opens.
2. Type a new name for the master method and click OK, or select a method name to
overwrite and click Overwrite.
The TraceFinder application saves the new method data in the following folder:
…\Thermo\TraceFinder\3.0\Forensic\Methods
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Figure 29. Detection page
Selected compound data
Chromatogram pane
Spectrum pane
Selected compound
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Table 20. Detection page panes
Pane
Description
Compound
Lists all compounds in the master method. The Compound list uses a right-click shortcut
menu. See “Using the Shortcut Menu Commands” on page 172.
QuanPeakn
Displays a chromatogram for the quantitative peak and its confirming ion peaks. The
quantitative peak and confirming peak panes include additional pages for retention time,
signal, detection, spectrum, and ratio parameters for the selected compound.
Trace
Displays a combination of the Detector and Trace values used for the raw data file.
Do not confuse this Trace parameter with the Trace parameter on the Signal page. This
Trace parameter combines both the Detector and Trace values specified on the Signal page.
See “Signal page for a mass spectrometer detector” on page 140.
Note When you select a detector option other than MS or PDA, the spectrum pane
reports “Not Available.”
Filter
Displays the filter used for the raw data file. Available only when you set the Trace parameter
to MS.
Reference
Chromatogram
and
Spectra
Displays a reference chromatogram and spectra for the raw data file.
When you view an analog trace, there is no spectra display. To close the spectra pane and use
the full width to display the chromatogram, click
.
Additional pages
Times
Defines the retention time and window for a quantitative peak.
See “Times” on page 133.
Signal
Defines the detector and detection parameters used to display each chromatogram trace. See
“Signal” on page 135.
Detect
Defines the peak detection algorithm and its options.
See “Detect” on page 144.
Spectrum
Defines a reference mass spectrum for a quantitative peak or compound. See “Spectrum” on
page 157.
Ratios
Defines the criteria for evaluating, confirming, or qualifying ions. See “Ratios” on page 162.
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Times
Use the Times page to define the expected retention time or a retention time range for a
quantitative peak.
Figure 30. Times page
Parameters for single
RT detection types
Parameters for RT
range detection types
Table 21. Times page parameters (Sheet 1 of 2)
Parameter
Description
Detection Type
Single - Detected: (Default) Specified as a centered retention time window. The application
integrates a distinct peak. In reports, the application displays the expected retention time
and actual retention time values as Method RT and Detected RT, respectively.
Range - Detected: Specified as a retention time start/end range.
Range - Integrated: Specified as a retention time start/end range. The application integrates
all peaks within the specified time range.
Expected RT (min)
Expected retention time for a single peak. Available only for the Single - Detected detection
type.
Window (sec)
Width of the window (in seconds) to indicate how far around the expected retention time
the system looks for a peak apex. Available only for the Single - Detected detection type.
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Table 21. Times page parameters (Sheet 2 of 2)
Parameter
Description
Start/End RT (min)
Beginning and ending retention time window that can encompass multiple peaks. Available
only for the Range - Detected and the Range - Integrated detection types. When you change
from a Single - Detected detection type, these values default to the previous beginning and
ending time calculated from the Expected RT and Window values.
View Width (min)
Viewable size of the ion chromatogram display. Changing the view width does not affect the
peak detection process; the TraceFinder application uses it only for graphical display. When
you select either Range - Detected or Range - Integrated as the detection type, you cannot
select a View Width value less than the retention time range (end time minus start time).
Shortcut menu
Set Peak Windows
Copies the View Width and Window values to all quantitative peaks for the compound and
Settings to All Peaks in updates the compound.
Compound
Available only when a compound has multiple quantitative peaks.
Set Peak Windows
Copies the View Width and Window values to all quantitative peaks for the method and
Settings to All Peaks in updates the method.
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Signal
Use the Signal page to define the detector and filters as you display each chromatogram trace.
For detailed descriptions of all the features on the Signal page, see “Signal page parameters” on
page 141. The TraceFinder application can use both analog detectors and mass spectrometer
detectors. See “Signal page for a mass spectrometer detector” on page 140 or “Signal page for
an analog detector” on page 141.
Follow these procedures:
• To specify ranges of ions for detection and integration
• To specify an XIC filter
• To specify an MS filter
 To specify ranges of ions for detection and integration
1. Select MS from the Detector list.
2. Select Mass Range from the Trace list.
3. In the Ranges area, click Edit.
Note The Ranges area is available only when you set the Detector parameter to MS
and the Trace parameter to Mass Range.
The Edit Mass Ranges dialog box opens where you can define mass ranges using a center
of mass or start and end values.
Figure 31. Edit Mass Ranges dialog box
4. Enter a value in the Center Mass box and click Add.
A new row with this value opens under Ranges. Center mass values are listed in the Start
m/z column. The application uses a range of one amu centered on this value.
5. Enter values in the Start m/z and End m/z columns and click Add.
The application adds a row with these start and end values.
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6. Add as many ranges as you want.
When you process a batch with this method, the application sums the multiple ions
specified by these ranges.
7. Click Apply.
The application applies the parameters to the list of ranges.
 To specify an XIC filter
1. Select MS from the Detector list.
2. Select Mass Range from the Trace list.
3. Select the XIC option.
Note The XIC option is available only when you set the Detector parameter to MS
and the Trace parameter to Mass Range.
4. Click the Filter browse button.
The XIC Filter dialog box opens. See XIC Filter dialog box.
5. Specify your filter options.
6. Click OK.
The application updates the chromatogram data using the specified XIC filter options.
The Filter box indicates the parameters of the specified XIC filter. For example:
MassAnalyzerFTMS analyzer
Positive polarity
MS2 order
Full scan mode
Data-dependent filter
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Figure 32. XIC Filter dialog box
Table 22. XIC Filter dialog box parameters (Sheet 1 of 2)
Parameter
Description
Mass Analyzer Any: Allows any mass analyzer.
Type
FTMS: Fourier Transform Mass Spectrometer
ITMS: Ion Trap Mass Spectrometer
Sector: Static electric or magnetic sectors, or a combination of the two
SQMS: Single Quad Mass Spectrometer
TOFMS: Time-of-Flight Mass Spectrometer
TQMS: Triple Quad Mass Spectrometer
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MSX
Any: Allows both MSX and non-MSX scans.
On: Allows only MSX scans.
Off: Allows only non-MSX scans.
Data
Dependent
Any: Allows both data-dependent and non-data-dependent filters.
On: Allows only data-dependent filters.
Off: Allows only non-data-dependent filters.
MS Order
Any: Allows any MS order.
MS: Single mass spec stage
MS2-MS3: Multiple mass spec stages
Polarity
Any: Allows both positive and negative.
Positive
Negative
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Table 22. XIC Filter dialog box parameters (Sheet 2 of 2)
Parameter
Description
Scan Mode
Any: Allows any scan mode.
Full: Full-scan mode
SIM: Selective ion monitoring
SRM: Selective reaction monitoring
CRM: Consecutive reaction monitoring
Q1MS: MS using quadrupole 1
Q3MS: MS using quadrupole 3
Activations
Any: Allows any activation method.
CID: Collision-induced dissociation
MPD: Multiple photodissociation
ECD: Electron capture dissociation
PQD: Pulsed dissociation
ETD: Electron transfer dissociation
HCD: Higher energy collision-induced dissociation
SAactivation:
PTRactivation:
NETDactivation: Negative electron-transfer dissociation activation
NPTRactivation:
This parameter is available only when the MS Order is set to MS2 or
MS3.
First Precursor This parameter is available only when the MS Order is set to MS2 or
MS3.
Second
Precursor
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This parameter is available only when the MS Order is set to MS3.
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 To specify an MS filter
1. Select the Filter option.
2. Select MS from the Detector list.
3. Select a trace type from the Trace list.
4. Select a filter from the Filter list.
The application applies the selected filter to the quantitative or confirming ion peak.
5. To apply this same filter to other peaks, right-click and choose one of the following from
the shortcut menu:
• Set Filter Options on All Peaks in This Compound: Applies this filter to all other
peaks in the compound.
• Set Filter Options on All Compounds: Applies this filter to all peaks in the method.
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Figure 33. Signal page for a mass spectrometer detector
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Figure 34. Signal page for an analog detector
Table 23. Signal page parameters (Sheet 1 of 3)
Parameter
Description
XIC
Available only when you select the MS detector. Specifies an Extracted Ion Chromatogram
experiment type that uses a single, full-scan mass filter that is post-processed to extract a peak for the
ions of interest.
Filter
Available only when you select the MS detector. Select from the list of mass filters to use for
processing the compound.
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Table 23. Signal page parameters (Sheet 2 of 3)
Parameter
Description
Detector
Options are determined by the detection options used to create the method. The method can use the
standard options (all the listed options) or only the detection options used to acquire an associated
raw data file.
MS: Mass spectrometer that ionizes sample molecules and then separates the ions according to their
mass-to-charge ratio (m/z).
PDA: Photodiode array detector providing a linear array of discrete photodiodes on an integrated
circuit chip. It is placed at the image plane of a spectrometer to allow a range of wavelengths to be
simultaneously detected.
Analog: Supplemental detectors (for example, FID, ECD). When you select this detector, any
reports that display a QIon value show the value as Analog and any reports that display spectra show
the spectra as Not Available.
A/D card: If you have a detector not under data system control, you can capture the analog signal
and convert it to digital using an interface box (for example, SS420X) for storage in the raw data file.
UV: A UV spectrophotometer (for variable-wavelength detection) or photometer (for
single-wavelength detection) equipped with a low-volume flow cell. This detector detects analytes
that readily absorb light at a selected wavelength.
Trace
Represents a specific range of the data. The TraceFinder application uses the trace to identify the
characteristic ions for a compound.
MS detector options: Mass Range, TIC, or Base Peak. When you select Mass Range, you are
prompted to enter the start and end m/z values for the ranges.
PDA detector options: Spectrum Maximum, Wavelength Range, or Total Scan.
Analog detector options: Analog 1, Analog 2, Analog 3, or Analog 4. You can configure these
channel names in your instrument configuration.
A/D Card detector options: AD Card ch1, AD Card ch2, AD Card ch3, or AD Card ch4. You can
configure these channel names in your instrument configuration.
UV detector options: Channel A, Channel B, Channel C, or Channel D. You can configure these
channel names in your instrument configuration.
Filter
Available only when you select the MS detector. Represents a particular data acquisition channel.
For example, the filter option + c Full ms [35.00-500.00] represents a positive ion centroid signal
acquired in single-stage, full-scan mode from m/z 35 to 500.
Ranges
Available only when you select the Mass Range trace for an MS detector.
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Table 23. Signal page parameters (Sheet 3 of 3)
Parameter
Description
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 135.
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. The Genesis and Avalon sensitivity modes are used for mass spectrometry detection.
The ICIS sensitivity mode is used primarily for analog detection.
On this page, you can specify how you want each mode to run. See the following for detailed
descriptions of all the features on the Detect page:
• For Genesis sensitivity, see “Detect page parameters for Genesis” on page 146.
• For ICIS sensitivity, see “Detect page parameters for ICIS” on page 150.
• For Avalon sensitivity, see “Detect page parameters for Avalon” on page 152.
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Figure 35. Detect page for Genesis
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Table 24. Detect page parameters for Genesis (Sheet 1 of 3)
Parameter
Description
Sensitivity
Specifies the Genesis peak detection algorithm.
Detection Method
Highest peak: Uses the highest peak in the chromatogram for component identification.
Nearest RT: Uses the peak with the nearest retention time in the chromatogram for
component identification.
Smoothing
Determines the degree of data smoothing to be performed on the active component peak
prior to peak detection and integration.
Default: 1
Range: Any odd integer from 1 through 15 points
S/N Threshold
Current signal-to-noise threshold for peak integration. Peaks with signal-to-noise values less
than this value are not integrated. Peaks with signal-to-noise values greater than this value
are integrated.
Range: 0.0 to 999.0
Enable Valley
Detection
Uses the valley detection approximation method to detect unresolved peaks. This method
drops a vertical line from the apex of the valley between unresolved peaks to the baseline.
The intersection of the vertical line and the baseline defines the end of the first peak and the
beginning of the second peak.
Expected Width (sec)
The expected peak width parameter (in seconds). This parameter controls the minimum
width that a peak is expected to have if valley detection is enabled.
With valley detection enabled, any valley points nearer than the expected width/2 to the top
of the peak are ignored. If a valley point is found outside the expected peak width, the
TraceFinder application terminates the peak at that point. The application always terminates
a peak when the signal reaches the baseline, independent of the value set for the expected
peak width.
Range: 0.0 to 999.0
Constrain Peak Width
Constrains the peak width of a component during peak integration of a chromatogram. You
can then set values that control when peak integration is turned on and off by specifying a
peak height threshold and a tailing factor. Selecting the Constrain Peak Width check box
activates the Peak Height (%) and Tailing Factor options.
Peak Height (%)
A signal must be above the baseline percentage of the total peak height (100%) before
integration is turned on or off. This text box is active only when you select the Constrain
Peak Width check box.
Range: 0.0 to 100.0%
Tailing Factor
A factor that controls how the TraceFinder application integrates the tail of a peak. This
factor is the maximum ratio of the trailing edge to the leading side of a constrained peak.
This text box is active only when you select the Constrain the Peak Width check box.
Range: 0.5 through 9.0
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Table 24. Detect page parameters for Genesis (Sheet 2 of 3)
Parameter
Description
Min Peak Height (S/N) For the valley detection approximation method to use the Nearest RT Peak Identification
criteria, this peak signal-to-noise value must be equaled or exceeded. For component
identification purposes, the TraceFinder application ignores all chromatogram peaks that
have signal-to-noise values that are less than the S/N Threshold value.
Range: 0.0 (all peaks) through 999.0
Available only for quantitation methods.
Peak S/N Cutoff
The peak edge is set to values below this signal-to-noise ratio.
This test identifies an edge of a peak when the baseline adjusted height of the edge is less
than the ratio of the baseline adjusted apex height and the peak S/N cutoff ratio.
When the S/N at the apex is 500 and the peak S/N cutoff value is 200, the TraceFinder
application defines the right and left edges of the peak when the S/N reaches a value less
than 200.
Range: 50.0 to 10000.0
Valley Rise (%)
The peak trace can rise above the baseline by this percentage after passing through a
minimum (before or after the peak).
This method drops a vertical line from the apex of the valley between unresolved peaks to
the baseline. The intersection of the vertical line and the baseline defines the end of the first
peak and the beginning of the second peak.
When the trace exceeds rise percentage, the TraceFinder application applies valley detection
peak integration criteria.
The TraceFinder application applies this test to both the left and right edges of the peak.
The rise percentage criteria is useful for integrating peaks with long tails.
Range: 0.1 to 500.0
Valley S/N
Specifies a value to evaluate the valley bottom. Using this parameter ensures that the
surrounding measurements are higher.
Default: 2.0
Range: 1.0 to 100.0
# Background Scans
Number of background scans performed by the TraceFinder application.
Report Noise As
Determines if the noise used in calculating S/N values is calculated using an RMS
calculation or a peak-to-peak resolution threshold. Options are RMS or Peak to Peak.
Shortcut menu
Apply to All Peaks in
Method
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Updates all compounds in the method with the current settings on the Detect page. These
updates apply to both quantitative and confirming ion peaks.
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Table 24. Detect page parameters for Genesis (Sheet 3 of 3)
Parameter
Description
Apply to All Peaks with Uses the current settings on the Detect page to update all compounds in the method that
Like Sensitivity Setting use the Genesis sensitivity mode. These updates apply to both quantitative and confirming
ion peaks that use the Genesis sensitivity mode.
Apply to All Peaks in
Compound
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Updates all peaks in the current compound with the current settings on the Detect page.
These updates apply to both quantitative and confirming ion peaks.
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Figure 36. Detect page for ICIS
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Table 25. Detect page parameters for ICIS (Sheet 1 of 2)
Parameter
Description
Sensitivity
Specifies the ICIS peak detection algorithm, used primarily with analog detectors.
Detection Method
Highest peak: Uses the highest peak in the chromatogram for component identification.
Nearest RT: Uses the peak with the nearest retention time in the chromatogram for
component identification.
Smoothing
Determines the degree of data smoothing to be performed on the active component peak
prior to peak detection and integration.
Default: 1
Range: Any odd integer from 1 through 15 points
Area Noise Factor
The noise level multiplier used to determine the peak edge after the location of the possible
peak.
Default: 5
Range: 1 through 500
Peak Noise Factor
The noise level multiplier used to determine the potential peak signal threshold.
Default: 10
Range: 1 through 1000
Baseline Window
The TraceFinder application looks for a local minima over this number of scans.
Default: 40
Range: 1 through 500
Constrain Peak Width
Constrains the peak width of a component during peak integration of a chromatogram. You
can then set values that control when peak integration is turned on and off by specifying a
peak height threshold and a tailing factor. Selecting the Constrain Peak Width check box
activates the Peak Height (%) and Tailing Factor options.
Peak Height (%)
A signal must be above the baseline percentage of the total peak height (100%) before
integration is turned on or off. This text box is active only when you select the Constrain
Peak Width check box.
Range: 0.0 to 100.0%
Tailing Factor
A factor that controls how the TraceFinder application integrates the tail of a peak. This
factor is the maximum ratio of the trailing edge to the leading side of a constrained peak.
This text box is active only when you select the Constrain the Peak Width check box.
Range: 0.5 through 9.0
Min Peak Height (S/N) For the valley detection approximation method to use the Nearest RT Peak Identification
criteria, this peak signal-to-noise value must be equaled or exceeded. For component
identification purposes, the TraceFinder application ignores all chromatogram peaks that
have signal-to-noise values that are less than the S/N Threshold value.
Range: 0.0 (all peaks) through 999.0
Available only for quantitation methods.
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Table 25. Detect page parameters for ICIS (Sheet 2 of 2)
Parameter
Description
Noise Method
The options are INCOS or Repetitive.
INCOS: Uses a single pass algorithm to determine the noise level.
Repetitive: Uses a multiple pass algorithm to determine the noise level. In general, this
algorithm is more accurate in analyzing the noise than the INCOS Noise algorithm, but the
analysis takes longer.
Min Peak Width
The minimum number of scans required in a peak.
Default: 3
Range: 0 to 100 scans
Multiplet Resolution
The minimum separation in scans between the apexes of two potential peaks. This is a
criterion to determine if two peaks are resolved.
Default: 10
Range: 1 to 500 scans
Area Tail Extension
The number of scans past the peak endpoint to use in averaging the intensity.
Default: 5
Range: 0 to 100 scans
Area Scan Window
The number of allowable scans on each side of the peak apex. A zero value defines all scans
(peak-start to peak-end) to be included in the area integration.
Default: 0
Range: 0 to 100 scans
RMS
Specifies that the TraceFinder application calculate noise as RMS. By default, the
application uses Peak To Peak for the noise calculation. RMS is automatically selected if you
manually determine the noise region.
Shortcut menu
Apply to All Peaks in
Compound
Updates all peaks in the current compound with the current settings on the Detect page.
These updates apply to both quantitative and confirming ion peaks.
Apply to All Peaks in
Method
Updates all compounds in the method with the current settings on the Detect page. These
updates apply to both quantitative and confirming ion peaks.
Apply to All Peaks with Uses the current settings on the Detect page to update all compounds in the method that
Like Sensitivity Setting use the ICIS sensitivity mode. These updates apply to both quantitative and confirming ion
peaks that use the ICIS sensitivity mode.
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Figure 37. Detect page for Avalon
Table 26. 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 26. Detect page parameters for Avalon (Sheet 2 of 2)
Parameter
Description
Smoothing
Determines the degree of data smoothing to be performed on the active component peak
prior to peak detection and integration.
Default: 1
Range: Any odd integer from 1 through 15 points
Autocalc Initial Events
Automatically calculates the events in the Event list.
Edit
Opens the Avalon Event List dialog box. See “Avalon Event List” on page 57.
Shortcut menu
Apply to All Peaks in
Compound
Updates all peaks in the current compound with the current settings on the Detect page.
These updates apply to both quantitative and confirming ion peaks.
Apply to All Peaks in
Method
Updates all compounds in the method with the current settings on the Detect page. These
updates apply to both quantitative and confirming ion peaks.
Apply to All Peaks with Uses the current settings on the Detect page to update all compounds in the method that
Like Sensitivity Setting use the Avalon sensitivity mode. These updates apply to both quantitative and confirming
ion peaks that use the Avalon sensitivity mode.
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Suitability
Use the Suitability page to determine if the column is degrading and to identify suspicious
peaks eluting at the same time as the target compound. Suspicious peaks caused by highly
retained compounds from a previous injection tend to have a broader than expected peak
profile. Tailing peaks frequently indicate a degrading column.
The Suitability page displays the parameter values that the application uses to check the
suitability of chromatographic peaks during processing. You can edit these parameters in the
System Suitability dialog box.
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 To set system suitability parameters
1. Click Edit.
The System Suitability dialog box opens. See “System Suitability dialog box” on
page 156.
2. To perform symmetry testing, do the following:
a. Select the Symmetry Parameters check box.
b. Type a peak height for symmetry testing in the Peak Height box.
c. Type a threshold for symmetry testing in the Symmetry Threshold box.
3. To carry out classification tests, do the following:
a. Select the Peak Classification Parameters check box.
b. To adjust Xcalibur peak width testing thresholds, type parameters in the Detect Peak
Width area.
• To enter a peak height for the test, type a value in the Peak Height box.
• To enter a minimum peak width threshold, type a value in the Min Peak Width
box.
c. To adjust the Xcalibur peak tailing test, type parameters in the Detect Tailing area.
• To enter a peak height for the test, type a value in the Peak Height box.
• To enter a threshold limit for peak tailing, type a value in the Failure Threshold
box.
d. To adjust the Xcalibur column overload test, type parameters in the Detect Column
Overload area.
• To enter a peak height for the test, type a value in the Peak Height box.
• To enter a threshold limit for peak tailing, type a value in the Failure Threshold
box.
e. To adjust the Xcalibur baseline clipping test, type parameters in the Detect Baseline
Clipping area.
To define the test window, type a value in the Number of Peak Widths for Noise
Detection box.
4. To save your settings, click OK.
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Figure 38. System Suitability dialog box
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Spectrum
Use the Spectrum page to store a reference mass spectrum for a quantitative peak or
compound.
For detailed descriptions of all the shortcut menu commands on the Spectrum page, see
“Spectrum page shortcut menu commands” on page 161.
Follow these procedures:
• To update confirming ion ratios
• To change the quantitation mass used for a quantitative peak
• To add ions together to get an accumulated signal
• To add a quantitative peak to an existing compound
• To add one or more confirming ions to an existing compound
• To zoom in on the chromatogram or spectrum displays
 To update confirming ion ratios
1. Click a peak in the quantitative peak chromatogram pane.
The mass spectrum for the peak is displayed in the Spectrum pane.
2. Right-click the Spectrum pane and choose Update Confirming Ion Ratios with This
Spectrum from the shortcut menu.
 To change the quantitation mass used for a quantitative peak
1. Click a peak in the chromatogram pane.
The mass spectrum for the peak is displayed in the Spectrum pane.
2. In the Spectrum pane, hold the cursor over the mass-to-charge value for an ion.
A red box around the ion’s m/z value indicates that the ion is selected.
3. Right-click and choose one of the following commands from the shortcut menu:
• Set This Mass as Quan Mass > Don’t Update Ion Ratios
• Set This Mass as Quan Mass > Update Ion Ratios Using This Reference Spectrum
The following examples show an original quantitative peak and a quantitative peak with an
updated quantitation mass.
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Figure 39. Original quantitative peak mass example
Original quantitative peak mass
The TraceFinder application replaces the original quantitation mass with the selected
mass.
Figure 40. Updated quantitative peak mass example
New quantitative 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 quantitative peak signal.
 To add a quantitative peak to an existing compound
1. Click the peak in the Quan Peak chromatogram pane.
The mass spectrum for the peak is displayed in the Spectrum pane.
2. In the Spectrum pane, hold the cursor over the m/z value for an ion.
A red box around the ion’s m/z value indicates that the ion is selected.
3. Right-click and choose Set This Mass as New Quan Peak from the shortcut menu.
The TraceFinder application adds this ion as a new quantitative peak.
New quantitative peak mass
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 To add one or more confirming ions to an existing compound
1. Click the quantitative peak in the chromatogram pane.
The mass spectrum for the peak is displayed in the Spectrum pane.
2. In the Spectrum pane, hold the cursor over the m/z value for an ion.
A red box around the ion’s m/z value indicates that the ion is selected.
3. Right-click and choose to Add This Mass as New Confirming Ion from the shortcut
menu.
The TraceFinder application adds the selected mass as a confirming peak for this
quantitative peak.
 To zoom in on the chromatogram or spectrum displays
1. Drag the cursor to delineate a rectangle.
The display zooms in on the specified rectangle.
2. To return to the original display, right-click and choose Reset Scaling from the shortcut
menu.
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Figure 41. Spectrum page
Table 27. Spectrum page shortcut menu commands
Command
Description
Update Confirming Ion Ratios
With This Spectrum
Updates the confirming ion ratios using the selected peak.
Set This Mass as Quan Mass
Adds the quantitation mass of the selected ion to the quantitation mass used for
the quantitative peak. You can choose to update the ion ratios or not update the
ion ratios using this reference spectrum.
Add This Mass to Existing Quan
Mass Range
Adds the selected mass to your existing quantitation mass range. You can choose
to update the ion ratios to adjust the confirming ion comparisons to the new
summed quantitative peak signal.
Set This Mass as New Quan Peak
Adds a new quantitative peak to an existing compound.
Add This Mass as New
Confirming Ion
Adds one or more confirming ion peaks to an existing compound.
Reset Scaling
Returns the chromatogram or spectrum display to its original size.
Copy to Clipboard
Copies the graphic display to the Clipboard.
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Ratios
Use the Ratios page (see “Ratios page” on page 163) 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 detailed descriptions of all the features on the Ratios page, see “Ratios page parameters”
on page 163.
 To specify ion ratio criteria
1. Select the Enable check box to activate the confirming ion.
2. In the Target Ratio box, select the theoretical ratio of the confirming ion’s response to the
quantification ion’s response.
3. In the Window Type list, select Absolute or Relative as the calculation approach for
determining the acceptable ion ratio range.
4. In the Window (+/-%) box, select the acceptable ion ratio range.
5. In the Ion Coelution box, select the maximum difference in retention time between a
confirming ion peak and the quantification ion peak.
In the following example
• The target ratio is expected to be 61.02% and the window is Absolute 20%, so the
acceptable window for this confirming ion peak is 41.02–81.02%.
• However, if the window type is Relative, the plus or minus value is 20% of 61.02%
(or 12.20%), so the acceptable window for this confirming ion peak is
48.82–73.22%.
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Figure 42. Ratios page
Table 28. Ratios page parameters
Parameter
Description
Enable
Makes the ion ratio criteria available.
Target Ratio (%)
The theoretical ratio of the confirming ion’s response to the quantification ion’s response.
Window Type
The absolute or relative calculation approach for determining the acceptable ion ratio range.
Window (+/-%)
The acceptable ion ratio range.
Ion Coelution (min)
The maximum difference in retention time between a confirming ion peak and the
quantification ion peak.
Shortcut menu
Set Ion Ratio to All
Confirming Peaks in
Compound
Copies the Window Type, Window, and Ion Coelution values to all confirming ion peaks
for the compound and updates the compound.
Available only when a compound has multiple confirming ion peaks.
Set Ion Ratio to All
Confirming Peaks in
Method
Copies the Window Type, Window, and Ion Coelution values to all quantitative peaks for
the method and updates the method.
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Calibration
Use the Calibration page to set or edit the mathematical model used for preparing the initial
calibration evaluation for one or more calibration standards.
Each target compound can have its own initial calibration settings, independent of the other
compounds. You can modify the calibration approach on this page or in Acquisition mode
when you view the results of an actual calibration batch.
Typically, general quantitation uses a measured response (area or height) to determine the
amount of a compound contained in a sample. The application compares the response of an
unknown, target compound to the response of a calibration sample that contains a known
amount of the compound by building a calibration curve to interpolate the amount in the
target compound.
To use a semi-quantitative process, you specify the compound’s standard type as Estimated
and then identify another compound as the linked compound. Instead of using the target
compound to create a calibration curve, the application uses a calibration curve from the
linked compound to calculate the amount in the target compound.
For detailed descriptions of all the features on the Calibration page, see Calibration page
parameters.
 To specify an internal standard for a compound
1. On the Identification page, specify at least one compound in the method as an internal
standard compound type.
See “Identification” on page 117.
2. On the Calibration page, do the following:
a. In the Standard Type column, select Internal.
b. In the ISTD column, select the compound that you want to use as the internal
standard for this compound.
The application lists only compounds specified as internal standards on the
Identification page.
To view the internal standard peak in the Analysis mode, see “Compound Details” on
page 437.
Figure 43. Calibration page
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Table 29. 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, External, or Estimated standards.
Response Via
The use of area or height. When you set the standard type to Estimated, this column is
inactive.
Curve Type
Specifies Linear, Quadratic, or AverageRF curve types. When you set the standard type to
Estimated, this column is inactive.
Origin
The origin treatment is Ignore, Include, or Force. The Origin and Weighting columns are
available only when you use Linear or Quadratic curve types. When you set the standard
type to Estimated, this column is inactive.
Weighting
Specifies the weighting as Equal, 1/X, 1/X^2, 1/Y, or 1/Y^2. When you set the standard
type to Estimated, this column is inactive.
Units
The units to be displayed with the calculated values.
ISTD
The internal standard (ISTD) for a target compound or surrogate. The list displays all
compounds with the compound type of Internal Standard. This column is available only
when you set the standard type to Internal.
Amount
The amount of the internal standard for ISTD compounds. When you set the standard type
to Estimated, this column is inactive.
Linked Compound
This column is available only when the standard type is set to Estimated. The list of
available compounds to be linked does not include any compounds whose standard type is
set to Estimated.
Estimation Method
This column is unavailable for editing when the standard type is set to Estimated.
• When the compound type for the associated linked compound is Target Compound,
the estimation method is automatically set to Ext Curve.
• When the compound type for the associated linked compound is Internal Standard, the
estimation method is automatically set to Ratio.
Shortcut menu
Thermo Scientific
The Calibration page uses a right-click shortcut menu. See “Using the Shortcut Menu
Commands” on page 172.
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Calibration Levels
On the Calibration levels page (see “Calibration Levels page” on page 167) for a master
method, you can define the standards for calibration. You can edit calibration levels and
concentrations for master methods only. The contents of this page are read-only when you are
editing a local method.
For detailed descriptions of all the features on the Calibration Levels page, see “Calibration
levels page parameters” on page 167.
 To specify calibration levels and concentrations
1. Select the compound whose calibration levels and concentrations you want to define.
2. In the Manage Calibration Levels area, type a value for the first calibration level.
The application adds a new, empty calibration level row beneath the edited row.
3. Continue adding calibration levels.
When you finish adding calibration levels, you can specify the concentrations for each
compound at each level.
4. To enter the concentrations 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 that you
want to copy, right-click, and choose Copy Down from the shortcut menu.
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Figure 44. Calibration Levels page
Table 30. 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.
Shortcut menu
The Calibration Levels page uses a right-click shortcut menu. See “Using the Shortcut
Menu Commands” on page 172.
QC Levels
Use the QC levels page for a master method to define the standards for QC levels. See “QC
Levels page” on page 169. 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 detailed descriptions of all
the features on the QC Levels page, see “QC levels page parameters” on page 169.
 To specify QC levels and concentrations
1. Select the compound whose QC levels, percentage test values, and concentrations that
you want to define.
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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.
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 that you
want to copy, right-click, and choose Copy Down from the shortcut menu.
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Figure 45. QC Levels page
Table 31. 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.
Shortcut menu
Thermo Scientific
The QC Levels page uses a right-click shortcut menu. See “Using the Shortcut Menu
Commands” on page 172.
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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 Status Pane” on page 323.
Figure 46. Real Time Viewer page
Table 32. Real Time Viewer page parameters (Sheet 1 of 2)
Parameter
Description
Show Quan Peaks
Only
Displays only quantitative peaks in the compounds list. Quantitative peaks are indicated
with a black dot in the Quan Peak column.
Displayable Traces
Quan Peak
Dots indicate quantitative peak traces. Unmarked traces indicate confirming ion peaks.
Compound Name
Names of all compounds in the method.
Trace
Lists the simple mass or precursor mass for all traces—both quantitative peak and
confirming ion peak—for each compound.
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Table 32. Real Time Viewer page parameters (Sheet 2 of 2)
Parameter
Description
Moves the selected trace to the Traces to Display in Real Time Viewer pane.
Moves the selected trace to the Displayable Traces pane.
Moves all traces to the Displayable Traces pane.
To move multiple traces to the Traces to Display... pane, hold down the SHIFT key, select
multiple traces, and then click
.
Traces to Display in
Real Time Viewer (n/25)
List the traces to be displayed and the display order used in the real-time display in the
Acquisition mode. See “Real-Time Trace Display” on page 335.
Maximum number of traces is 25.
Move to Top
Moves the selected trace to the top of the Traces to Display... list and the second position in
the real-time display. The TIC is always the first position in the real-time display in the
Acquisition mode.
Move Up
Moves the selected trace up one position in the list.
Move Down
Moves the selected trace down one position in the list.
Move to Bottom
Moves the selected trace to the bottom of the list.
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Using the Shortcut Menu Commands
Each page on the Compounds page (except the Acquisition List and Real Time Viewer pages)
uses right-click shortcut menu commands to display or hide the retention column, remove
compounds from the method, copy and paste data, or save the compound list to a .csv file.
Table 33. Compounds page shortcut menu commands (Sheet 1 of 2)
Command
Description
Copy Down
Copies the value in the selected row to all rows below it. This
command is available only when you have selected a value that
can be copied down. See Appendix B, “Using Copy Down and
Fill Down.”
Display Retention Time Displays or hides the RT column in the compound list.
Column
Delete Compound From Removes the selected compound from the current master
Method
method.
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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.
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Table 33. Compounds page shortcut menu commands (Sheet 2 of 2)
Command
Description
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.
Sort by Compound
Name
Sorts the compounds alphabetically from A to Z.
Sort by Retention Time
Sorts the compounds from shortest retention time to longest
retention time.
Add This Compound to Adds the selected compound to the compound database. When
CDB
the compound already exists in the compound database, the
TraceFinder application updates the compound database with the
current compound information.
Add All Compounds to
CDB
Thermo Scientific
Adds all compounds in the current method to the compound
database. When any of these compounds already exist in the
compound database, the TraceFinder application updates the
compound database with the current compound information.
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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.
 To open the QAQC page
Click QAQC in the Method View navigation pane.
Available only when you activate
Intelligent Sequencing in
the Application Configuration mode.
From the QAQC page of the Method View, you can access these additional pages:
• Limits
• Calibration
• QC Check
• Negative
• ISTD
• Solvent Blank
• Hydrolysis
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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 47. Limits page
Table 34. 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.
Cutoff
Also called limit of reporting (LOR) in some industries. This is the lowest amount that can
be reported, as determined by each laboratory’s standard operating practices.
ULOL
(Linearity Limit)
Upper limit of linearity. This is usually the highest calibrator amount.
Carryover Limit
The highest amount of a substance that does not leave a residual amount in the instrument.
If a substance has a carryover limit of 5, amounts higher than 5 usually dirty the instrument
and leave residue behind, tainting the following sample. A carryover limit of less than 5 does
not leave any residual amounts of the substance.
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Calibration
Use the Calibration page to define acceptable criteria for initial calibration. The TraceFinder
application 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 48. Calibration page
Table 35. 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).
CV Test (%)
Coefficient of Variance test. The coefficient of variance percentage is the standard deviation
of the multiple samples of one level, multiplied by 100, and then divided by the average of
the multiple samples of that level. This calculation is based on the areas of the peaks.
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QC Check
Use the QC Check 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 Quality Control report, the TraceFinder application flags the calculated values for
internal standard compounds that exceed these limits.
For linear and quadratic modes, the maximum difference for the calculated concentration in
the QC sample versus the theoretical value is set on the QC Levels page of the Compounds
page.
Figure 49. QC Check page
Table 36. QC Check page parameters
Thermo Scientific
Parameter
Description
RT
Retention time. The time after injection when the compound
elutes. The total time that the compound is retained on the
column.
Compound
The compound name.
Max RF Diff (%)
The maximum deviation between the response factor (RF) of the
QC sample and the average response factor from the calibration
(when in average RF mode).
Min RF
The minimum response factor for the QC sample (when in
average RF mode).
CV Test (%)
Coefficient of Variance test. The coefficient of variance percentage
is the standard deviation of the multiple samples of one level,
multiplied by 100, and then divided by the average of the multiple
samples of that level. This calculation is based on the areas of the
peaks.
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Negative
Use the Negative 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.
For detailed descriptions of all the features on the Negative page, see Negative page
parameters.
On the Negative 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 50. Negative page
Table 37. Negative page parameters
Parameter
Description
RT
Retention time. The time after injection when the compound elutes. The total time that the
compound is retained on the column.
Compound
The compound name.
Method
The evaluation process used for comparing the calculated concentration. You can specify no
maximum, a specific concentration, or a percentage of the LOR, LOD, or LOQ.
Percentage
The percentage of the LOR, LOD, or LOQ if you are using the percentage approach.
Max Conc
The maximum concentration if you are using an absolute value.
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ISTD
Use the ISTD page to review the response and retention time of internal standards (when
available). The TraceFinder application 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 if you have not
identified any compounds as internal standards, this page does not show any values.
Figure 51. ISTD page
Table 38. 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 52. Solvent Blank page
Table 39. Solvent Blank page parameters
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Parameter
Description
RT
Retention time. The time after injection when the compound
elutes. The total time that the compound is retained on the
column.
Compound
The compound name.
Method
The evaluation process to use as a response for the quantitation ion
only (Quan Ion RT) or as a summed response for the quantitation
ion and any confirming ions (All Ion RT). To deactivate the
solvent blank test for a specific compound, select None.
Upper Limit
Specifies an upper limit for each compound in the sample when
you select an evaluation process. These values are not
concentrations; they are raw response values.
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Hydrolysis
Use the Hydrolysis page to specify the hydrolysis checks for compounds.
Figure 53. Hydrolysis page
Table 40. Hydrolysis page parameters (Sheet 1 of 2)
Parameter
Description
RT
Retention time. The time after injection at which the compound elutes. The total time
that the compound is retained on the column.
Compound
The compound name.
Method
The evaluation process to use, specified as either a lower threshold or a range. To
deactivate the hydrolysis test for a specific compound, select None.
Threshold/Lower Limit
For compounds using the Threshold method, this specifies the threshold value for the
hydrolysis test. Values below this threshold are flagged in the Hydrolysis report.
For compounds using the Range method, this specifies the lower limit of the range.
Upper Limit
For compounds using the Range method, this parameter specifies the upper limit of the
range.
Shortcut menu
Copy Down
Copies the selected column value to all rows in that column. For detailed instructions
about using the Copy Down command, 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 Removes the selected compound from the current master method.
Method
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 compound information to another application,
such as an Excel spreadsheet.
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Table 40. Hydrolysis page parameters (Sheet 2 of 2)
Parameter
Description
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 Groups Page
Use the Groups page of the Method View (see ““Groups page” on page 184”) to organize
compounds into functional or logical groups. You can use these groups for creating a subset of
target compounds. For detailed descriptions of all the features on the Groups page, see
“Groups page parameters.”
For quantitative processing, the TraceFinder application processes all compounds in the
method and stores the complete result set, but only those in the selected group are visible in
the Acquisition mode. Limiting the displayed compounds to those in the selected group can
be useful when working with a master method containing a large list of compounds, only
some of which are required for analysis in certain samples. In that case, the application
requires only a single method and can reduce the results. To display only those compounds to
be used in quantitative processing, select Quan Compounds from the Show list.
You can create multiple groups and include the same compound in more than one group.
 To open the Groups page
Click Groups in the Method View navigation pane.
Available only when you activate
Intelligent Sequencing in
the Application Configuration mode.
 To create a group
1. At the bottom of the Groups area, click Add Group.
The Add a New Group dialog box opens.
2. Type a name for the new group and click OK.
The new group appears in the Groups area.
3. Drag a compound from the Compounds area onto a group name (as if you were moving
files into a folder).
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4. To remove all the compounds from a group, rename the group, or delete it, right-click the
group name and choose from the shortcut menu.
5. To remove a single compound, right-click the compound name in the group and choose
Remove from Group from the shortcut menu.
Figure 54. Groups page
Table 41. 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.
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Empty Group
Removes all compounds from the selected group.
Rename Group
Changes the name of the selected group.
Delete Group
Removes the selected group and all the compounds in it.
Remove From Group
Removes the selected compound from its group.
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Editing the Intelligent Sequencing Page
Use the Intelligent Sequencing page to specify the actions you want the application to take
when there are acquisition failures with each sample type. The Intelligent Sequencing page is
available only when you activate Intelligent Sequencing in the Application Configuration
mode. See “Intelligent Sequencing” on page 66.
 To open the Intelligent Sequencing page
Click Intel Seq in the Method View navigation pane
 To specify actions for sample acquisition failures
1. In the Sample Types list, select a sample type.
Each sample type has a specific set of failure flags. See “Sample-Specific Failure Flags” on
page 188.
2. For each failure flag, select a failure action.
The failure action choices are the same for each failure flag except flags for Solvent or
Negative sample types. The Solvent and Negative sample types do not have Auto Sample
or Auto Sample and Reinject failure actions.
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Each Failure Action requires one or more of the following values:
• Sample Type
• Priority
• Max Action Count
• Failure Continuation
For a detailed description of each of these parameters, see “Actions” on page 187.
3. Select a sample type to use for the failure action.
This value is available only for Auto Sample and Auto Sample and Reinject failure
actions. When you create your samples list on the Auto Samples page, you must include
at least one sample with this sample type for the autosampler to use when it encounters
this error condition. See “Auto Samples Page” on page 376.
4. In the Priority column, type a priority value for this action.
The priority value can be any positive or negative integer.
• The application performs the failure action for the highest priority failure it
encounters and ignores all others.
• When you assign the same priority to two or more failures, the application performs
the failure action for the first failure it encounters and ignores all others.
5. In the Max Action Count column, type a value for the maximum number of times the
application should repeat a sample.
6. In the Failure Continuation column, do one of the following:
• Select the check box to skip this sample and continue to the next sample when this
sample exceeds the Max Action Count value.
• Clear the check box to stop the batch when this sample exceeds the Max Action
Count value.
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Actions
Use the Actions pane to specify what action the application takes when it encounters a
submission failure for the type of failure flag associated with each sample type.
Table 42. Actions parameters (Sheet 1 of 2)
Parameter
Description
Flag
Flag (error) types specific to each sample type. See Sample-Specific
Failure Flags. Each flag type has a set of user-specified actions that
the application follows when it encounters this error.
Failure Action
In the event of a failed sample, the application does one of the
following:
• Continue: Continues to the next sample in the batch.
• Stop: Stops the batch.
• Auto Sample: Injects the sample type specified for the Auto
Sample Type parameter and continues to the next sample.
• Reinject: Reinjects the current sample by inserting a “reinject”
sample in the batch.
• Auto Sample and Reinject: Injects the sample type specified
for the Auto Sample Type parameter and then reinjects the
failed sample.
Sample Type
Specifies either a Solvent or Negative sample type to use for the
auto sample injection.
Default: Solvent
Priority
The priority value can be any positive or negative integer.
When two or more failures have the same priority, the application
performs the failure action for the first failure it encounters and
ignores all others.
The application performs the failure action for the highest priority
failure and ignores all others.
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Table 42. Actions parameters (Sheet 2 of 2)
Parameter
Description
Max Action Count
Specifies the maximum number of times the application should
repeat a sample before it continues to the next sample or stops the
sequence, as determined by the value in the Failure Continuation
parameter.
Default: 1
Failure Continuation
When this check box is selected, samples that exceed the value
specified for the Max Action Count parameter cause the
application to skip the sample and continue to the next sample.
Default: Selected
When this check box is cleared, samples that exceed the value
specified for the Max Action Count parameter cause the
application to stop the batch.
Sample-Specific Failure Flags
Each sample type has a specific set of failure flags.
Sample Type
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• Negative
Calibrator
• Cal Out of Range
• Ion Ratio Failure
• Carryover
QC
• Ion Ratio Failure
• Out of Range
Hydrolysis
• Ion Ratio Failure
• Hydrolysis
Solvent
• Solvent Flag
Unextracted
• Ion Ratio Failure
Specimen
• Ion Ratio Failure
• Carryover
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Editing the Reports Page
Use the Reports page to specify how you want to save or print your reports. For detailed
descriptions of the features on the Reports page, see “Reports page parameters” on page 190.
For the quantitation report types, you can modify quantitation limits flags, user interface
options, and quantitation flag options on the Quan Report Settings page.
For ToxID report types, you can modify default report options, semi-quantitative results
options, ion ratio calculation methods, the exact mass window, and Exactive™ options on the
Target Screening Export Settings page.
This section includes instructions for the following tasks:
• Specifying Report Formats
• Specifying Quan Report Settings
• Specifying Target Screening Export Settings (for ToxID Reports)
Specifying Report Formats
• For each Standard report type, you can create a hardcopy printout, a PDF file, or an XML
file.
• For each Custom report type, you can create a hardcopy printout or an Excel
Macro-Enabled Workbook (.xlsm) file.
• For each ToxID report type, you can create a hardcopy printout or a PDF file.
 To open the Reports page
Click Reports in the Method View navigation pane.
Available only when you activate
Intelligent Sequencing in
the Application Configuration mode.
The Reports page opens with a list of all configured reports.
To configure which reports are available when you create a master method or which
reports create a batch-level report, see “Specifying the Reports Configuration” on page 39.
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 To specify report types and output formats
1. To edit the Report Title, double-click the name and type your new custom title.
The TraceFinder application uses this title for all reports that use this master method. You
cannot edit the Report Title from other report views.
2. To specify the type of report output to create for each report type, select the check box in
the appropriate column.
3. To duplicate an output type for all reports, click the cell to select it, and then right-click
and choose Copy Down from the shortcut menu.
All check boxes in the column below the selected cell duplicate the selected or cleared
state of the selected cell. This action applies only to reports where this output format is
available. By default, all report types are cleared.
Figure 55. Reports page
Table 43. Reports page parameters
Parameter
Description
Example
Opens a PDF that displays an example of the report type.
Report Name
The name of a report.
Report Title
The user-defined description to be used on a report.
Report Type
The type of report: Standard, Custom, or ToxID.
Print
Sends reports to the printer. Available for all report types.
Create PDF
Saves reports as PDF files. Available only for Standard and ToxID report types.
Create XML
Exports reports in XML format. Available only for Standard report types.
Create XLSM
Exports reports in Excel Macro-Enabled Workbook (.xlsm) format. Available only for Custom
report types.
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 39.
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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 the concentration calculation method
• To track the use of the tune file
 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 174.
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 seven 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 that 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 “Quan Report Settings page
parameters” on page 194.
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 To specify the concentration calculation method
In the Calculate Concentration As box, select Rounded or Truncated.
• Rounded: Rounds the calculated amount to the nearest value using the number of
decimal places specified in the Quan Limits Flags area.
• Truncated: Truncates the calculated amount at the number of decimal places
specified in the Quan Limits Flags area.
See “To specify quantitation limits” on page 191.
 To track the use of the tune file
1. Select the Enable Tune Time Tracking check box.
This option tracks the number of hours between the last instrument tune and each
sample acquisition.
2. In the Tune File Lifetime box, enter the number of hours that you want to allow between
the last instrument tune and a sample acquisition.
Any sample acquired outside this maximum allowable time is flagged on the Batch report.
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Figure 56. Quan Report Settings page
Table 44. 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 reports for only the compounds that are found in a sample. If a compound is above
the specified Quan Flag Options limits, the TraceFinder application reports the compound.
This prevents generating “empty” reports for the compounds that are not found.
User Interface Options
Shade Row When
Sample is Outside of
Evaluation Criteria
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 an analysis.
Use Alternate
Calibration Report
Format
Uses an alternate format for the Calibration Report that is designed to print more concisely
(this report is limited to a maximum of seven calibration standards).
Display Quan Flags
and Legend
Displays manual flags, confirming manual flags, quantitation flags, and a legend on
high-density reports.
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Table 44. 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.
Calculated Amount Option
Calculate
Concentration As
Specifies the Rounded or Truncated method for reporting concentration amounts.
Tune Time Tracking Options
Enable Tune Time
Tracking
Tracks the number of hours between the last instrument tune and each sample acquisition.
Tune File Lifetime
Specifies the maximum number of hours between the last instrument tune and a sample
acquisition. Any sample acquired outside this maximum allowable time is flagged on the
Batch report.
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Specifying Target Screening Export Settings (for ToxID Reports)
Use the options on the Target Screening Export Settings page to set the parameters required to
produce ToxID reports. For detailed descriptions of the features on the Target Screening
Export Settings page, see “Target Screening Export Settings page parameters” on page 200.
The TraceFinder application uses these parameters to process a raw data file and create a
report similar to a ToxID report.
Note The Target Screening Export Settings page is available only when you activate the
ToxID features. See “ToxID” on page 64.
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
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Based on MS3 scans
Based on accurate mass scans
Based on SRM scans
Based on Exactive screening method
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 the 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 the 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 quantitation ion.
For example, when the Ion Ratio Window is 20% and the quantitation 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.
To add or remove adducts from the default lists, see “Specifying Adducts Configuration”
on page 60.
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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 the 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.
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.
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Figure 57. Target Screening Export Settings page
Table 45. Target Screening Export 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.
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.
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Table 45. Target Screening Export Settings page parameters (Sheet 2 of 2)
Parameter
Description
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 SemiQuantitative Result
Includes the semi-quantitative results in the target screening reports.
Measurement Unit
Units used for labeling purposes.
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(%)
Specifies the acceptable ion ratio range.
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
represent a gain or loss to the neutral mass. 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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Editing a Target Screening Master Method
You can open a target screening master method to specify method instructions, reporting
options, peak filter settings, screening databases, identification and confirmation settings, and
peak detection parameters.
This section includes instructions for the following tasks:
• Opening a Target Screening Master Method
• Editing the General Page
• Editing the Reports Page
• Editing the Screening Page
• Editing the Peak Detection Page
Opening a Target Screening Master Method
For target screening methods, you select which databases to use in the Compound Databases
area of the Target Screening Settings pane. The available databases are the compound
databases stored in
C:\Thermo\TraceFinder\3.0\Forensic\Databases\filename.cdb
The target screening method uses only the target list of compounds in the selected compound
databases to identify the compounds in the samples.
 To open a saved master method
1. Click Method Development from the navigation pane.
2. Choose File > Open > Master Method from the main menu.
The Open Master Method dialog box opens, displaying all available methods.
Tip You can also open one of your most recently used master method files. Choose
Files > Recent Files > MethodName.
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3. Select a target screening master method and click Open.
The General page for the selected method opens in the Method View. For detailed
descriptions of all the features on the General page, see “General page parameters” on
page 206.
The Method View for a target screening method includes General, Reports, Screening,
and Peak Detection pages.
Editing the General Page
Use the General page to define basic information about the master method.
 To edit the parameters on the General page
1. Click General in the Method View navigation pane.
The General page for the screening method opens. See “General page for a screening
method” on page 206.
2. In the Lab Name box, type the name to be displayed on the top of each printed, saved, or
exported report.
The default name is Default Laboratory.
3. In the Assay Type box, type the assay type to be targeted by the method.
4. From the Injection Volume box, select the injection volume (in μL) to be used for sample
injection.
Range: 0.1 to 2000 μL
Use the up/down arrows to change the volume in increments/decrements of 1 μL, or use
the keyboard to enter non-integer injection volumes.
IMPORTANT The TraceFinder application uses this injection volume in the master
method, not the injection volume in the instrument method.
5. From the Mass Precision box, select the number of decimal places to be used in reports
and in peak and spectrum displays.
Valid values: Integers from 2 to 6, inclusive
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6. From the Instrument Method list, select an instrument method.
7. To edit the instrument method, click Edit.
The Thermo Xcalibur Instrument Setup dialog box opens. This example of an
instrument setup shows multiple configured instruments.
8. Edit the values on the instrument page for your instrument.
9. From the main menu in the Thermo Xcalibur Instrument Setup dialog box,
choose File > Save and then choose File > Exit.
The TraceFinder application returns you to the General page of the Method View.
10. Select the units of measure that you want to use.
• (Default) MMU (millimass units): A static calculation to the extracted mass.
• PPM (parts per million): 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.
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11. From the Mass Tolerance box, select the number of millimass units or parts per million to
use as the m/z ± tolerance value.
Use the up/down arrows to change the volume in increments/decrements of 1 unit, or use
the keyboard to enter non-integer tolerances.
The application applies this mass tolerance to the extracted chromatograms.
12. From the Library Search Type list, select the type of library to use for target screening.
• NIST: Uses the NIST library that you installed with the TraceFinder application. See
“Installing the NIST and QED Libraries” on page 16.
Note Because the NIST library is large, using this library can slow sample
processing.
• Library Manager: Uses the library that you specified in the Application
Configuration mode. See “Screening Library” on page 68.
The application searches the library to identify or confirm the sample compound,
matches the fragment ion spectrum in the library to the compound’s ion spectrum, and
returns the highest score (best match).
13. To display all compounds specified in the method, including those that are not found in
the sample, select the Show All Compounds check box.
14. Type in the Notes box, or paste text from another application using CTRL+V.
You can add a note to explain what makes this method unique.
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Figure 58. General page for a screening method
Table 46. General page parameters (Sheet 1 of 2)
Parameter
Description
Lab Name
The laboratory name to be displayed on the top of each printed, saved, or exported report.
Default: Default Laboratory
To specify this default laboratory name, see “Specifying Application Defaults” on page 44.
Assay Type
The name for the analysis type to be targeted by the method. The assay type associates the
method with the analysis of a compound or specific class of compounds (for example, you
might use an assay type of PAH for the analysis of Polynuclear Aromatic Hydrocarbons).
Injection Volume
The system uses the injection volume (in μL) for sample injection. For a more detailed
explanation, refer to the documentation for the autosampler.
The injection volume in the master method overrides the injection volume in the
instrument method.
The injection volume in the batch overrides the injection volume in the master method.
Range: 0.1 to 2000 μL
Mass Precision
Number of decimal places used in reports and in peak and spectrum displays.
Valid values: Integers from 2 to 6, inclusive.
Instrument Method
Instrument method used for acquiring samples.
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Table 46. General page parameters (Sheet 2 of 2)
Parameter
Description
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.
Mass Tolerance
Upper limit of MMU or PPM.
Default: 500
Range: 0.1 through 50 000
• (Default) MMU (millimass units): A static calculation to the extracted mass.
• PPM (parts per million): 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.
Library Search Type
Specifies the type of library to use for target screening.
• NIST: Uses the NIST library that you installed with the TraceFinder application. See
“Installing the NIST and QED Libraries” on page 16.
• Library Manager: Uses the library that you specified in the Application Configuration
mode. See “Screening Library” on page 68.
Show All Compounds
Display all compounds specified in the method, including those that are not found in the
sample.
Notes
Optional notes about the method.
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Editing the Reports Page
Use the Reports page to specify the reports and report output formats that you want to create
for the method. You can also specify options for exporting compounds to Excel spreadsheets
or CSV files.
Follow these procedures:
• To open the Reports page
• To specify report types and output formats
• To specify options for exporting compounds to an Excel worksheet
• To specify options for exporting compounds to a CSV file
• To specify report options
 To open the Reports page
Click Reports in the Method View navigation pane.
The Reports page for the screening method opens. See “Reports page for a target
screening method” on page 210. The reports list displays only the Target Screening report
types.
For information about configuring the Target Screening Summary Report or Target
Screening High Density Sample Report when you create a target screening method, see
“Specifying the Reports Configuration” on page 39.
 To specify report types and output formats
1. To edit the Report Title, double-click the name and type your new title.
The TraceFinder application uses this title for all reports that use this master method. You
cannot edit the Report Title from other report views.
2. To specify the type of report output to create for each report type, select the check box in
the appropriate column.
3. To duplicate an output type for all reports, click the cell to select it, and then right-click
and choose Copy Down from the shortcut menu.
All check boxes in the column below the selected cell duplicate the selected or cleared
state of the selected cell. This action applies only to reports where this output format is
available.
By default, all report types are cleared.
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 To specify options for exporting compounds to an Excel worksheet
1. In the Excel Export Settings area on the Target Screening Export/Report Settings page,
select one of the following worksheet formats:
Multiple Worksheets: Writes one sample to each Excel worksheet tab.
Single Worksheet: Write all samples to a single Excel worksheet tab.
The application uses the selected worksheet format when you export a batch compound
list to an Excel spreadsheet file.
For instructions about exporting a compound list from the Analysis mode, see “To export
compounds to an Excel spreadsheet” on page 459.
2. In the Peaks area, select the type of peaks to export: All Peaks, Confirmed Only, or
Identified and Confirmed.
For detailed descriptions of the criteria used to identify and confirm peaks, see “To specify
identification and confirmation settings” on page 216.
For detailed descriptions of the Format and Peaks parameters, see Reports page parameters.
 To specify options for exporting compounds to a CSV file
1. In the CSV Export Settings area on the Target Screening Export/Report Settings page,
select one of the following file formats:
Multiple Files: Writes one sample to each file.
Single Rile: Write all samples to a single file.
The application uses the selected file format when you export a batch compound list to a
CSV file.
For instructions about exporting a compound list from the Analysis mode, see “To export
compounds to a CSV file” on page 459.
2. In the Peaks area, select the type of peaks to export: All Peaks, Confirmed Only, or
Identified and Confirmed.
For detailed descriptions of the criteria used to identify and confirm peaks, see “To specify
identification and confirmation settings” on page 216.
 To specify report options
Use the Report Options on the Target Screening Export/Report Settings pane to specify
the compounds to use in reports: all compounds in the method or only the compounds
found in the sample. These settings affect all reports created with this method.
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Figure 59. Reports page for a target screening method
Table 47. Reports page parameters
Parameter
Description
Report list columns
Example
This option is not available for target screening reports.
Report Name
The name of a report.
Report Title
The user-defined description to be used on a report.
Report Type
In a target screening method, all reports are the Target Screening report type.
Print
Sends reports to the printer.
Create PDF
Saves reports as PDF files.
Create XML
Exports reports as XML files.
Create XLSM
This option is not available for target screening reports.
Batch Level
This option is not available for target screening reports.
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Figure 60. Target Screening Export/Report Settings page for a target screening method
Table 48. Target Screening Export/Report Settings page parameters
Parameter
Description
Excel Export Settings
Format
Specifies one of the following formats for exporting reports to an Excel spreadsheet file:
• Multiple Worksheets: Writes one sample to each Excel worksheet tab.
• Single Worksheet: Writes all samples to a single Excel worksheet tab.
Peaks
Specifies one of the following options for reporting peaks:
• All Peaks: All peaks found in the sample data.
• Identified and Confirmed: Reports peaks that are considered identified and peaks that
are considered confirmed.
• Confirmed Only: Reports only peaks that are considered confirmed.
CSV Export Settings
Format
Specifies one of the following formats for exporting reports to a comma-separated-value
(.csv) file:
• Multiple Files: Writes one sample to each file.
• Single File: Writes all samples to a single file.
Peaks
Specifies one of the following options for reporting peaks:
• All Peaks: All peaks found in the sample data.
• Identified and Confirmed: Reports peaks that are considered both identified and
confirmed.
• Confirmed Only: Reports only peaks that are considered confirmed.
Report Options
Include All
Compounds
Reports all compounds in the method, including those that are not found in the sample.
Include Only Found
Compounds
Reports only compounds that are found in the sample.
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Editing the Screening Page
Use the Screening page to specify peak filter settings, screening databases, and identification
and confirmation settings for a screening method.
 To open the screening page
Click Screening in the Method View navigation pane.
The Screening page for the screening method opens. See “Screening page for a target
screening method” on page 218.
This section includes instructions for the following tasks:
• Specifying Peak Filter Settings
• Specifying Compound Databases
• Specifying Identification and Confirmation Settings
Specifying Peak Filter Settings
The Peak Filter Settings pane displays parameters for limiting unwanted data.
 To specify peak filter settings
1. To set a retention time range that excludes searching for peaks outside the range, do the
following:
a. Select the Use RT Limits check box.
The application activates the Search From and To options.
b. In the Search From box, enter the lower limit; in the To box, enter the upper limit.
2. To use one or more negative samples for subtraction to filter the resulting peaks, do the
following:
a. Select the Use Matrix Blank check box.
The application activates the Amplifier option.
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During automatic processing, the TraceFinder application subtracts the areas of the
peaks in the negative samples from the matching areas in the specimen samples.
To determine the pair of peaks to subtract from each other, the application selects the
two peaks with the mass and the retention time that are closest to each other (as
defined in the compound database), within the mass tolerance specified in the
method.
When the same compound peak (same mass and retention time within the
predefined tolerance windows) is in multiple selected negative samples, the
application subtracts only the one with the highest area.
When a compound peak in one negative sample has the same primary ion as another
peak in a different negative sample but has different adducts, the application uses all
the adducts from both these peaks for subtraction purposes. For example, if a
compound has the M+H and M+Na ions in one negative sample, and this same
compound has the M+H and M+NH4 ions in another negative sample, the
application uses for subtraction the area that results from all of these ions.
When no negative sample exists in the sequence, or if one or more negative samples
exist but you do not select the Use Matrix Blank check box, then subtraction does not
occur. If subtraction occurs and the subtracted area is less than 0, the application sets
the subtracted area to 0.
b. In the Amplifier box, type an amplifier value.
Use the up/down arrows to change the value in increments/decrements of 1 unit, or
use the keyboard to enter non-integer values.
The TraceFinder application multiplies a negative area by this value before
performing subtraction. The larger the amplifier value, the more peaks the
application filters from the final results.
In the Batch View for sequences created with this method, you can select which negative
samples to use for subtraction. See “Blank Subtraction in Target Screening Batches” on
page 348.
3. In the Chromatogram View Width box, type a value to define the chromatogram viewing
range in the Data Review view.
4. To use source CID scans for target screening confirmation (fragment ion or library
search), select the Use Source CID Scans check box.
When you select this check box, the TraceFinder application uses the source CID scans
when they are available in the data file. If they are not available, then the application uses
AIF or MS/MS scans when available.
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Specifying Compound Databases
The Target Screening Settings pane displays the compound databases stored in the following
folder:
C:\Thermo\TraceFinder\3.0\Forensic\Databases
 To specify compound databases
1. Select the Enabled check box for at least one compound database.
2. (Optional) To edit a database, click Open and do the following:
a. Edit the database.
See “Editing Compounds in the Database” on page 251.
b. When you finish editing the database, click Screening in the Method View
navigation pane to return to the Screening page.
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Specifying Identification and Confirmation Settings
The TraceFinder application automatically uses the mass-to-charge ratio (m/z) for filtering
compound peaks. In the Identification and Confirmation Settings area, you can select
additional criteria to help increase confidence using either of the following:
• Compound identification for identifying a sample compound as a minimum requirement
for a match to be displayed in the results.
To identify a compound, the application searches within the specified RT window (or the
RT window override if specified in the method) and compares the measured m/z of the
sample peak against the calculated (expected) m/z of the target compound. When the
sample peak’s m/z is within the default ±5 ppm tolerance of the target compound’s m/z,
the application considers that this target compound is identified.
• Compound confirmation for confirming a sample compound and to increase confidence
in the match results.
To confirm a compound, the application searches the entire raw data file and compares
the measured m/z of the sample peak against the calculated (expected) m/z of the target
compound. When the sample peak’s m/z is within the tolerance of the target compound’s
m/z, the application considers that this target compound is confirmed.
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 To specify identification and confirmation settings
1. To set a target threshold override and include only peaks with areas above this designated
threshold, do the following:
a. Select the Threshold Override check box.
b. In the associated box, type the threshold as an area value.
This threshold overrides the Response Threshold value set in the compound
database. The application ignores the peaks with areas below your specified threshold.
c. To include only peaks with signal-to-noise ratios (S/Ns) that are above a specified
value, in the S/N Ratio Threshold box, type the threshold as a ratio value.
The application ignores the peaks with S/Ns that are below the specified threshold.
2. To specify the Retention Time option, do the following:
a. Select either the Identity or Confirm check box.
b. Select the Window Override check box and type the window value.
This window overrides the RT Window value that was set in the compound database
and includes only peaks within this designated window. The application identifies or
confirms the presence of a compound only when its measured retention time matches
the target compound’s expected retention time within the specified Window
Override retention time.
3. To specify the Fragment Ions option, do the following:
a. Select either the Identity or Confirm check box.
b. In the Max. # of Fragments box, type the maximum number of fragments to use to
identify or confirm the presence of a compound.
4. To specify the Isotopic Pattern option, do the following:
a. Select either the Identity or Confirm check box.
b. In the Fit Threshold box, type the fit threshold percentage.
To identify or confirm the presence of a compound, the resulting score percentage
from isotopic pattern matching must be higher than the specified fit threshold
percentage.
c. In the Allowed Intensity Deviation box, type a value to specify the allowed intensity
deviation of the mass spectrometer relative to the monoisotopic ion, as a percentage
of the base peak height.
The TraceFinder isotopic pattern algorithm considers an isotope peak as not found if
its intensity, relative to the monoisotopic ion’s intensity, is more than the deviation
percentage from the theoretical relative intensity of the isotope ion. For best results,
set this value to a number that causes up to 98% of all intensity deviations to be
smaller than the allowed intensity deviation value.
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d. To specify that isotopic pattern calculations use internal mass calibration instead of
external mass calibration, select the Use Internal Mass Calibration check box.
When this check box is selected, the application applies a requirement that an
isotope’s m/z must be closer to its theoretical value to avoid a score penalty.
5. To specify the Library Search option, do the following:
a. Select either the Identity or Confirm check box.
b. Type the threshold value in the Score Threshold box.
The resulting score percentage from a library search match must be higher than your
entered threshold value to identify or confirm the presence of a compound.
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Figure 61. Screening page for a target screening method
Table 49. Screening page parameters (Sheet 1 of 3)
Parameter
Description
Peak Filter Settings
Use RT Limits
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Specifies a lower and upper limit for searches.
Ranges: 0.00 to 999.99 minutes
Default: 0.00 minutes for lower limit; 999.00 minutes for upper limit
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Table 49. Screening page parameters (Sheet 2 of 3)
Parameter
Description
Use Matrix Blank
Specifies that during automatic processing, the TraceFinder application subtracts the areas of
the peaks in the selected negative samples from the matching areas in the specimen samples.
Amplifier
The application multiplies a negative area by this value before performing subtraction. The
larger the amplifier value, the more peaks the application filters from the final results.
Range: .01 to 1000.00
Default: 1.00
Chromatogram View
Width
Specifies a a window width to define the chromatogram viewing range in the Data Review
view.
Range: 0.10 to 999.00 minutes
Default: 0.75 minutes
Use Source CID Scans
Specifies that the application use the source CID scans when they are available in the data
file. If they are not available, then the application uses AIF or MS/MS scans when available.
Compound Databases
Enabled
Specifies databases to use for target screening processing.
Database Name
Lists available databases in the Databases folder.
Identification and Confirmation Settings
Peaks
Specifies that the application use the mass-to-charge ratio (m/z) for filtering compound
peaks.
Threshold Override
This threshold overrides the Response Threshold value set in the compound database. The
application ignores the peaks with areas below this specified threshold.
Range: 1000 to 1 000 000 000
Default: 5000
S/N Ratio Threshold
Includes only peaks with signal-to-noise ratios (S/Ns) above the specified value.
Range: 1.0 to 100 000
Default: 5.0
Retention Time
Specifies either the Identify or Confirm option for a retention time search. To identify a
compound, the application searches the specified RT window for a match. To confirm a
compound, the application searches the entire raw data file.
Window Override
Specifies the number of seconds to override the RT Window value set in the compound
database and include only peaks within this designated window. The application identifies
or confirms the presence of a compound only when its measured retention time matches the
target compound’s expected retention time within the specified Window Override retention
time.
Range: 0 to 999 seconds
Default: 30 seconds
Fragment Ions
Specifies either the Identify or Confirm option for a fragment ion match. To identify a
fragment, the application searches the specified RT window for a match. To confirm a
fragment, the application searches the entire raw data file.
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Table 49. Screening page parameters (Sheet 3 of 3)
Parameter
Description
Max. # of Fragments
Specifies the maximum number of fragments to use to identify or confirm the presence of a
compound.
Range: 1 to 5
Default: 1
Isotopic Pattern
Specifies either the Identify or Confirm option for an isotopic pattern match. To identify a
compound, the application searches the specified RT window for a match. To confirm a
compound, the application searches the entire raw data file.
Fit Threshold (%)
To identify or confirm the presence of a compound, the resulting score percentage from
isotopic pattern matching must be higher than the specified fit threshold percentage.
Default: 90%
Allowed Intensity
Deviation
Specifies the allowed intensity deviation of the mass spectrometer, relative to the
monoisotopic ion, as a percentage of the base peak height.
The TraceFinder isotopic pattern algorithm considers an isotope peak as not found if its
intensity relative to the monoisotopic ion’s intensity is more than this deviation percentage
from the theoretical relative intensity of the isotope ion. For best results, set this value to a
number that causes up to 98% of all intensity deviations to be smaller than the allowed
intensity deviation value.
Default: 10%
Use Internal Mass
Calibration
Specifies that the application require an isotope’s m/z to be closer to its theoretical value to
avoid a score penalty.
Allowed Mass
Deviation
Specifies the allowed mass deviation in the spectrum data.
The TraceFinder isotopic pattern algorithm considers an isotope peak as found if its
measured m/z is less than this amount away from its expected m/z. For best results, set this
value to a number that causes up to 98 percent of all mass deviations to be smaller than the
allowed mass deviation value.
Range: 3 to 100 ppm
Default: 3 ppm
Library Search
Specifies either the Identify or Confirm option for a library search. To identify a compound,
the application searches the specified RT window for a match. To confirm a compound, the
application searches the entire raw data file.
Score Threshold
The resulting score percentage from a library search match must be higher than your
specified threshold value to identify or confirm the presence of a compound.
Default: 80%
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Editing the Peak Detection Page
The TraceFinder application can use any of the following peak detection algorithms: Genesis,
ICIS, or Avalon.
 To specify peak detection parameters
1. Click Peak Detection in the Method View navigation pane.
The Peak Detection page for the screening method opens.
2. Select a detection algorithm: Genesis, ICIS, or Avalon.
• 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.
3. Specify the peak detection parameters for your method.
Figure 62. Parameters on the Genesis peak detection page for a target screening method
Genesis peak detection parameters for screening methods are the same as for quantitation
methods. See “Detect page parameters for Genesis” on page 146.
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Figure 63. Parameters on the ICIS peak detection page for a target screening method
ICIS peak detection parameters for screening methods are the same as for quantitation
methods. See “Detect page parameters for ICIS” on page 150.
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Figure 64. Parameters on the Avalon peak detection page for a target screening method
Avalon peak detection parameters for screening methods are the same as for quantitation
methods. See “Detect page parameters for Avalon” on page 152.
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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. The application uses the settings in the method template to
identify the data to display in the Qualitative View. See “Qualitative View” on page 416.
Only quantitation methods use method templates. Target screening methods do not use
method templates.
Follow these procedures:
• To open the Method Template Editor
• To specify peak criteria
• To identify the peaks
• To specify confirming ions
• To calibrate the compounds
• To enter a note for the method
• To save the method template
 To open the Method Template Editor
1. Click Method Development in the navigation pane.
The Method Development navigation pane opens.
2. Click Method View.
3. From the main menu, choose File > New > Method Template.
The Method Template Editor opens. For a complete description of the features on the
Method Template Editor, see “Method Template Editor dialog box” on page 231.
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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
height or area of the largest peak.
4. To display a specific number of the largest peaks by height or area, select the Only Select
Top Peaks check box and enter the number of peaks to display.
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 To identify the peaks
1. In the Use these Libraries box, select the libraries that you want to search.
All libraries loaded on your instrument are displayed in the Use these Libraries box.
2. To limit the number of hits returned when the system searches a spectrum against the
selected libraries, set a value in the Limit Library Hits box.
3. To specify how to sort the library searches, select a value from the Best Match Method
list.
 To specify confirming ions
1. To set the number of confirming ions, select the Include Confirming Ions check box
and enter a value in the Number of Confirming Ions box.
This value is the number of other ions in the spectrum whose ratio is compared to the
quantitation ion. Using this ratio, you can then determine if it is the target compound or
something else. You can set this value to integers from 1 to 10, inclusive. This value
defaults to 2 because you typically perform a 3-ion experiment with one quantitation
mass and two confirming ions.
The system selects the most intense ion to use as the quantitation mass and uses this mass
for the mathematical operations.
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2. To define the criteria for evaluating confirming or qualifying ions, select the Specify
Default Ion Ratio Ranges check box and set the following values:
a. To specify the maximum difference in retention time between a confirming ion peak
and the quantification ion peak, set a value in the Ion Coelution (min) box.
b. To specify an absolute or relative calculation approach for determining the acceptable
ion ratio range, select Absolute or Relative from the Window Type list.
c. To specify the acceptable ion ratio range, set a value in the Window (+/– %) box.
3. To include the peak spectrum in the processing method, select the Include Compound
Peak Spectrum as Reference Spectrum check box.
 To calibrate the compounds
1. From the Calibration Method list, select Internal or External.
2. From the Curve Type list, select one of the following:
• Linear: All other settings are available with this exception: When you select Include in
the Origin list, the Weighting parameter is unavailable.
• Quadratic: All other settings are available with this exception: When you select
Include in the Origin list, the Weighting parameter is unavailable.
• Average RF: The Weighting and Origin parameters are unavailable.
3. From the Origin list, select one of the following:
• Ignore: Specifies that the origin is not included as a valid point in the calibration
curve when the curve is generated. When you select Ignore, the calibration curve
might or might not pass through the origin.
• Force: Specifies that the calibration curve passes through the origin of the data point
plot when the calibration curve is generated.
• Include: Specifies that the origin is included as a single data point in the calculation
of the calibration curve. When you select Include, the calibration curve might or
might not pass through the origin.
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4. From the Weighting list, select one of the following:
• Equal: Specifies that the origin is included as a single data point in the calculation of
the calibration curve. When you select Equal, the calibration curve might or might
not pass through the origin.
• 1/X: Specifies a weighting of 1/X for all calibration data points during the
least-squares regression calculation of the calibration curve. Calibrants are weighted
by the inverse of their quantity.
• 1/X^2: Specifies a weighting of 1/X^2 for all calibration data points during the
least-squares regression calculation of the calibration curve. Calibrants are weighted
by the inverse of the square of their quantity.
• 1/Y: Specifies a weighting of 1/Y for all calibration data points during the
least-squares regression calculation of the calibration curve. Calibrants are weighted
by the inverse of their response (or response ratio).
• 1/Y^2: Specifies a weighting of 1/Y^2 for all calibration data points during the
least-squares regression calculation of the calibration curve. Calibrants are weighted
by the inverse of the square of their response (or response ratio).
5. From the Response Via list, select Area or Height.
• Area: Specifies that the TraceFinder application use this area value in response
calculations.
• Height: Specifies that the application use this height value in response calculations.
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 To specify qualitative peak processing
1. Select the Use Genesis Algorithm for Qual Processing check box and specify a value for
internal standard matching.
The application uses the Genesis algorithm to match internal standards in a range
plus/minus the value that you specify. For additional information about the Genesis
algorithm, see “Genesis Detection Method” on page 50.
This parameter is available only when you set the Sensitivity parameter in the Find the
Peaks area to ICIS or Avalon. When you select the Use Genesis Algorithm for Qual
Processing check box, the application ignore the Sensitivity parameter in the Find the
Peaks area.
2. Select or clear the Exclude Matching Quan Peaks check box and specify a value for the
exclusion window.
The application excludes quantitative peaks in a range plus or minus the value that you
specify.
3. To process samples that include data-dependent scans, select the Use Data Dependent
Scans check box.
When you process a sample using this feature, the application uses the TIC trace to find
all data-dependent full scans, lists them, and performs a library search against the
data-dependent MS/MS or MSn scan.
This option constrains the Data Review to only data-dependent scan spectra. See
“Working in the Report View” on page 468.
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.”
4. To indicate whether to select peaks above a minimum percentage of the nearest internal
standard peak that results in compound selection, select the Enable ISTD Threshold
check box and specify a minimum percentage.
To consider a peak for a processing method, the TraceFinder application uses the Enable
ISTD Threshold filter to determine which peaks meet the specified percentage of the
height of the nearest internal standard peak.
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When you select the Enable ISTD Threshold parameter, the method ignores values set for
the Enable Peak Threshold and Only Select Top Peaks parameters. See “To specify peak
criteria” on page 225.
Note When you create a method with the Method Forge, the application ignores the
parameters in the Qualitative Peak Processing area.
 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\3.0\Forensic\Templates\Methods
Saved method templates are available when you create a method using Method Forge. See
“Creating a New Method with Method Forge” on page 85.
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Figure 65. Method Template Editor dialog box
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Table 50. Method Template Editor dialog box parameters (Sheet 1 of 3)
Parameter
Description
Find the peaks
Sensitivity
Defines how extensively the peak detector algorithm searches for low-level peaks.
Limit the Retention
Time Range
Min RT specifies the beginning of the range. Max RT specifies the end of the range.
Enable Peak Threshold
Specifies whether to select peaks by relative height or area and the percentage of the highest
peak that results in compound selection.
Only Select Top Peaks
Displays a specific number of the largest peaks by height or area.
Identify the peaks
Use These Libraries
Lists the libraries that you can search.
Limit Library Hits
Specifies the number of hits returned when the system searches a spectrum against the
selected libraries.
Best Match Method
Specifies how to sort the library searches.
Valid values: Search Index, Reverse Search Index, Match Probability
Handle confirming ions
Include Confirming
Ions/
Number of Confirming
Ions
Specifies the number of confirming ions, which are other ions in the spectrum whose ratio
is compared to the quantitation ion to identify the compound.
This value defaults to 2 because you typically perform a 3-ion experiment with one
quantitation mass and two confirming ions.
Range: Integers from 1 to 10, inclusive.
Specify Default Ion
Ratio Ranges
Enables the ion ratio range features.
Ion Coelution specifies the maximum difference in retention time between a confirming
ion peak and the quantification ion peak.
Window Type specifies an Absolute or Relative calculation approach for determining the
acceptable ion ratio range.
Window (+/-%) specifies the acceptable ion ratio range.
Include Compound
Peak Spectrum as
Reference Spectrum
Includes the peak spectrum in the processing method. Use this setting to perform a spectra
comparison in Data Review.
Calibrate the compounds
Calibration Method
Specifies an internal or external calibration method.
Curve Type
Specifies a linear, quadratic, or average RF curve type.
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Table 50. Method Template Editor dialog box parameters (Sheet 2 of 3)
Parameter
Description
Origin
Specifies that the origin is ignored, forced, or included in the generated calibration curve.
• Ignore: Specifies that the origin is not included as a valid point in the calibration curve
when the curve is generated. When you select Ignore, the calibration curve might or
might not pass through the origin.
• Force: Specifies that the calibration curve passes through the origin of the data point
plot when the calibration curve is generated.
• Include: Specifies that the origin is included as a single data point in the calculation of
the calibration curve. When you select Include, the calibration curve might or might
not pass through the origin.
Weighting
Specifies the weighting for the calibration data points.
• Equal: Specifies that the origin is included as a single data point in the calculation of
the calibration curve. When you select Equal, the calibration curve might or might not
pass through the origin.
• 1/X: Specifies a weighting of 1/X for all calibration data points during the least-squares
regression calculation of the calibration curve. Calibrants are weighted by the inverse
of their quantity.
• 1/X^2: Specifies a weighting of 1/X^2 for all calibration data points during the
least-squares regression calculation of the calibration curve. Calibrants are weighted by
the inverse of the square of their quantity.
• 1/Y: Specifies a weighting of 1/Y for all calibration data points during the least-squares
regression calculation of the calibration curve. Calibrants are weighted by the inverse
of their response (or response ratio).
• 1/Y^2: Specifies a weighting of 1/Y^2 for all calibration data points during the
least-squares regression calculation of the calibration curve. Calibrants are weighted by
the inverse of the square of their response (or response ratio).
Response Via
Specifies if the TraceFinder application uses area or height in response calculations.
• Area: Specifies that the application use this peak area value in response calculations.
• Height: Specifies that the application use this peak height value in response
calculations.
Qualitative Peak Processing
Use Genesis Algorithm
For Qual Processing
The application uses the Genesis algorithm to match internal standards.
ISTD Matching
Excludes all the target compounds found in the method and does not list these compounds
in the TIC Report or in the Qual Mode view in the Data Review.
Exclude Matching Quan Compares the retention time of the internal standard in the method to the found retention
Peaks
time of the internal standard in the library search and excludes peaks outside the Exclusion
Window range.
Exclusion Window
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Defines a range plus/minus the Exclusion Window value that you specify.
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Table 50. Method Template Editor dialog box parameters (Sheet 3 of 3)
Parameter
Description
Use Data Dependent
Scans
Constrains the Data Review to only data-dependent scan spectra. See “Working in the
Report View” on page 468. In addition to the peak information, the TIC Report and TIC
Summary Report display information about the data-dependent filtered data.
Enable ISTD Threshold Specifies that, when identifying a peak, qualitative peak processing use the minimum
threshold specified as a percentage of the nearest internal standard peak, rather than the
threshold specified in the Enable Peak Threshold and Only Select Top Peaks parameters.
See Enable Peak Threshold or Only Select Top Peaks in this parameter table.
% of Internal
Standard
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Percentage of the nearest internal standard peak to use as the minimum threshold for
identifying a peak.
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Importing Published Master Methods
In the TraceFinder application, you can import published methods to use for detecting,
processing, and reporting. The Tracefinder installation provides the following folder of
published methods:
…\Thermo\TraceFinder\3.0\Forensic\Published Master Methods
 To import a published master method
1. Choose Method View > Import Published Method from the main menu.
The Import Published Method dialog box opens.
2. Select a method to import.
3. Click Import.
The application reports that the method successfully imported and saves the method in
the following folder:
…\Thermo\TraceFinder\3.0\Forensic\Methods
You can use any of the Open Method commands to open this method just as you would a
method that you created.
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Exporting SRM Data
In the TraceFinder application, you can export the selected reaction monitoring (SRM) data
from a quantitation method to an XML file that can be read by a TSQ or Q Exactive
application. You can export SRM transitions only from quantitation methods.
 To export SRM data to an XML file
1. Open the master method whose SRM data you want to export.
If you make changes to the method, you must save it before you can export the SRM
transitions.
2. To view a list of your SRM transitions, click the Acquisition List tab on the Compounds
page.
You do not have to display the Acquisition List to export the data, but the compounds in
the Acquisition List must contain at least one SRM experiment type. For information
about displaying SRM experiment types, see “Acquisition List” on page 115. For
information about editing SRM experiment types, see “Editing Compounds in the
Database” on page 251.
3. Choose Method View > Export SRM Data from the main menu.
The application writes the transitions to the following folder, using a format compatible
with your configured instrument:
…\Thermo\TraceFinder\3.0\Forensic\Methods\method
IMPORTANT If you have neither a TSQ nor an Exactive instrument configured, a
message asks which format you want to export: Triple Quadrupole or Q Exactive.
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Triple Quadrupole Format
The TraceFinder application writes the data in the SRM table to the following file:
…\Thermo\TraceFinder\3.0\Forensic\Methods\method\method.xml
The data in this file matches the TSQ XML data, which you can use in the instrument
method editor of that application.
Example SRM data file in TSQ format:
<?xml version="1.0" encoding="utf-8" ?>
- <TSQMassList>
- <TSQListItem>
<ParentMass>356.1</ParentMass>
<ProductMass>321.1</ProductMass>
<CollisionEnergy>14</CollisionEnergy>
<EnergyRamp>0</EnergyRamp>
<RT>0</RT>
<Width>60</Width>
<PreWidth>0</PreWidth>
<PostWidth>0</PostWidth>
<StartTime>0</StartTime>
<StopTime>0.5</StopTime>
<TubeLens>0</TubeLens>
<S-Lens>0</S-Lens>
<Polarity>0</Polarity>
<Name>15-acethyldeoxynivalenol+NH4</Name>
- </TSQListItem>
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Q Exactive Format
The TraceFinder application writes the data in the SRM table to the following file:
C:\Thermo\TraceFinder\3.0\Forensic\Methods\method\method.xml.include-masses
The data in this file matches the Exactive XML data, which you can use in the instrument
method editor of that application.
Example SRM data file in Q Exactive format:
<?xml version="1.0" encoding="utf-8"?>
<IncludeMasses xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
FullInternalName="Framework.IncludeMassesContainer">
<Masses FullInternalName="Framework.IncludeMasses">
<Mass id="1">
<Value unit="m/z" FullInternalName="decimal">321.1</Value>
<Polarity>0</Polarity>
<Start unit="min" FullInternalName="decimal">5</Start>
<End unit="min" FullInternalName="decimal">5</End>
<NormalizedCollisionEnergy
FullInternalName="decimal">14</NormalizedCollisionEnergy>
<ChargeState FullInternalName="int">0</ChargeState>
<Comment />
</Mass>
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Working with the Compound Database
When user security is activated, as a user in either the LabDirector or ITAdmin role, you can
manage compound definitions in the current database in the Compound Database view.
This section includes the following topics:
• Opening and Saving a Database
• Editing Compounds in the Database
• Choosing Experiment Types
• Exporting and Importing Compounds
For a description of all the parameters in the Compound Database view, see “Compound
Database Views” on page 243.
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Opening and Saving a Database
You can load a compound database that was included with your TraceFinder installation, or
you can create your own database. For detailed descriptions of all parameters and functions in
the Compound Database view, see “Compound Database Views” on page 243.
When you save the edits for a compound, the application saves the changes to the compound
database file. For instructions about editing compounds, see “Editing Compounds in the
Database” on page 251.
Follow these procedures:
• To open the Compound Database editor
• To load a compound database into the editor
• To create a new compound database
• To save the database to a new name
 To open the Compound Database editor
1. Click Compound Database in the Method Development navigation pane.
The current database opens in the Compound Database view.
If there is no compound database displayed in the editor, see the instructions To load a
compound database into the editor.
You can add compounds to the database by importing a file of compounds into the new
database, or you can manually add compounds one at a time.
See “To import compounds” on page 262 or “To add a compound to the database” on
page 251.
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 To load a compound database into the editor
1. Choose File > Open Compound Database.
The Open Compound Database dialog box opens.
2. Double-click the name of the database that you want to open.
The selected database opens in the Compound Database view. See “Compound Database
Views” on page 243.
Note Or, you can choose File > Recent Files > filename from the main menu to load
a previously opened database.
 To create a new compound database
1. Choose File > New Compound Database from the main menu.
The New Compound Database dialog box opens.
2. Type a file name for the new database and click OK.
The application stores the database as
C:\Thermo\TraceFinder\3.0\Forensic\Databases\filename.cdb
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 To save the database to a new name
1. Choose File > Save Compound Database As from the main menu.
The Save Compound Database As dialog box opens.
2. Do one of the following:
Type a file name for the new database and click OK.
–or–
Select the name of a database to overwrite, and click Overwrite.
If you attempt to overwrite the compound database that you currently have open, the
application warns that you cannot overwrite the compound database because it is being
used.
The application stores the database as
C:\Thermo\TraceFinder\3.0\Forensic\Databases\filename.cdb
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Compound Database Views
The parameters in the compound database are different depending on which experiment type
the compound uses.
• Compound Database view for SRM experiments
• Compound Database view for SIM experiments
• Compound Database view for XIC experiments
For detailed descriptions of all parameters used in the compound database, see “Compound
Database view parameters” on page 246.
Figure 66. Compound Database view for SRM experiments
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Figure 67. Compound Database view for SIM experiments
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Figure 68. Compound Database view for XIC experiments
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Table 51. Compound Database view parameters (Sheet 1 of 5)
Parameter
Description
Search
Displays only compounds that match the typed text.
Displays one of these experiment types that each use a different structure for the mass filter.
See “Choosing Experiment Types” on page 258.
• SRM: Selected Reaction Monitoring
• XIC: Extracted Ion Chromatogram
• SIM: Single Ion Monitoring
Compound
Alphabetically lists the compounds in the database followed by the experiment type. Some
long names are truncated in the list. Hold your cursor over the name to display a ToolTip
with the entire name.
Formula
Chemical formula for the compound. Used to calculate the neutral mass for the
compound.
Compound Detail
Compound
Alphanumeric name assigned to the compound.
Experiment
Experiment type: SRM, XIC, or SIM. For details about the differences, see “Choosing
Experiment Types” on page 258.
Category
(Optional) Alphanumeric identifier.
CAS
The Chemical Abstract Service (CAS) number that the TraceFinder application matched
with the compound.
Formula
Alphanumeric chemical identifier.
Ionization
Alphanumeric identifier.
Valid values: None, ESI, APCI, EI, CI, or APPI
Default: None
Response Threshold
The application integrates only peaks with a response greater than this threshold. The
response threshold is a minimum response that must be met to allow peak confirmation.
Used only for target screening methods. Available only for XIC experiments.
Default: 5000
Range: 1000 or greater
Neutral Mass
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Mass calculated from the chemical formula. The neutral mass is the sum of all AMU
elements in the compound. This parameter is informational only; it is not used for peak
detection.
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Table 51. Compound Database view parameters (Sheet 2 of 5)
Parameter
Description
Target Peaks
Precursor Mass
The mass-to-charge ratio (m/z) of a target peak. The location of the center of a target
precursor-ion peak in mass-to-charge ratio units.
In confirming peaks, the precursor mass is the same as the target peak precursor mass.
Default: 0.0
Range: 10.000 to 2999.999
Available for all SRM experiments and for XIC experiments with the MS Order set to
MS2.
For mass values in XIC experiments when the MS Order set to MS1, see Extracted Mass.
Product Mass
The mass-to-charge ratio of the confirming peak. The location of the center of a target
quan-ion peak in mass-to-charge ratio (m/z) units.
Default: 0.0
Range: 10.000 to 2999.999
Available for all SRM experiments and for XIC experiments with the MS Order set to
MS2.
For mass values in XIC experiments when the MS Order set to MS1, see Extracted Mass.
Mass
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The mass-to-charge ratio of the confirming peak. The location of the center of a target
quan-ion peak in mass-to-charge ratio (m/z) units.
Available only for SIM experiments.
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Table 51. Compound Database view parameters (Sheet 3 of 5)
Parameter
Description
Extracted Mass
The mass-to-charge ratio of the target peak. The location of the center of a target quan-ion
peak in mass-to-charge ratio (m/z) units.
You can enter a value for the Extracted Mass, but when you change the values for Formula,
Adduct, Polarity, or Charge State, the application recalculates the Extracted Mass value,
overwriting the value you entered.
Default: 0.0
Range: 10.000 to 2999.999
Available only for XIC experiments with the MS Order set to MS1.
For mass values in XIC experiments when the MS Order set to MS2, see Precursor Mass or
Product Mass.
Polarity
Positive or Negative
Adduct
Lists the adducts specified in the configuration file. To add or remove adducts from the
default lists, see “Specifying Adducts Configuration” on page 60.
Adducts affect the calculated amount of the extracted mass by adding to or subtracting
from the neutral mass.
Adducts are polarity sensitive. Select the Polarity parameter before selecting the Adduct
value.
Default Positive Valid Values: Neutral, NH4, H, Na, K
Default Negative Valid Values: Neutral, H, H3C2O2, HCO2
Default: Neutral
Charge State
Specifies the charge state of the ion (the z value in m/z). For example, a charge state of 2
with a negative polarity means that the compound has 2 more electrons than protons.
Valid Values: 1 through 10
Default: 1
MS Order
Specifies whether the confirming peaks come from the same scan (MS1) or are fragments
from an adjacent scan (MS2).
Available only for XIC experiments.
Time Range Peak
Specifies whether the acquisition time is specified as a window around a specified RT value
or as a retention time range in minutes.
This parameter is visible only when you are editing a compound.
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Table 51. Compound Database view parameters (Sheet 4 of 5)
Parameter
Description
Window (sec)
The application uses RT and Window values to determine the start and stop time for the
acquisition. Available only when the Time Range Peak option is not selected.
Range: 0.00 to 499.50
Start time = RT – (Window/2)
Stop time = RT + (Window/2)
Start and stop range: 0.00 to 999.00
RT (min)
Retention time. The application uses RT and Window values to determine the start and
stop time for the acquisition. When the Time Range Peak option is selected, the RT value
is specified as a range.
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
Lens
Range: –400 to 400
Collision Energy
The energy used when ions collide with the collision gas.
Available only for SRM experiments.
Range: –250.00 to 250.00
Energy Ramp
Range: 0.00 to 200.00
Confirming Peaks
Confirming peak parameters are used only in quantitative methods.
Precursor
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 or XIC experiments with the MS Order set to MS2.
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
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The mass-to-charge ratio of the confirming peak. The location of the center of a target
quan-ion peak in mass-to-charge ratio (m/z) units.
Available only for SIM experiments.
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Table 51. Compound Database view parameters (Sheet 5 of 5)
Parameter
Description
Extracted Mass
The mass-to-charge ratio of the target peak. The location of the center of a target quan-ion
peak in mass-to-charge ratio (m/z) units.
Available only for XIC 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
MS Order
Fragments
Extracted Mass
Specifies whether the confirming peaks or fragments come from the same scan (MS1) or an
adjacent scan (MS2).
Available only for XIC experiments.
Fragment parameters are used for XIC experiment types in target screening methods. The
application uses fragments to define masses that are present in an adjacent scan (MS2).
The mass-to-charge ratio of the target peak. The location of the center of a target quan-ion
peak in mass-to-charge ratio (m/z) units.
Available only for XIC experiments.
Default: 0.0
Range: 10.000 to 2999.999
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Editing Compounds in the Database
In the Compound Database view, you can import compounds into the database, add or
remove compounds from the database, add target or confirming peaks to a compound, or
remove target or confirming peaks from a compound.
Follow these procedures:
• To add a compound to the database
• To remove a compound
• To make a compound editable
• To add a target peak to a compound
• To add a confirming peak to a target peak
• To copy target peaks from one compound to another
• To copy window values from one peak to another
• To add a fragment to a target peak
 To add a compound to the database
1. Click the Add Compound icon,
.
The application adds a new, empty compound page and highlights the required
parameters in red.
2. Click the Compound box, and type the required Compound name.
3. Select the Experiment type: SRM, SIM, or XIC.
The required parameters are different for each experiment type. See “Choosing
Experiment Types” on page 258.
4. In the Target Peaks area, do the following:
• For SRM experiments, enter values for Precursor Mass and Product Mass.
• For SIM or XIC experiments, enter a value for Extracted Mass.
5. In the Confirming Peaks area, do the following:
• For SRM experiments, enter values for Precursor and Product Mass.
• For SIM or XIC experiments, enter a value for Precursor and Extracted Mass.
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6. Enter or edit any of the other optional parameters described in the “Compound Database
view parameters” on page 246.
Tip You cannot add another new compound or access the menu commands until you
enter all required parameters or cancel
the new compound.
 To remove a compound
1. In the Compound list, select the compound that you want to delete.
2. Click the Remove Compound icon,
.
3. If you are sure you want to delete the selected compound, at the prompt, click OK.
The application removes the selected compound and all its peak information.
4. The application supports the following methods to delete multiple compounds:
• CTRL+A to select all compounds
• CTRL+click to select noncontiguous compounds
• SHIFT+click to select contiguous compounds
 To make a compound editable
1. In the Compound list, select the compound that you want to edit.
2. Click the Edit Compound icon,
.
The application makes the compound parameters editable and displays the
Add icons,
, so that you can add target peaks, confirming peaks, and fragments to the
compound details.
Note If you are adding a new compound, it is “editable” by default.
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 To add a target peak to a compound
1. Click the Add Peak icon in the Target Peaks header.
Add Target Peak icon
The application adds a new target peak to the compound. A target peak includes
quantitative values for the compound.
Delete Target Peak icon
2. Enter all required parameters.
The required target peak values differ for each experiment type. See “Choosing
Experiment Types” on page 258.
For a list of required and optional parameters, see the list of “Compound Database view
parameters” on page 246.
Tip You cannot add another new target peak or save the compound until you enter all
required peak parameters or delete
the new target peak.
3. Repeat these steps to add as many as six target peaks to the compound.
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 To add a confirming peak to a target peak
1. Click the Add Confirming Peak icon in the Confirming Peaks header.
Add Confirming Peak icon
The application adds a new confirming peak to the target peak.
Delete Confirming Peak icon
2. Type the required values for the confirming peak.
The required confirming peak values differ for each experiment type. See “Choosing
Experiment Types” on page 258.
For a list of required and optional parameters, see “Compound Database view
parameters” on page 246.
3. Repeat these steps to add as many as 10 confirming peaks to the target peak.
Tip You cannot add another new confirming peak or save the compound until you
enter all required peak parameters or delete
the new confirming peak.
 To copy target peaks from one compound to another
1. In the compounds list, select the compound whose target peak you want to copy.
Source compound
2. When the target peak includes more than one peak, in the Target Peaks area for the
selected compound, scroll to the peak you want to copy.
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3. In the compounds list, keep the source compound selected and use the SHIFT or CTRL
keys to select the compounds that you want to copy the target peak to.
Source compound
IMPORTANT Be careful to keep the source compound selected.
4. In the Target Peaks area for the selected compound, right-click the target peak area and
choose Add Peak 1 to N Selected Compounds from the shortcut menu.
Right-click the target peak area.
The application reports that the peak was copied to the specified number of compounds.
The application copies the peak information to the selected compounds, adding this peak
to the peaks already defined for the compounds.
5. Click OK.
 To copy window values from one peak to another
1. In the compounds list, select the compound with the window value that you want to
copy.
Source compound
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2. In the Target Peaks area for the selected compound, identify the peak whose window you
want to copy.
3. In the compounds list, keep the source compound selected and use the CTRL key to
select the compounds that you want to copy the window to.
Source compound
IMPORTANT Be careful to keep the source compound selected.
4. In the Target Peaks area for the selected compound, right-click the target peak area and
choose Set the Window for All Peaks of selectedCompounds to windowValue from the
shortcut menu.
Right-click the target peak area.
The application reports that the retention time and window were copied to the specified
number of compounds, including the source compound when it has multiple peaks.
The application copies the retention time and window information to all peaks in the
selected compounds and all additional peaks in the source compound, overwriting the
values for these parameters.
5. Click OK.
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 To add a fragment to a target peak
1. Click the Add Fragment icon in the Fragments header.
Add Fragment icon
The application adds a new fragment to the target peak.
Delete Fragment icon
2. Click the Extracted Mass box, and type a value between 10 and 2999.999.
3. Repeat these steps to add as many fragments as you want.
Tip You cannot save the compound until you enter all required fragment parameters
or delete
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Choosing Experiment Types
The TraceFinder application uses three experiment types: SRM, SIM, and XIC.
Each of these experiment types uses a different structure for the mass filter. The target peak
and confirming peak parameters for each experiment type are defined in the “Compound
Database view parameters” on page 246.
A compound database can include multiple experiment types for a single compound;
however, each compound name and experiment type combination must be unique.
SRM: Selected Reaction Monitoring
The SRM experiment type supports triple quadrupole LC/MS. The mass filter includes
precursor mass and narrow mass ranges to identify product masses. Imported compounds
with no experiment type are treated as SRM data.
Confirming peaks include values for precursor mass, product mass, and collision energy.
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SIM: Single Ion Monitoring
The SIM experiment type supports single quadrupole LC/MS, GC/MS, and Exactive
systems. The mass filter includes narrow mass ranges to identify product masses.
Confirming peaks include an extracted mass value.
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XIC: Extracted Ion Chromatogram
The mass filter is a single, full scan which is post-processed to extract a peak for the ions of
interest.
Confirming peaks include an extracted mass value and a choice of mass order: MS1 or MS2.
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Exporting and Importing Compounds
From the Compound Database, you can export compounds to a CSV file or import
compounds from an XML, a CSV, or a CDB file.
Follow these procedures:
• To export compounds
• To import compounds
• To convert a legacy compound database to TraceFinder 3.0 format
In addition to procedures for importing and exporting compound data, this section also
contains the following topics:
• Compound Database Names Mapped to CSV Column Names
• Data Columns with Default Values
 To export compounds
1. Choose Compound Database > Export Compounds from the main menu.
The Export Compounds dialog box opens.
2. (Optional) Click Browse and locate a different folder or file name where you want to
write the exported compound database.
Each parameter in the compound database editor is represented by a column of data in
the spreadsheet. When you export compound data to a CSV file, each parameter is
assigned to a column and each row is assigned to a compound.
3. Select one of these options:
• Export Only Columns with Data: Writes only columns that contain nondefault
data for at least one compound. This option does not export columns that contain
only default data. See “Data Columns with Default Values” on page 267.
• Export All Columns: Writes all columns to the CSV file, including columns that
contain no data for any compound.
4. Click Export and Overwrite.
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The application stores the database as
C:\Thermo\TraceFinder\3.0\Forensic\Databases\databaseName.csv
A Microsoft Excel window opens with the compound data in spreadsheet format.
Figure 69. Compound data in an Excel spreadsheet
Column names in an exported Excel spreadsheet do not always match the parameter names in
the compound database editor. See “Compound Database Names Mapped to CSV Column
Names” on page 266.
You can use the tools in the spreadsheet to edit the data in the compound database and then
import the data in the CSV file back into the TraceFinder application. If you delete a column
from the spreadsheet and then import the CSV file, the TraceFinder application replaces the
data in that column with default values. For a list of default values, see “Data Columns with
Default Values” on page 267.
 To import compounds
1. Choose Compound Database > Import Compounds from the main menu.
The Select File to Import into the Current Compound Database dialog box opens.
You can import compounds from the following file types:
• ToxID Exactive CSV
• ToxID MS2 CSV
• TraceFinder CSV
• TraceFinder MassList XML
• TraceFinder 2.1 Legacy CDB
• ExactFinder 2.0 CDB
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IMPORTANT Before you import data from a CSV file, verify that the following
required columns have data for each compound. These columns have no default
values and must have a value before you can import .csv data into the TraceFinder
compound database:
• CompoundName
• ExperimentType
• ProductMass (target peak)
• Confirm Product (confirming peak)
• Fragment
If you delete one of these columns from the spreadsheet and attempt to import
the .csv data into the TraceFinder application, the application warns that it is unable
to parse the file and identifies the missing columns.
2. Locate the CDB, CSV, or XML compounds file that you want to import and click Open.
The Import Compounds dialog box opens.
Note If the import file is missing required compound information, the application
warns that it is unable to parse the file and identifies the missing columns. For a list of
required columns, see “To convert a legacy compound database to TraceFinder 3.0
format” on page 264.
3. To select a different compound database, click Browse, locate an XML, a CSV, or a CDB
compounds file, and click Open.
4. Confirm that the import file and the target database are correct.
The dialog box reports the total number of compounds in the import file, the number of
compounds with validation errors, and the number of compounds that already exist in
the target database.
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5. Select one of these options:
• Skip: Imports only those compounds that do not already exist in the target database.
• Overwrite: Replaces compounds that already exist in the target database with the
imported compounds.
6. Click Import.
The TraceFinder application imports the compounds from the imported file, adds them
to any compounds already in the database, and alphabetically sorts them.
The application reports the number of imported compounds.
7. Click OK.
 To convert a legacy compound database to TraceFinder 3.0 format
1. Choose File > New Compound Database from the main menu.
The New Compound Database dialog box opens.
2. In the Database Name box, type a name for the new compound database that you will
create.
3. Click OK.
The application creates a new, empty database.
4. Choose Compound Database > Import Compounds from the main menu.
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5. In the Select File to Import into the Current Compound Database dialog box, select a
legacy compound database CDB, CSV, or XML file to import.
The Import Compounds dialog box opens.
6. Confirm that the import file and the target database are correct.
The dialog box reports the total number of compounds in the import file, the number of
compounds with validation errors, and the number of compounds that already exist in
the target database. Because you are importing compounds into a new, empty database,
the number of compounds already found should be zero.
7. Click Import.
The application reports the number of imported compounds.
8. Click OK.
Note You can use the Import Compounds command to add compounds from a legacy
database to your current compound database. See “To import compounds” on page 262.
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Compound Database Names Mapped to CSV Column Names
Column names in an Excel spreadsheet do not always match the parameter names in the
compound database editor. The following table maps the parameter names to the column
headings in a CSV spreadsheet.
Table 52. CSV column names for compound parameters (Sheet 1 of 2)
CDB parameter
CSV column heading
Compound Detail
Compound
CompoundName
Experiment
ExperimentType
Category
Category
CAS
CAS
Formula
ChemicalFormula
Ionization
Ionization
Response Threshold
(XIC only)
ResponseThreshold
Target Peaks
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Precursor Mass
(SRM only)
PrecursorMass
Product Mass
(SRM only)
ProductMass
Mass
(SIM only)
ProductMass
Extracted Mass
(XIC only)
Extracted Mass
Product Mass
Mass
Extracted Mass
Extracted Mass
(when CDB contains any combination of SRM, XIC, and
SIM experiments)
Adduct
Adduct
Polarity
Polarity
Charge State
ChargeState
Window
Window
RT
RT
Collision Energy
(SRM only)
CollisionEnergy
Lens
Lens
Energy Ramp
EnergyRamp
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Table 52. CSV column names for compound parameters (Sheet 2 of 2)
CDB parameter
CSV column heading
Confirming Peaks
Precursor
(SRM and XIC only)
Confirm Precursor
Product Mass
(SRM only)
Confirm Product
Mass
(SIM only)
Confirm Product
Extracted Mass
(XIC only)
Confirm Extracted
Product Mass
Mass
Extracted Mass
Confirm Extracted
(when CDB contains any combination of SRM, XIC, and
SIM experiments)
Collision Energy
(SRM only)
Confirm Energy
Fragments
(XIC only)
Extracted Mass
Fragment
Data Columns with Default Values
When you export compounds to a CSV file with the Export Only Columns with Data
option, the application writes only columns that contain nondefault data for at least one
compound. This option does not export columns that contain only default data.
When you import compounds from a CSV data file that has missing columns, the application
replaces the missing columns and uses default values for all compounds.
Table 53. Default values for compound parameters (Sheet 1 of 2)
CDB parameter
Default value
Compound Detail
Formula
Blank
CAS
Blank
Category
Blank
Ionization
None
Response Threshold
(XIC only)
5000
Target Peaks
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Blank
Collision Energy
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Table 53. Default values for compound parameters (Sheet 2 of 2)
CDB parameter
Default value
Adduct
Neutral
Lens
0
Energy Ramp
0
Confirming Peaks
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0
Collision Energy
Blank
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Working with Instrument Methods
Working with Instrument Methods
An instrument method is a set of experiment parameters that define the operating settings for
an autosampler, mass spectrometer, and so on. Instrument methods are saved as file
type .meth.
IMPORTANT Do not open the Thermo Foundation Instrument Configuration window
while the TraceFinder application is running.
Follow these procedures:
• To open the Instrument View
• To create a new instrument method
• To create a new multiplexing instrument method
• To open an instrument method
• To import an instrument method
 To open the Instrument View
1. Click Method Development from the navigation pane.
The Method Development navigation pane opens.
2. Click Instrument View.
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 To create a new instrument method
1. Choose File > New Instrument Method from the main menu.
The Thermo Xcalibur Instrument Setup window opens.
Figure 70. Example instrument setup showing multiple configured instruments
2. Click the icon for the instrument that you want to use for the method.
3. Edit the values on the instrument page.
4. From the main menu in the Thermo Xcalibur Instrument Setup window, choose File >
Save As.
The Save As dialog box opens.
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5. Select an instrument method name to overwrite, or type a new name for the instrument
method, and click Save.
The File Summary Information dialog box opens.
6. (Optional) Type a comment about the new instrument method.
7. Click OK.
The TraceFinder application saves the new instrument method in the following folder:
…\Xcalibur\methods
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 To create a new multiplexing instrument method
1. Choose File > New Instrument Method from the main menu.
The Thermo Xcalibur Instrument Setup window opens.
Figure 71. Example instrument setup showing a configured multiplexed instrument
2. Click the icon for the instrument that you want to use for the method.
3. Edit the values for the instrument method.
For information about specifying multiplexing values, refer to the documentation for
your multiplexed instrument.
4. Specify the channels that you want to use for acquisition. 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
 To open an instrument method
1. Click Open Instrument Method on the Instrument View navigation pane.
An instrument method browser opens.
2. In the browser, do one of the following:
• Select an instrument method from the list and click Open.
• Click Xcalibur Instrument Method, select a method from the list of recent
methods, and click Open.
The selected method opens in the Thermo Xcalibur Instrument Setup window. You can
edit this method and save the changes, or you can save this method with another name.
Note To open Help for any of your configured instruments, click Help on the
instrument page.
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 To import an instrument method
1. From the main menu, choose Instrument View > Import Published Method.
The Import Published Method dialog box opens. This dialog box lists the master
methods in the Published Master Methods folder. You can import instrument methods
that are associated with these published master methods.
2. Select a method that includes the instrument method that you want to import.
For instructions about importing the master methods, see “Importing Published Master
Methods” on page 235.
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 in the navigation pane.
The Method Development navigation pane opens.
2. Click Development Batch.
The Development Batch view opens a new, empty batch.
Note The Channel column is available only when you have activated multiplexing in
the Application Configuration mode. See “Multiplexing” on page 66.
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 To specify a location for development batch data
1. To specify a location for the files, choose Development Batch > Select Batch Location
from the main menu.
By default, the TraceFinder application writes the temporary files, raw data files, and SLD
method file to the following folder:
…\Thermo\TraceFinder\3.0\Forensic\Temp
2. In the browser, do one of the following:
Locate the folder that 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 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.
 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–
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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 that 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.
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.”
A development batch uses the same shortcut menu features as a batch in the Batch View in
the Analysis mode. For detailed descriptions of the right-click shortcut menu, see “Batch View
Shortcut Menu” on page 355.
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.
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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 activated multiplexing in
the Application Configuration mode. See “Multiplexing” on page 66.
Figure 72. Completed development batch
 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 that 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.
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 To remove all samples from the list
1. Choose File > New Sample List from the main menu.
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 that 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:
C:\Thermo\TraceFinder\3.0\Forensic\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
From the main menu, choose Go > Launch 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
On the 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
Using Quick Acquisition
Use the quick acquisition feature to quickly submit a single sample from any view of the
Acquisition mode.
Note The Quick Acquisition feature is available only when you activate it in the
Application Configuration mode. See “Quick Acquisition” on page 64.
 To run a quick acquisition
1. Choose Go > Quick Acquire Sample from the main menu or click the Quick Acquire
Sample icon,
.
The Quick Acquisition dialog box opens.
2. Select an instrument method.
3. Type a name for the raw data file that you acquire.
Do not enter the .raw file extension.
4. For the path, browse to 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:
i.
Select the Manual Injection option.
ii. Click OK.
The application submits the sample to the Acquisition queue. See “Acquisition Page”
on page 324.
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Using Quick Acquisition
• To perform autosampler injection, do the following:
i.
Select the Use Autosampler option.
ii. In the Vial Position box, type a vial position.
iii. 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.
iv. Click OK.
The Quick Acquisition dialog box opens.
v.
Select the Use check box for the device that you want to use for this acquisition.
vi. (Optional) Select the Start Device check box to indicate the device that will
initiate communication with the other instruments.
This is usually the autosampler.
vii. (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.
viii. (Optional) Select the Priority check box to place the sample immediately after
any currently acquiring sample.
ix. (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.
x. Click OK.
The application submits the sample to the Acquisition queue. See “Acquisition Page”
on page 324.
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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
Application Configuration mode. See “Batch Wizard Style” on page 65.
Contents
• Working with Batches
• Using Quick Acquisition
• Real Time Status Pane
• Sample Types
When you plan to work with multiple samples or use similarly designed batches, use the
Acquisition mode to reduce the amount of data you must enter.
Because the nature and types of batches are often similar (in some cases specified by laboratory
standard practices), you can define a batch template that supplies the basic structure of a
batch.
Note When user security is activated, only a user in the LabDirector or Supervisor role
can create a batch template.
Using a master method, you can create a batch and run the samples. A batch represents one or
more samples that are to be acquired, processed, reviewed, and reported as a set. After you
create a batch of samples, you can submit the batch and review the results in the Analysis
mode or you can go directly to viewing and printing reports.
You can set up a calibration batch with known concentrations of the target compounds and
compare the calibration values against samples in future batches.
You can also use the Quick Acquisition feature to quickly submit a single sample from any
page in the Acquisition mode. See “Using Quick Acquisition” on page 321.
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Working with Batches
This section includes instructions for the following tasks:
• Opening and Navigating the Acquisition Mode
• Creating and Submitting Batches
Opening and Navigating the Acquisition Mode
 To access the Acquisition mode
Click Acquisition in the navigation pane.
The navigation pane for the Acquisition mode opens.
As you progress through the Acquisition mode using any of these methods for creating a
batch, the task pane at the top of the view tracks your progress. As you complete each
stage, you can hold your cursor over the view name in the task pane to display the
parameters that you specified for the batch. See Example task pane when you have
completed the Acquisition mode.
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Figure 73. Example task pane when you have completed the Acquisition mode
Hold your cursor over Batch Selection, Sample Definition,
or Report Selection to view the parameters for your batch.
Categories in the Sample Definition list:
QC Samples: QC
Calibration Samples: Calibrator
Blank Samples: Negative
Unknown Samples: All other samples
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Creating and Submitting Batches
To create and submit a batch, the Acquisition mode uses a wizard-style interface to guide you
through these major steps:
1. Selecting a Batch
2. Defining the Sample List
3. Selecting and Reviewing Reports
4. Submitting the Batch
The Acquisition mode provides multiple techniques for creating either a batch or a batch
template.
• To start a new quantitative batch
• To start a new screening batch
• To select a prepared batch
• To reinject samples in a previously acquired batch
• To create a quantitative batch template
• To create a screening batch template
Each batch creation technique has an associated workflow, as shown in the following
flowcharts. Each workflow uses a different combination of Acquisition mode views.
Workflow for Creating an Original Batch
Batch and
Method
Samples
Reports
Finish
To create an original batch, start with the instructions “To start a new quantitative batch” on
page 290 or “To start a new screening batch” on page 292.
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Workflow for Acquiring a Prepared Batch
Batch
Finish
Samples
To acquire a prepared batch, start with the instructions “To select a prepared batch” on
page 294.
Workflow for Reinjecting a Previously Acquired Batch
Batch
Samples
Finish
To process a previously acquired batch, start with the instructions “To reinject samples in a
previously acquired batch” on page 295.
Workflow for Creating or Editing a Batch Template
Template and
Method
Samples
Finish
Note When user security is activated, in either the LabDirector or ITAdmin role, you can
create a batch template.
To create a batch template, start with the instructions “To create a quantitative batch
template” on page 296 or “To create a screening batch template” on page 297.
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Working with Batches
Selecting a Batch
In a Batch Selection view of the Acquisition mode, you can create a new quantitative or
screening batch in any of your current projects/subprojects. Or, you can submit a batch that
you previously prepared and saved, reinject the samples in a batch that you previously
acquired, or create a batch template to use for future batches.
Follow these procedures:
• To start a new quantitative batch
• To start a new screening batch
• To start a new batch from a template
• To select a prepared batch
• To reinject samples in a previously acquired batch
• To create a quantitative batch template
• To create a screening batch template
 To start a new quantitative batch
1. Click Create a New Batch in the navigation pane.
2. Select the Quantitative Batch option.
3. Select the project and subproject where you want to create the new batch.
4. Type a name for the new batch in the Batch Name box.
If the name you enter is not unique, a red warning flashes.
5. Select a method from the Method Selection list.
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The Method Compound Data pane displays the compounds in the method. You cannot
edit the compounds list from the Acquisition mode.
6. To continue to the next view, click Next.
The Sample Definition view opens. See “Defining the Sample List” on page 298.
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 To start a new screening batch
1. Click Create a New Batch in the navigation pane.
2. Select the Screening Batch option.
3. Select the project and subproject where you want to create the new batch.
4. Type a name for the new batch in the Batch Name box.
If the name you enter is not unique, a red warning flashes.
5. Select a method from the Method Selection list.
The Method Compound Databases pane displays the compound databases in the
method. The application uses these databases to identify the compounds in the samples.
You cannot edit the compound database list from the Acquisition mode.
6. To continue to the next view, click Next.
The Sample Definition view opens. See “Defining the Sample List” on page 298.
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 To start a new batch from a template
1. Click Create a New Batch in the navigation pane.
2. Select either the Screening Batch or the Quantitative Batch option.
The Available Templates pane displays only batch templates for the selected option.
3. In the Available Templates pane, select the template and method combination that you
want to use.
The system creates a batch name with the selected template name and appends the date
and time stamp. You can change the default project, subproject, or method associated
with this template.
4. (Optional) Select a different project and subproject where you want to create the new
batch.
5. (Optional) Select a different method to use for the new batch.
6. To continue to the next view, click Next.
The Sample Definition view of the Acquisition mode opens. See “Defining the Sample
List” on page 298.
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 To select a prepared batch
1. Click Submit a Prepared Batch in the navigation pane.
The application displays all your unacquired, saved batches. The TraceFinder application
stores all unacquired batches in the following folder:
…\Thermo\TraceFinder\3.0\Forensic\Projects\projectname\subprojectname
2. Select the batch that 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
sample list for this batch.
• If the batch is unreadable, the application reports that the batch file is not valid and
cannot be opened.
• If a sample in the batch is unreadable, the application cannot open the sample. The
application creates a new sample with the same name and flags the sample. You must
complete the missing information such as Sample Type, Level, and so forth, and then
save the batch before you submit it for acquisition. Or, you can browse in a new raw
data file to replace the corrupt file.
4. Do one of the following:
• To edit the sample list, click Previous.
For detailed instructions, see “Defining the Sample List” on page 298.
–or–
.
• To prepare the batch for acquisition, click Submit,
For detailed instructions, see “Submitting the Batch” on page 313.
–or–
• To save the batch to be acquired later, click Save,
.
The TraceFinder application saves your batch in the following folder:
C:\Thermo\TraceFinder\3.0\Forensic\Projects\projectname\subprojectname
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 To reinject samples in a previously acquired batch
1. Click Reinject Samples in the navigation pane.
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, both quantitative and screening.
4. In the Batch pane, select the batch that 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 298.
• If the batch is unreadable, the application reports that the batch file is not valid and
cannot be opened.
• If a sample in the batch is unreadable, the application creates a new sample with the
same name and flags the sample. You must complete the missing information, such as
Sample Type, Level, and so forth, and then save the batch before you submit it for
acquisition. Or, you can browse in a new raw data file to replace the corrupt file.
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 To create a quantitative batch template
1. Click Create or Edit a Template in the navigation pane.
Note When user security is activated, this page is available only to users in the
LabDirector or Supervisor role.
2. Select the Quantitative Batch option.
3. Select the project and subproject where you want to create the new batch template.
4. Type a name for the new batch template in the Template Name box.
5. Select a method from the Method Selection list.
The Method Compound 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.
The Sample Definition view of the Acquisition mode opens. See “Defining the Sample
List.”
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 To create a screening batch template
1. Click Create or Edit a Template in the navigation pane.
Note When user security is activated, this page is available only to users in the
LabDirector or Supervisor role.
2. Select the Screening Batch option.
3. Select the project and subproject where you want to create the new batch template.
4. Type a name for the new batch template in the Template Name box.
5. Select a method from the Method Selection list.
The Method Compound 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.
The Sample Definition view of the Acquisition mode opens. See “Defining the Sample
List.”
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Defining the Sample List
Use the Samples page in the Sample Definition view of the Acquisition mode, to create a list
of samples for the batch. See “Samples page in the Sample Definition view” on page 306. You
can add samples, insert samples, import a sample list, or remove samples from the list. You can
use the Reference Sample page to select a reference sample to use as a reference peak in the
Data Review. See “Reference Sample page in the Sample Definition view” on page 308.
To create the sample list, you can use either of two sets of function buttons (described in the
following graphic) or you can use commands on the shortcut menu (see the Shortcut Menu
section of the “Samples page parameters” on page 306).
As you enter sample values, you can use the Copy Down and Fill Down commands to quickly
enter column values. For detailed instructions on using Copy Down and Fill Down to enter
column values, see Appendix B, “Using Copy Down and Fill Down.”
Use any of the following procedures to create a sample list. When you finish defining the list
of samples, click Next.
• When you are creating a batch from scratch, creating a batch from a template, or
editing a batch template and you click Next, the Report Selection view opens. See
“Selecting and Reviewing Reports” on page 309.
• When you are editing a prepared batch or reinjecting samples and you click Next, the
Finish Selection view opens. See “Submitting the Batch” on page 313.
Follow these procedures:
• To add samples to the list
• To insert samples into the list
• To import samples into the list
• To remove samples from the list
• To reinject a sample from a previously acquired batch
• To select channels for the batch
• To assign a specific channel to a sample
• To select a reference sample
 To add samples to the list
1. Select the number of sample rows to add
and then click the Add icon,
or
.
2. Type a file name in the Filename column for each sample.
Each file name must be unique.
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3. Select a sample type from the Sample Type list for each sample.
Available sample types
Specimen
QC
Solvent
Calibrator
Unextracted
Negative
Hydrolysis
For a detailed description of each sample type, see “Sample Types” on page 337.
4. For each Calibrator or QC sample, select a level from the Level list.
The sample levels are defined in the master method. If there are no levels to select in the
Level list, ask a user with Supervisor or LabDirector permissions to edit the method and
specify the levels. Then return to the Acquisition mode, and begin the batch again. The
application does not save a batch when you leave the Acquisition mode.
If you have Supervisor or LabDirector permission, do the following:
a. Return to the Method Development mode.
b. Open the method.
c. Click the Compounds tab.
d. Click the Calibration Levels tab.
e. Add the levels.
f.
Save the method.
For detailed instructions, see “Calibration Levels” on page 166.
5. For each sample, type a vial position in the Vial Position column.
Tip Use the Fill Down command to make entering vial positions easier.
6. For each sample, type a volume in the Injection Volume column.
The minimum injection volume value allowed is 0.1 μL; the maximum injection volume
value allowed is 5000 μL.
7. (Optional) Type or edit the values for the remaining columns.
Note When you use the horizontal scroll bar at the bottom of the sample 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.”
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 To insert samples into the list
1. Select the sample above which you want to insert new Specimen samples.
You cannot use the Insert command to create the first sample row.
2. Select the number of samples to insert
and then click the Insert icon,
or
.
The application inserts the Specimen samples above the selected sample.
Inserted
samples
3. For each sample, type a file name in the Filename column.
Each file name must be unique.
4. For each sample, select a sample type from the Sample Type list.
For a detailed description of each sample type, see “Sample Types” on page 337.
Available sample types
Specimen
QC
Solvent
Calibrator
Unextracted
Negative
Hydrolysis
5. For each Calibrator or QC 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. Then return to the Acquisition mode, and begin the batch again.
The application does not save a batch when you leave the Acquisition mode.
If you have Supervisor or LabDirector permission, follow the instructions in step 4 of the
procedure “To add samples to the list” on page 298.
6. Type a vial position in the Vial Position column for each sample.
Tip Use the Fill Down command to make entering vial positions easier.
7. For each sample, type a volume in the Injection Volume column.
The minimum injection volume allowed is 0.1 μL; the maximum injection volume
allowed is 5000 μL.
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8. (Optional) Type or edit the values for the remaining columns.
Note When you use the horizontal scroll bar at the bottom of the sample list, the
Status, Filename, Sample Type, and Level columns stay fixed while the other columns
scroll right and left.
 To import samples into the list
1. Click Import,
.
The Sample Import Tool dialog box opens.
Use this dialog box to import a sample list from a CSV, an XML, or an SLD file.
2. Click Browse and select a CSV, an XML, or an SLD file with the sample definitions that
you want to import.
Note The .csv, .xml, or .sld file format must match the TraceFinder file format.
3. From the Imported Samples Will Be list, select either Appended to the End of the List
or Inserted at the Selected Row.
4. Click Import.
The Sample Import Tool dialog box closes, and the application adds the specified samples
to the sample list.
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.
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Xcalibur sample type
TraceFinder sample type
Blank
Negative
Std Bracket
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5. For each Calibrator or QC 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. Then return to the Acquisition mode, and begin the batch again.
The application does not save a batch when you leave the Acquisition mode.
If you have Supervisor or LabDirector permission, follow the instructions in step 4 of the
procedure “To add samples to the list” on page 298.
For detailed instructions about defining calibration levels, see “Calibration Levels” on
page 166.
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 sample 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.
 To remove samples from the list
1. Select the samples that you want to remove.
Tip Use the CTRL or SHIFT keys to select multiple samples.
2. Right-click and choose Remove Selected Samples from the shortcut menu.
 To reinject a sample from a previously acquired batch
1. In the sample list, select the sample to reinject.
2. Right-click and choose Reinject Selected Samples from the shortcut menu.
The TraceFinder application creates a copy of the selected sample and appends INJ001 to
the file name. Additional reinjections of the same sample are numbered INJ002, INJ003,
and so forth.
The TraceFinder application copies all parameter values from the original sample.
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A green status icon indicates previously acquired samples (acquired and processed) and
the sample name is grayed out. A blue status icon indicates samples created for reinjection
(not acquired).
When you submit this batch, the application acquires only the reinjection samples.
 To select channels for the batch
Note These features are available only when you have activated multiplexing in the
Application Configuration mode. See “Multiplexing” on page 66.
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 Application Configuration mode. See “Multiplexing”
on page 66.
Clearing a channel in the Multiplexing Channels area does not remove this channel
selection from the Channels list for each sample. When you assign a channel to a sample,
be careful not to assign a channel that is not available.
 To assign a specific channel to a sample
1. Scroll to the Channel column.
Note The Channel column is available only when you have activated multiplexing in
the Application Configuration mode. See “Multiplexing” on page 66.
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.
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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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 To select a reference sample
1. Click the Reference Sample tab.
The Reference Sample page in the Sample Definition view opens. See “Reference Sample
page in the Sample Definition view” on page 308.
You can select one reference sample to use as a reference peak in the Data Review.
2. Right-click the Reference Sample page and choose Add Reference Sample from the
shortcut menu.
The Open Chromatograph Reference Sample dialog box opens.
Note If you are using a new method, you will not see any reference samples here. You
must create and save a batch using the current method to see the reference samples in
this list.
3. Select a project from the list of projects.
4. Select a subproject from the list of subprojects.
5. Select a batch from the list of batches.
The TraceFinder application displays only batches that were created using the current
master method.
6. Select a sample from the list of processed samples on the right.
The TraceFinder application displays all the processed samples in the selected batch. To
use a sample as a reference sample, the sample must have been processed with the current
master method.
7. Click Open.
8. The application adds the reference sample to the Reference Sample page.
9. (Optional) Enter values for Sample ID, Sample Name, Comment, and Barcode Actual.
10. (Optional) Change the Vial Position for the sample.
The application uses the peak in this sample as a reference peak in the Analysis mode. See
“Reference Peak” on page 451.
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Figure 74. Samples page in the Sample Definition view
Table 54. Samples page parameters (Sheet 1 of 2)
Parameter
Definition
Previous
Returns you to the previous Acquisition mode view.
Next
Takes you to the next Acquisition mode view.
Status color codes
Sample is not acquired.
Sample is acquired but not processed.
Sample is acquired and processed.
Sample is currently acquiring.
Sample Controls
Add
Adds the specified number of empty rows to the sample grid.
Insert
Inserts the specified number of empty rows above the selected row.
Import
Opens the Sample Import Tool where you can import samples defined in a CSV file or
an XML file.
Multiplexing Channels
These features are available only when you have activated multiplexing in the Application
Configuration mode. See “Multiplexing” on page 66.
All Channels
Uses all configured channels to acquire this batch.
Channel 1-n
Uses only the selected channels to acquire this batch.
Shortcut menu commands
Add Sample
Adds a single empty row to the sample grid.
Insert Sample
Inserts a single empty row to the sample grid above the selected row.
Insert Copy Sample
Copies the currently selected row and inserts a copy above the row.
Reinject Selected
Samples
Creates a copy of the selected sample and appends INJ001 to the file name. Additional
reinjections of the same sample are numbered INJ002, INJ003, and so forth.
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Table 54. Samples page parameters (Sheet 2 of 2)
Parameter
Definition
Remove Selected
Samples
Removes selected samples from the sample grid.
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.”
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 345.
Enable/Disable Sample
Weight Calculation
Displays or hides the Sample Volume, Dilution Factor, Sample Weight, Calculation Type,
and Final Units columns.
Copy
Copies the data in the selected rows or columns to the Clipboard. Use this command to
copy sample information to 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
a Microsoft Excel spreadsheet. You cannot paste this data back into the Acquisition mode
sample list.
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.
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Figure 75. Reference Sample page in the Sample Definition view
Table 55. Reference Sample page parameters
Parameter
Status
Description
Sample is not acquired.
Sample is acquired but not processed.
Sample is acquired and processed.
Sample is currently acquiring.
Filename
Name of the raw data file that contains the sample data.
Sample ID
A user-defined, alphanumeric string that identifies a sample.
Sample Name
A user-defined name that identifies a sample.
Vial Position
The tray vial number used for an autosampler acquisition.
Barcode Actual
A user-entered barcode for the vial.
Shortcut menu commands
Add Reference Sample
Opens the Open Chromatogram Reference Sample dialog box where you can select a
reference sample.
Delete Selected
Deletes the reference sample.
Copy
Copies the data in the selected rows or columns to the Clipboard. Use this command to
copy sample information to another application, such as an Excel spreadsheet. You cannot
paste this data back into the reference sample list.
Copy With Headers
Copies the data in the selected rows or columns and the associated column headers to the
Clipboard. Use this command to copy sample information to another application, such as
an Excel spreadsheet. You cannot paste this data back into the reference sample list.
Paste
Pastes a single column of copied data from another application, such as an Excel
spreadsheet, into the selected column.
Export to CSV File
Opens the Save As dialog box where you can save the current sample list to a CSV file.
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Selecting and Reviewing Reports
On the Report Selection view, you can specify the types of reports that you want to create. See
“Report Selection view” on page 311. 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 that you generate, you can create a hardcopy printout, a PDF
file, or an XML file.
• For each custom report that you generate, you can create a hardcopy printout or an
XLSM file.
• For each target screening report that you generate, you can create a hardcopy printout or
a PDF file.
• For each ToxID report that you generate, you can create a hardcopy printout or a PDF
file.
Use any of the following procedures to create a reports list. When you finish specifying your
report options, click Next to go to the Finish view and submit your batch. See “Submitting
the Batch” on page 313.
The application writes the resulting output files for your reports to the following folder:
…\TraceFinder\3.0\Forensic\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, an XML, or an XLSM file
• To specify a custom report in hardcopy or XLSM format
• To specify a ToxID or target screening report in hardcopy format or as a PDF file
• To export reports to a specific folder
 To edit a report description
Select the Report Title column and edit the default title.
The default report title is the same as the report name.
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 To preview a standard report
1. Click
(magnifier 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
.
Note Only Standard report types have preview documents.
 To specify a standard report in print format or as a PDF, an XML, or an XLSM file
1. For each type of report that you want to create, select the check box in the Print, Create
PDF, or Create XML 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 ToxID or 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 lower left corner of the view.
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The Browse For Folder dialog box opens.
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 76. Report Selection view
Table 56. Report Selection view parameters (Sheet 1 of 2)
Parameter
Description
Example
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 Title
User-editable description to be used on a report.
Report Type
The type of report: Standard, Custom, ToxID, or Target Screening.
Print
Reports to be sent to the printer.
Create PDF
Reports to be saved as PDF files.
Available only for standard, ToxID, 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 56. Report Selection view 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 39.
Shortcut menu:
Copy Down
Copies the selected or cleared state to all subsequent reports in the column.
Export Results
Writes all reports to the specified folder in addition to the batch Reports folder.
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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 320.
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.
 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 57. Instrument states (Sheet 1 of 2)
Instrument state
Description
Turn Device On
Keeps the system in the On state when the current run finishes,
so you can begin another run without waiting. All power and
flows are maintained at operational levels.
Default: On
Turn Device Standby
Keeps the system in the Standby state when the current run
finishes, so you can begin another run with only a short delay
between runs.
Some devices do not have a Standby feature. For devices with
this feature, the device enters a power-saving or
consumable-saving mode, and you can switch the device back
on in approximately 15 minutes. Depending on the
instrument, this state turns liquid flows off but maintains
heaters and other subsystems in an On state so that there is no
warm-up time required when you change from Standby to On.
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Table 57. Instrument states (Sheet 2 of 2)
Instrument state
Description
Turn Device Off
Keeps the system in the Off state when the current run
finishes. The Off state indicates that all power to the
instrument, which the TraceFinder application can control, is
turned off. This includes power to all heaters and
subassemblies, but in some cases not all subassemblies.
Some devices do not have an Off feature. For devices that do
have this feature, the device enters a power-saving or
consumable-saving mode, and you can switch the device back
on. When several runs are queued, the application uses the
system power scheme of the last submitted run.
Instrument status indicators
Green indicates that the device is turned on or is running.
Yellow indicates that the device is in standby mode or is
waiting for contact closure.
Red indicates that the device is turned off or that there is an
error with the device.
 To save a batch for later acquisition
From the Finish view, click Save,
.
The TraceFinder application saves your batch as a prepared file.
 To start an acquisition
1. Click Submit,
.
The Submit Options dialog box opens. For detailed descriptions of the parameters, see
“Submit Options dialog box” on page 317.
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.
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6. (Optional with multiplexing activated) Select the Priority Sequence check box.
The application acquires the priority batch on the next available channel or the assigned
channel.
7. (Optional without multiplexing activated) Select the Priority Sequence check box and
then select one of the following priority options to place the batch in the queue:
• Next Available Batch places the batch immediately after the currently acquiring
batch.
• Next Available Sample places the batch immediately after the currently acquiring
sample.
Note When you select Full Sequence Submission in the Application Configuration
mode, these options are unavailable because the current batch and the current sample
are, in effect, the same thing.
8. Do one of the following:
To start the selected processes, click OK.
The selected processes begin, and the TraceFinder application shows the real-time display
at the bottom of the current window. You can begin another batch in the Acquisition
mode while you watch the real-time display of the currently acquiring batch.
–or–
Click Cancel to exit the Acquisition mode without performing any tasks.
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Figure 77. 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
Number of samples to be submitted for acquisition,
processing, or reporting.
Acquire Data
(Default) Submits the current batch to acquisition.
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Table 58. Submit Options dialog box parameters (Sheet 2 of 2)
Parameter
Description
Process Data
(Default) Processes the data for the current batch.
Create Reports
Creates reports for the current batch.
Priority Sequence
With multiplexing activated, places the batch immediately
after the currently acquiring batch.
Without multiplexing activated, specifies one of the following
priority options to place the batch in the queue:
Next Available Batch: Places the batch immediately after the
currently acquiring batch.
Next Available Sample: Places the batch immediately after
the currently acquiring sample.
Note When you select Full Sequence Submission in the
Application Configuration mode, these options are
unavailable because the current batch and the current
sample are, in effect, the same thing.
Acquisition pane
Device Name
Lists all configured instruments.
If the instrument that you want to use is not configured, close
the TraceFinder application, configure the instrument, and
then reopen the TraceFinder application. You cannot
configure an instrument while the TraceFinder application is
running.
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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.
Post-run System
State
Specifies the system state after it acquires the last batch.
On (default), Standby, or Off.
Hide/Show Details
Collapses or expands the acquisition details of the Submit
Options dialog box.
OK
Begins the selected processes.
Cancel
Closes the Submit Options dialog box without submitting any
tasks.
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Working with Batches
 To view the output files
Locate the files to view from the following directories:
• The TraceFinder application writes saved batches to the subproject folder:
…\TraceFinder\3.0\Forensic\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 78. Finish view
Table 59. Finish view parameters
Parameter
Description
System Status
The System Status pane displays the following:
• Devices used for the acquisition
• Project, subproject, and name of the batch
• Number of 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.
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 prepared batch.
Submit
Opens the Submit Options dialog box where you can optionally choose to generate reports.
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Using Quick Acquisition
Using Quick Acquisition
Use the quick acquisition feature to quickly submit a single sample from any view of the
Acquisition mode.
Note The Quick Acquisition feature is available only when you activate it in the
Application Configuration mode. See “Quick Acquisition” on page 64.
 To run a quick acquisition
1. Choose Go > Quick Acquire Sample from the main menu or click the Quick Acquire
Sample icon,
.
The Quick Acquisition dialog box opens.
2. Select an instrument method.
3. Type a name for the raw data file that you acquire.
Do not enter the .raw file extension.
4. For the path, browse to 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:
i.
Select the Manual Injection option.
ii. Click OK.
The application submits the sample to the Acquisition queue. See “Acquisition Page”
on page 324.
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Using Quick Acquisition
• To perform autosampler injection, do the following:
i.
Select the Use Autosampler option.
ii. In the Vial Position box, type a vial position.
iii. 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.
iv. Click OK.
The Quick Acquisition dialog box opens.
v.
Select the Use check box for the device that you want to use for this acquisition.
vi. (Optional) Select the Start Device check box to indicate the device that will
initiate communication with the other instruments.
This is usually the autosampler.
vii. (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.
viii. (Optional) Select the Priority check box to place the sample immediately after
any currently acquiring sample.
ix. (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.
x. Click OK.
The application submits the sample to the Acquisition queue. See “Acquisition Page”
on page 324.
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Real Time Status Pane
Real Time Status Pane
You can access the Real Time Status pane from any mode in the TraceFinder application.
 To access the Real Time Status Pane from any mode
Click Real Time Status in the upper right corner of the TraceFinder window.
The Real Time Status pane opens at the bottom of the current view.
Figure 79. Real Time Status pane
The Real Time Status pane has four pages of information and a real-time trace pane:
• Acquisition Page
• Instrument Page
• Devices Page
• Queues Page
• Real-Time Trace Display
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Real Time Status Pane
Acquisition Page
Use the Acquisition page to monitor the progress as the application acquires the samples.
Use the Start,
, Stop,
, or Pause,
,
icons to control batches in the Acquisition queue.
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Instrument Page
Use the Instrument page to monitor the currently acquiring sample.
When you run single sample
submission, this displays the
sample name.
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Devices Page
Use the Devices page to monitor the status of the instrument. The feedback you see on the
Devices page depends on the instrument you are using. The following examples show an
Accela autosampler and an Aria™ multiplexing device.
Accela Autosampler Feedback
Aria Multiplexing Feedback
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Follow these procedures:
• To pause the autosampler
• To control the channels
• To view the pressure trace
• To control the channels
 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 control the channels
Right-click the channel name and choose a command from the shortcut menu.
Table 60. Autosampler shortcut menu commands
Command
Description
On
Turns on a stopped pump and continues acquiring the sample
list assigned to that channel.
Off
After the current sample completes, the application stops
acquiring and the pump shuts down.
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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 To access the Aria multiplexing controls
Click Direct Control.
The Aria MX Direct Control dialog box opens.
For detailed descriptions of the features in this dialog box, refer to the Transcend Systems
with Xcalibur Software User Guide.
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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 332.
Follow these procedures:
• To pause all batches in a queue
• To remove a single batch from a queue
• To remove all batches in a queue
• To remove all pending batches
 To pause all batches in a queue
1. Select a queue (Acquisition, Processing, or Reporting).
Note When multiplexing is activated, you can have as many as four samples acquiring
at once. Pausing the Acquisition queue does not affect any acquiring samples.
2. Right-click and choose Pause Queue from the shortcut menu.
After the current sample completes, the application pauses all batches and samples in the
specified queue. Only the selected queue is affected.
3. To restart a paused queue, select the queue, right-click, and choose Resume Queue from
the shortcut menu.
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 To remove a single batch from a queue
1. Select a queue (Acquisition, Processing, or Reporting).
2. Right-click and choose Stop Active Batch from the shortcut menu.
Note This command is available only when there are active batches in the queue.
Paused batches and batches that contain only pending samples are not “active.”
The application confirms that you want to remove the active batch from the selected
queue. After the current sample completes, the application removes the batch and all
pending samples from the queue. Only the selected queue is affected.
 To remove all batches in a queue
1. Select a queue (Acquisition, Processing, or Reporting).
2. Right-click and choose Stop All Batches from the shortcut menu.
The application removes all batches with pending samples from the selected queue. The
current sample continues to acquire. Only the selected queue is affected.
 To remove all pending batches
1. Select a queue (Acquisition, Processing, or Reporting).
2. Right-click and choose Remove Pending Batches from the shortcut menu.
Note A pending batch is a batch in which all samples are pending. If any sample in
the batch is active, the batch is not affected by this command.
The application removes all batches that contain only pending samples. Only the selected
queue is affected.
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Figure 80. Queue-level shortcut menu
Table 61. Queue-level shortcut menu commands
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Command
Description
Pause Queue
After the current sample completes, the application pauses the
specified queue. Only the selected queue is affected.
Resume Queue
Returns the paused queue to active status.
Stop Active Batch
Removes all pending samples from the specified queue. The active
sample is not affected.
Stop All Batches
Removes all pending samples and batches from the specified
queue. The active sample is not affected.
Reactivate All Batches
Returns all paused batches to active status.
Remove Pending
Batches
Removes all pending batches from the specified queue. The active
batch is not affected.
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Batch-Level Commands
Use the batch-level commands to pause or remove entire batches or samples within batches
from any of the queues on the Queues page. See “Batch-level shortcut menu.”
Follow these procedures:
• To remove a single pending sample from a batch
• To remove all pending samples from a batch
• To stop a batch
• To remove a pending batch
 To remove a single pending sample from a batch
1. Select a pending sample.
2. Right-click the sample and choose Remove Sample from the shortcut menu.
The application confirms that you want to remove the selected sample from the batch and
then removes the sample.
 To remove all pending samples from a batch
1. Select a batch in any of the queues (Acquisition, Processing, or Reporting).
The batch must have at least one pending sample.
2. Right-click and choose Remove Pending Samples from the shortcut menu.
The application confirms that you want to remove all pending samples from the batch
and then removes the samples. If the batch includes only pending samples, the
application removes the batch from the queue.
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 To stop a batch
1. Select an active batch in any of the queues (Acquisition, Processing, or Reporting).
Note The batch must have at least one active sample and one pending sample.
2. Right-click and choose Stop Batch from the shortcut menu.
The application confirms that you want to remove the selected batch from the queue.
After the current sample completes, the application removes the batch and all pending
samples from the queue.
 To remove a pending batch
1. Select a pending batch in any of the queues (Acquisition, Processing, or Reporting).
Note A pending batch is a batch in which all samples are pending. If any sample in
the batch is active, this command is not available.
2. Right-click and choose Remove Pending Batch from the shortcut menu.
The application confirms that you want to remove the selected batch from the queue and
then removes the batch from the queue.
Figure 81. Batch-level shortcut menu
Table 62. Batch-level shortcut menu commands
Command
Description
Stop Batch
After the current sample completes, the application removes all
samples in the selected batch.
Remove Pending Batch Removes all samples from the selected pending batch.
Remove Pending
Samples
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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 Status pane shows only the TIC trace as each sample acquires. To
observe specific traces, such as the internal standard, use the RTV Display Traces function to
display multiple traces.
When you create your method, you can specify additional traces to display in the real-time
viewer and in which order the traces are displayed. The application always displays the TIC
trace in the top pane. See “Real Time Viewer” on page 170.
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 To display multiple traces
Right-click the chromatogram pane and choose the number of traces to display.
The chromatogram pane displays real-time chromatograms for the selected number of
traces.
The TIC is always displayed at the top. When there are more traces than can fit in the
pane, you can scroll through the traces.
For each trace, the application displays the mass or precursor mass.
Figure 82. Real-time trace display with multiple traces
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Sample Types
Sample Types
The TraceFinder application uses the following sample types in all sample definitions and
reports. To view example standard reports specific to a sample type, see Appendix A,
“Reports.”
Table 63. Sample type definitions
Thermo Scientific
Sample type
Definition
Negative
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.
Unextracted
Similar to a Negative sample, but contains target compounds. By
analyzing a sample, you can confirm that there are no residual
compounds in the solvent system that can cause erroneous results.
Calibrator
(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
(Quality Check) 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 sample, it
compares the measured quantity with the expected value and an
acceptability range. The quantitative analysis of a QC sample is
classified as passed if the difference between the observed and expected
quantities is within the user-defined tolerance. A QC sample is classified
as failed if the difference between the observed and expected quantities is
outside the user-defined tolerance.
Solvent
Contains only solvent.
Specimen
Used for quantitative analysis of samples.
Hydrolysis
Checks the degradation of compounds dissolved in water.
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Using the Analysis Mode
This chapter includes instructions about 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 for Quantitation Methods
• Working in Data Review for Target Screening Methods
• Working in the Report View
• Working in the Project Administration View
• Working in the Local Method View
• Working in the Batch Template Editor
Use the Analysis mode to do the following:
• 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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 To access the Analysis mode
Click Analysis in the navigation pane.
The Analysis navigation pane opens.
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Using Quick Acquisition
Using Quick Acquisition
Use the quick acquisition feature to quickly submit a single sample from any view of the
Acquisition mode.
Note The Quick Acquisition feature is available only when you activate it in the
Application Configuration mode. See “Quick Acquisition” on page 64.
 To run a quick acquisition
1. Choose Go > Quick Acquire Sample from the main menu or click the Quick Acquire
Sample icon,
.
The Quick Acquisition dialog box opens.
2. Select an instrument method.
3. Type a name for the raw data file that you acquire.
Do not enter the .raw file extension.
4. For the path, browse to 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:
i.
Select the Manual Injection option.
ii. Click OK.
The application submits the sample to the Acquisition queue. See “Acquisition Page”
on page 324.
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Using Quick Acquisition
• To perform autosampler injection, do the following:
i.
Select the Use Autosampler option.
ii. In the Vial Position box, type a vial position.
iii. 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.
iv. Click OK.
The Quick Acquisition dialog box opens.
v.
Select the Use check box for the device that you want to use for this acquisition.
vi. (Optional) Select the Start Device check box to indicate the device that will
initiate communication with the other instruments.
This is usually the autosampler.
vii. (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.
viii. (Optional) Select the Priority check box to place the sample immediately after
any currently acquiring sample.
ix. (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.
x. Click OK.
The application submits the sample to the Acquisition queue. See “Acquisition Page”
on page 324.
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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 includes the following topics:
• Samples Page
• Auto Samples Page
• Reference Samples Page
 To open the Batch View
1. Click Analysis in the navigation pane of the current mode.
2. In the Analysis navigation pane, click Batch View.
The Batch View navigation pane opens.
Available only when you activate
Intelligent Sequencing in the Application
Configuration mode.
Available only for quantitative batches.
The Analysis mode includes a toolbar:
Use the toolbar or the equivalent commands on the Batch View shortcut menu to create the
sample list and submit samples for acquisition. See “Toolbar” on page 351 or “Batch View
Shortcut Menu” on page 355.
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Samples Page
To open the Samples page, click Samples in the Batch View navigation pane.
This section contains information about the following topics:
• Samples Page Features
• Creating a New Batch
• Editing a Batch
• Submitting a Batch
Samples Page Features
The Samples page is divided into three panes:
• Samples pane
Use the sample list pane to create a batch. See “Samples Pane” on page 345.
• Automated Batch Reports pane
Use the Automated Batch Reports pane to select the type of output formats that you want
to generate for the reports. See “Automated Batch Reports Pane” on page 357.
• Compound Active Status pane
Use the Compound Active Status pane to make specific compounds active or inactive. See
“Compound Active Status Pane” on page 359.
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Working in the Batch View
Samples pane
Automated Batch Reports pane
Compound Active Status pane
Tip To resize the panes, drag the separators that divide the panes.
Samples Pane
The samples pane includes the following features:
• Column Display
• Status Indicators
• Blank Subtraction in Target Screening Batches
• Sample Weight Calculation
• Toolbar
• Batch View Sample List
• Batch View Shortcut Menu
Column Display
The sample list contains many columns of information. You can scroll to see all the columns
of information, and you can customize which columns to display and their display order.
Follow these procedures:
• To scroll the sample list
• To customize the column display
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 To scroll the sample list
Use the horizontal scroll bar at the bottom of the sample list to view all the information.
When you use the scroll bar at the bottom of the sample list, the Status, Filename, Sample
Type, and Level columns stay fixed while the other columns scroll right and left.
 To customize the column display
1. Right-click the sample list and choose Modify Columns from the shortcut menu.
The Modify Columns dialog box opens. See “Modify Columns dialog box.”
2. Use the arrow buttons to move all the columns that you want displayed to the Displayed
Columns pane.
These columns are displayed after the Status, Filename, Sample Type, and Level columns.
3. To arrange the order of the columns, do the following:
a. In the Displayed Columns pane, select a column name.
b. Use Up or Down to move the selected column up or down in the list.
The first column in the list represents the leftmost column in the Batch View sample
list, and the last column in the list represents the rightmost column in the Batch View
sample list.
Note You cannot move the Status, Filename, Sample Type, or Level column.
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. Repeat step 4 for all columns whose widths you want to change, and click OK.
The columns in the sample list immediately reflect your changes. The application uses
these settings for all sample lists in the Batch View.
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Figure 83. Modify Columns dialog box
Table 64. Modify Columns function buttons
Function
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 column.
Moves all columns except Status, Filename, Sample Type, and 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 column.
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 column.
Note In target screening batches only, a Blank Subtraction column is added to the fixed
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
Blank Subtraction in Target Screening Batches
In target screening batches only, use the Blank Subtraction feature to select which negative
samples you want to use for peak subtraction. The application subtracts the areas of the peaks
in the selected negative samples from the matching areas in the specimen samples.
When you process the batch sequence, the application subtracts the peaks in a selected
negative sample from all specimen samples that follow it, until it encounters another negative
sample.
To activate the Blank Subtraction feature, see “To specify peak filter settings” on page 212.
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Sample Weight Calculation
Use the sample weight features to calculate the conversion factor for a sample. The application
uses different methods to calculate the conversion factor for liquid or solid calculation types.
Liquid: SampleVolume DilutionFactor
Solid: (SampleVolume × DilutionFactor) SampleWeight
Manual: The application does not calculate the Conversion Factor. Instead, you can enter the
Conversion Factor value.
Follow these procedures:
• To display the features for calculating sample weight
• To calculate the conversion factor for a liquid sample
• To calculate the conversion factor for a solid sample
• To manually specify the conversion factor for a sample
 To display the features for calculating sample weight
If the Conversion Factor, Sample Volume, Dilution Factor, Sample Weight, Calculation
Type, and Final Units columns are not visible, right-click and choose Enable Sample
Weight Calculation from the shortcut menu.
 To calculate the conversion factor for a liquid sample
1. From the Calculation Type list, select Liquid.
For a liquid sample, the Sample Weight value is not editable.
2. In the Sample Volume column, type the volume in ng/mL for your sample.
3. In the Dilution Factor column, type the value for the dilution.
For example, if you have 1000 ng/mL of a substance that is too concentrated for the mass
spectrometer, you can dilute it by 1000. Then your injection volume is 1, your conversion
factor is 1000, and your sample amount is 1000.
4. In the Final Units column, type the units that you want to use for the calculated amount
in the Data Review view, on the Active View page in the Report View, or in reports.
The application uses the following formula to calculate the Conversion Factor:
SampleVolume DilutionFactor
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 To calculate the conversion factor for a solid sample
1. From the Calculation Type list, select Solid.
2. In the Sample Weight column, type the weight in ng for your sample.
3. In the Sample Volume column, type the volume in ng/ml for your sample.
4. In the Dilution Factor column, type the value for the dilution.
For example, if you have 1000 ng/ml of a substance that is too concentrated for the mass
spectrometer, you can dilute it by 1000. Then your injection volume is 1, your conversion
factor is 1000, and your sample amount is 1000.
5. In the Final Units column, type the units that you want to use for the calculated amount
in the Data Review view, on the Active View page in the Report View, or in reports.
The application uses the following formula to calculate the Conversion Factor:
(SampleVolume × DilutionFactor) SampleWeight
 To manually specify the conversion factor for a sample
1. From the Calculation Type list, select Manual.
For a manually calculated sample, the only available columns are the Conversion Factor
and the Final Units.
2. In the Conversion Factor column, type the conversion factor to use for your sample.
3. In the Final Units column, type the units that you want to use for the calculated amount
in the Data Review view, on the Active View page in the Report View, or in reports.
The application uses the specified conversion factor when it calculates the amount for the
sample.
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Toolbar
The Analysis mode includes this toolbar for creating and submitting a batch.
Table 65. Toolbar functions
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 363.
Inserts a new, empty sample or samples above the selected sample. See
the instructions “To insert samples into the list” on page 363.
Removes the selected samples from the sample list. See the
instructions “To remove samples from the list” on page 364.
Adds imported samples from a CSV, an XML, or an SLD file to the
sample list. See the instructions “To import samples into the list” on
page 363.
Submits only the selected samples for acquisition, processing, or
report generation. See the instructions “To submit samples in the
batch” on page 371.
Submits the batch for acquisition, processing, or report generation.
See the instructions “To submit samples in the batch” on page 371.
Opens the Batch Wizard where you can use a batch template to define
a standard sequence composed of various sample types to be assembled
into a batch of samples. See “Creating a Batch Using the Batch
Wizard” on page 379.
Opens the Batch Template Editor where you can create a batch
template that contains the basic settings and sample types for your
batches. See “Working in the Batch Template Editor” on page 500.
Opens the Quick Acquisition dialog box where you can quickly
submit a single sample. See “Using Quick Acquisition” on page 341.
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Batch View Sample List
The sample list displays all the quantitative data for the samples of a batch.
Status indicators for each sample indicate if the sample is currently acquiring, not acquired,
acquired, or processed.
The sample list includes the following columns of information:
Figure 84. Batch View sample list
Note
• In target screening batches only, the sample list includes a Blank Subtraction column
after the Sample Type column.
• Cells in the sample list that are not editable, such as Barcode Actual, are shaded and
empty.
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Table 66. Batch View sample list columns (Sheet 1 of 2)
Column
Status
Description
Sample is not acquired.
Sample is acquired but not processed.
Sample is acquired and processed.
Sample is currently acquiring.
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:
Specimen, QC, Solvent, Calibrator, Hydrolysis, Unextracted, or Negative
Default: Specimen
Qual Processing
Indicates samples to be processed with the qualitative peak processing criteria specified in
the method. The Qualitative View displays processed data for the selected samples.
Blank Subtraction
Specifies a negative sample to use for blank subtraction.
Level
The level defined for a calibration sample or quality control sample.
Sample ID
A user-defined, alphanumeric string that identifies a sample.
Sample Name
A user-defined name that identifies a sample.
Vial Position
The tray vial number used for an autosampler acquisition.
Injection Volume
The injection volume (in microliters) of the injected sample.
When you are using an autosampler, you can set the default injection volume in the
Autosampler dialog box in the Instrument View. The minimum and maximum injection
volumes that you can use depend on the Autosampler you configure. The usable range
depends on the injection mode and might be smaller than the displayed range.
The Injection Volume value set in the master method overwrites the value in the instrument
method.
Range: 0.1 through 5000 μL
Calculation Type
Liquid: The application calculates the Conversion Factor as
SampleVolume DilutionFactor
Solid: The application calculates the Conversion Factor as
(SampleVolume × DilutionFactor) SampleWeight
Manual: Sample Volume, Dilution Factor, Sample Weight, and Final Units columns are not
available, and the Conversion Factor value is editable.
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Table 66. Batch View sample list columns (Sheet 2 of 2)
Column
Description
Conversion Factor
Editable only when Calculation Type is Manual. Default: 1
Sample Volume
Default: 1
Dilution Factor
Default: 1
Sample Weight
Available only when Calculation Type is Solid. Default: 1
Final Units
Specifies the calculated amount in the Data Review view, on the Active View page in the
Report View, or in reports.
Default: 1
Instrument Method
Specifies the instrument to use for the acquisition.
Channel
Specifies the channel on which the sample was run. If the sample is not acquired, the value is
Pending. The Channel column is available only when you have activated multiplexing in the
Application Configuration mode. See “Multiplexing” on page 66.
Barcode Expected
A user-entered barcode for the vial.
Barcode Actual
An actual barcode for the vial. This value is not editable.
Comment
A user-defined comment for the sample.
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Batch View Shortcut Menu
The Batch View includes a shortcut menu for creating a batch.
Table 67. 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 363.
Browse In Raw File
Opens a dialog box where you can select a raw data file to use for the selected sample row.
Map Raw Files to
Samples
Opens a dialog box where you can select multiple raw data files to use for the selected
sample rows.
Copy Down
Copies the value in the selected row to all rows below it. This command is available only
when you have selected a value that can be copied down.
Fill Down
Enters sequential values in the column starting with the value in the selected row and
ending with the last row in the column. This command is available only when you have
selected a value that can be filled down.
Modify Columns
Opens the Modify Columns dialog box. See “Column Display” on page 345.
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
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Table 67. Batch View shortcut menu commands (Sheet 2 of 2)
Command
Description
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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Automated Batch Reports Pane
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 about specifying which reports and output formats are
generated, see “Specifying the Reports Configuration” on page 39.
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 about specifying which reports and output formats are generated
and which reports are batch-level, see “Specifying the Reports Configuration” on page 39.
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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Compound Active Status Pane
In the Compound Active Status pane, you can choose specific compounds to be active or
inactive.
 To set a compound as active or inactive
1. In the sample list, select a sample.
All compounds in the selected sample are listed in the Compound Active Status pane.
The default active/inactive status is determined by the identification settings in the local
method. For information about setting the identification parameters, see “Identification”
on page 117.
• To display compounds alphabetically, right-click and choose Sort by Compound
Name from the shortcut menu.
• To display compounds from shorter to longer retention time, right-click and choose
Sort by Retention Time from the shortcut menu.
2. Select or clear the Active check box for the compound.
For instructions about changing the active/inactive status in the Data Review view, see
“Inactive and Excluded Compounds” on page 435.
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Compound Active/Inactive Status
You can specify which compounds are active or inactive in the Local Method View or the
Batch View.
Figure 85. Active and inactive compounds in the Local Method View
For details about setting the status on the Identification page, see “Identification” on
page 117.
Figure 86. Active and inactive compounds in the Batch View
For details about setting the status in the Batch View, see “Compound Active Status Pane” on
page 359.
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Creating a New Batch
In the Batch View, you can create a new batch.
Follow these procedures:
• To create a new batch
• To add samples to the list
• To insert samples into the list
• To import samples into the list
• To remove samples from the list
• To copy a sample
• To reinject a sample
• To edit sample values
• To browse in raw data files
• To customize the column display
 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.
2. Select to create either a quantitative batch or a screening batch.
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3. Select a master method from the Method list.
The application displays all available methods, either quantitative or screening.
4. Select a drive from the Storage Location list.
Tip The application does not display drives that do not have a project and subproject.
The project list displays all projects, subprojects, and batches on the selected drive.
You cannot use network drives to acquire data. For more information about network
drives, see “Working with Drives” on page 493.
5. Select a project and a subproject and type a name for your new batch.
Tip To activate the Save button, you must select a subproject and enter a unique
batch name. If the Save button is not activated, either you have entered a name that is
already used or you have not selected a subproject.
6. Click Save.
A new batch opens with one Specimen sample.
The batch name in the title bar indicates that you are creating a quantitative or screening
batch.
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 To add samples to the list
1. To add a single sample row, right-click the sample list and choose Add Sample from the
shortcut menu.
2. To add multiple sample rows, select the number of rows and then click the Add Sample
icon,
.
The application adds the specified number of new, empty samples to the end of the
sample list.
 To insert samples into the list
Select the sample above which you will insert new, Specimen samples, and then do one of
the following:
• To insert a single sample row, right-click and choose Insert Sample from the shortcut
menu.
• To insert multiple sample rows, select the number of rows and then click the Insert
Sample icon
.
The application inserts the Specimen samples above the selected sample.
Inserted
samples
 To import samples into the list
1. Choose Batch > Import Samples from the main menu, or click the Import Samples
icon,
.
The Sample Import Tool dialog box opens.
From this dialog box, you can import samples from a CSV, an XML, or an SLD file.
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2. Click Browse and select a CSV, an XML, or an SLD file that contains the samples to
import.
3. From the Imported Samples Will Be list, select Appended to the End of the List or
Inserted at the Selected Row.
4. Click Import.
The Sample Import Tool dialog box closes, and the application adds the specified samples
to the sample list.
When you import samples from an Xcalibur sequence file (SLD), the TraceFinder
application makes the following column name substitutions:
Xcalibur column
TraceFinder column
Position
Vial Position
Inj Vol
Injection Volume
Dil Factor
Conversion Factor
When you import samples from an Xcalibur sequence file (.sld), the TraceFinder
application makes the following sample type substitutions:
Xcalibur sample type
TraceFinder sample type
Blank
Negative
Std Bracket
Calibrator
5. (Optional) When using multiplexing, select a channel for each imported sample.
Imported samples default to Auto.
Note The Channel column is available only when you have activated multiplexing in
the Application Configuration mode. See “Multiplexing” on page 66.
 To remove samples from the list
1. Select the samples that you want to remove.
Tip Use the CTRL or SHIFT keys to select multiple samples.
2. Right-click and choose Remove Selected Samples from the shortcut menu.
 To copy a sample
1. Select the sample that you want to copy.
2. Right-click and choose Insert Copy Sample from the shortcut menu.
The TraceFinder application inserts the copy above the selected sample.
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 To reinject a sample
1. In the sample list, select the sample that you want to reinject.
2. Right-click and choose Reinject This Sample from the shortcut menu.
The TraceFinder application creates a copy of the selected sample and appends INJ001 to
the file name. Additional reinjections of the 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
Specimen
QC
Solvent
Calibrator
Unextracted
Negative
Hydrolysis
3. For each Calibrator or QC sample, select a level from the Level list.
The sample levels are defined in the master method. If there are no levels to select in the
Level list, do the following:
a. Return to the Method Development mode.
b. Open the method.
c. Click the Compounds tab.
d. Click the Calibration Levels tab.
e. Add the levels.
f.
Save the method.
g. Return to the Analysis mode, and then click Update.
The application updates the local method with the new sample levels.
For detailed instructions, 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 sample 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 adds any additional browsed in files below the selected sample.
For all browsed-in raw data files, the application sets the Status to Acquired,
the Sample Type to Specimen.
, and sets
Note You cannot overwrite an acquired sample. When you select a sample that is
acquired, the application adds all browsed in files below the selected sample.
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 To customize the column display
1. Right-click the Batch View sample list and choose Modify Columns from the shortcut
menu.
The Modify Columns dialog box opens.
Table 68. Modify Columns dialog box function buttons
Function
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 that you want displayed 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 Up or Down to move the selected column up or down in the list.
The first column in the list represents the leftmost column in the Batch View sample
list, and the last column in the list represents the rightmost column in the Batch View
sample list.
Note You cannot move the Status, Filename, Sample Type, 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 sample list. You can add samples,
edit samples, or remove samples. If the batch has already been acquired, you can select specific
samples for reinjection. If the batch has unacquired samples when you complete your edits,
you can save it as a “ready to acquire” batch.
Follow these procedures:
• To open a saved batch
• To open a recent batch
• To edit samples in a batch
• To reinject a sample from a previously acquired batch
• To submit samples in the batch
 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
Choose File > Recent Files > batchname from the main menu.
The selected batch opens in the Batch View.
 To edit samples in a batch
Use the commands described in “Working in the Batch View” on page 343.
You can add new samples, edit samples, or delete samples.
 To reinject a sample from a previously acquired batch
1. In the sample list, select the sample that you want to reinject.
2. Right-click and choose Reinject This Sample from the shortcut menu.
The TraceFinder application creates a copy of the selected sample and appends INJ001 to
the file name. Additional reinjections of the 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).
3. To save this batch with the new samples for reinjection, choose File > Save > Batch from
the main menu.
The batch is saved as a prepared batch that is ready to submit. You can open this batch
from the Reinject Samples page in the Acquisition mode and submit the batch. The
application acquires only the samples that have not been previously acquired.
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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 372.
For a description of commands on the shortcut menu, see “Batch View shortcut menu
commands” on page 355.
 To submit samples in the batch
1. Do one of the following:
• To submit all samples in the batch, click the Submit Batch icon,
.
• To submit specific samples, select the samples and click the
Submit Selected Samples icon,
.
The Submit Options dialog box opens. See “Submit Options dialog box” on page 372.
2. Select the tasks that 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 activated) 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 activated) Select the Priority Sequence check box and
then select one of the following priority options to place the batch in the queue:
• Next Available Batch places the batch immediately after the currently acquiring
batch.
• Next Available Sample places the batch immediately after the currently acquiring
sample.
9. To start the selected processes, click OK.
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Figure 87. Submit Options dialog box
Table 69. Submit Options dialog box parameters (Sheet 1 of 2)
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Parameter
Description
User Name
Name of the current user.
Samples
Range of samples to be submitted for acquisition, processing, or
reporting.
Acquire Data
(Default) Submits the current batch to acquisition.
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Table 69. Submit Options dialog box parameters (Sheet 2 of 2)
Parameter
Description
Process Data
(Default) Processes the data for the current batch.
Create Reports
Creates reports for the current batch.
Priority Sequence
With multiplexing activated, places the batch immediately after
the currently acquiring batch.
Without multiplexing activated, specifies one of the following
priority options to place the batch in the queue:
• Next Available Batch places the batch immediately after the
currently acquiring batch.
• Next Available Sample places the batch immediately after the
currently acquiring sample.
Acquisition pane
Device Name
Lists all configured instruments.
If the instrument that you want to use is not configured, close the
TraceFinder application, configure the instrument, and then
reopen the TraceFinder application. You cannot configure an
instrument while the TraceFinder application is running.
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.
Post-run System State
Specifies the system state after it acquires the last batch.
On (default), Standby, or Off.
Function 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
tasks.
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Saving a Batch to a New Location
You can move the current batch to a different project and subproject, or you can make a copy
of the current batch and save the copy to a different project and subproject.
Follow these procedures:
• To save a batch to another project or subproject
• To move a batch to another project or subproject
 To save a batch to another project or subproject
1. Choose File > Save > Save Batch As from the main menu in the Analysis mode.
The Batch Save dialog box opens.
2. Select a storage location.
3. Select a project.
4. Select a subproject.
5. Type a name for the new batch.
If you are saving the batch to a different subproject, you must give it a unique name. You
cannot overwrite an existing batch in the new subproject.
6. Click Save.
When you save the batch to a different subproject, the reports reflect the original
project/subproject and the application does not save the calibration history.
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 To move a batch to another project or subproject
1. Choose File > Save > Move Batch from the main menu in the Analysis mode.
The Batch Save dialog box opens.
2. Select a storage location.
3. Select a project.
4. Select a subproject.
5. Type a name for the new batch.
You must give the batch a unique name in the new subproject. You cannot overwrite an
existing batch.
6. Click Save.
When you move the batch, the reports reflect the original project/subproject and the
application does not save the calibration history.
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Auto Samples Page
The Auto Samples page identifies the Solvent or Negative samples to use for any Auto Sample
or Auto Sample and Reinject failure actions as specified on the Intelligent Sequencing page of
the method. See “Editing the Intelligent Sequencing Page” on page 185.
Each sample type that you specify for a failure action on the Intelligent Sequencing page must
be defined on the samples list on the Auto Samples page.
 To open the Auto Samples page
Click Auto Samples in the Batch View navigation pane.
The Auto Samples page opens. See Auto Samples page.
 To add an auto sample type
1. Right-click and choose Add Auto Sample from the shortcut menu, or click the Add New
Auto Sample icon,
.
The application adds a Solvent sample to the sample list.
You can add, insert, or remove samples from this list as you would any sample list. See
“Samples Page” on page 344.
2. To change the sample type to a Negative, click the Sample Type column and select
Negative from the list.
3. In the Injection Volume column for the sample, type a volume.
The minimum injection volume value allowed is 0.1 μL; the maximum injection volume
value allowed is 5000 μL.
4. In the Number of Injections column, type the number of injections available in the
designated Solvent or Negative vial.
After auto sample injections have occurred, you can return to this page to view the
number of Injections Used in each vial.
5. In the Vial Position column, type the vial position for the Solvent or Negative sample.
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Figure 88. Auto Samples page
Table 70. Auto Samples page parameters
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Column
Description
Sample Type
The sample type for the auto sample injection as specified on the
Intelligent Sequencing page—either Solvent or Negative.
Default: Solvent
Injection Volume
The injection volume used for the sample acquisition as specified on
the Samples page.
Range: 0.1 through 5000 μL
Injections Used
The number of times a vial has been used. The count is cumulative
across all batches.
Number of
Injections
The number of injections available in the designated Solvent or
Negative vial.
Vial Position
Vial position for this sample type as specified on the Samples page.
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Reference Samples Page
The Reference Samples page displays the reference samples that you selected for this batch.
 To specify a chromatogram reference sample
1. In the Batch View, click Reference Samples.
An empty reference sample table opens.
2. Click the Add Reference Sample icon,
Reference Sample from the shortcut menu.
, or right-click and choose Add
The Open Chromatogram Reference Sample dialog box opens.
Note If you are using a new method, no reference samples appear here. You must first
process a batch using the current method to see the reference samples in this list.
3. Select a project from the list of projects.
4. Select a subproject from the list of subprojects.
5. Select a batch from the list of batches.
The application displays only batches that were created using the current master method.
6. Select a sample from the list of processed samples.
The application displays all the processed samples in the selected batch. Before using a
sample as a reference sample, you must have processed the sample with the current master
method.
7. Click Open.
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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 84 and “Working in the Batch Template Editor” on page 500.
Note This batch wizard is available only when you select the Batch Template Wizard
(EnviroLab/ToxLab/QuanLab forms) style in the Application Configuration mode. See
“Batch Wizard Style” on page 65.
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
Calibration and Compound
Selection
Finish
 To open the Batch Wizard
Choose File > New > Batch Using Wizard from the main menu in the Analysis mode,
or click the Batch Wizard icon,
.
Note Creating a batch using the Batch Wizard requires that you have previously
created at least one batch template. See “Working in the Batch Template Editor” on
page 500.
The Batch Template Selection page of the Batch Wizard opens. For descriptions of the
parameters on the Batch Template Selection page, see “Batch Template Selection page” on
page 381.
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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.”
 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 your layout preference.
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 89. Batch Template Selection page
Table 71. Batch Template Selection page 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\3.0\Forensic\Templates\Batches
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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.
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Table 71. Batch Template Selection page parameters (Sheet 2 of 2)
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Parameter
Description
Help
Opens the “Creating a Batch Using the Batch Wizard” topic (this
topic) in the application Help tool.
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 383.
Cancel
Immediately exits the Batch Wizard and does not save the batch.
There is no confirming message.
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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 387.
 To enter a required 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.
When you are not using Quick Mode, follow these procedures:
• To change the file names
• 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
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 To change the file names
1. Select the file name.
Not selected for renaming
Selected for renaming
By default, all samples specified on the Batch Template Selection page are named with a
date stamp and the designation “aNNN” as in this example: 9262012_a001.
2. Type a new 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 386.
 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 Specimen sample to the end of the sample list.
2. In the Filename column for each sample, do one of the following:
• Accept the default file name: UnknownN.
• Change the default file name. Follow the instructions “To change the file names.”
• Browse in a raw data file name. Follow the instructions “To browse in a raw data file”
on page 386.
3. Select a sample type from the Sample Type list for each sample.
Available sample types
Specimen
QC
Solvent
Calibrator
Unextracted
Negative
Hydrolysis
4. For detailed descriptions of sample types, see “Sample Types” on page 337.
5. For each Calibrator or QC 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. Click Cancel in the Batch Wizard.
b. Return to the Method Development mode.
c. Open the method.
d. Click the Compounds tab.
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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.”
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 The Add Sample function is not available in Quick Mode.
 To remove samples from the batch
1. Select the samples 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 The Remove Selected Samples 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 Specimen sample above the selected sample.
Note The Insert Sample function is not available in Quick Mode.
 To copy a sample
1. Select the sample that you want to copy.
2. Right-click and choose Insert Copy Sample from the shortcut menu.
The application inserts the copy above the selected sample.
Note The Insert Copy Sample function is not available in Quick Mode.
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 To move a sample up or down in the sample list
1. Select the sample that 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 The Move Sample functions are not available in Quick Mode.
 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 The Browse in Raw File function is not available in Quick Mode.
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Figure 90. Batch Specification page
Table 72. Batch Specification parameters (Sheet 1 of 2)
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, Specimen 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.
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Table 72. Batch Specification parameters (Sheet 2 of 2)
Parameter
Description
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.”
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, Specimen 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.”
Renumber Vial Positions Renumbers vial positions for all samples after the currently selected sample. The selected
sample retains its vial position. All subsequent samples are renumbered sequentially.
Available only after you add or move samples.
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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.”
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 371.
 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 391.
 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 391.
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Figure 91. Finish page
Table 73. Finish parameters
Parameter
Description
Modify Calibrations or
Active Compounds by
Group
Activates the Next button that lets you access the Calibration and Compound Selection
page. When you have already used the Calibration and Compound Selection page, this
option is not available.
Batch Name
Name of the default batch in this 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 383.
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 371.
Next
Opens the Calibration and Compound Selection page where you can edit the calibration
file or edit the list of compounds that you want to identify.
Available only when Modify Calibrations or Active Compounds by Group is checked.
Cancel
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Immediately exits the Batch Wizard and does not save the batch. There is no confirming
message.
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Selecting Calibration Files and Compounds
From the Calibration and Compound Selection page, you can edit the calibration file or edit
the list of compounds that you want to identify. For descriptions of the parameters on the
Calibration and Compound Selection page, see “Calibration and Compound Selection Page.”
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.
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 389.
 To identify specific compounds or groups of compounds
1. In the Compound Groups area, select the groups that include the compounds 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 389.
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Figure 92. Calibration and Compound Selection Page
Table 74. Calibration and Compound Selection parameters
Parameter
Description
Calibration File
Name of the current batch in this 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.
Extend Calibrations
Adds calibration data from the current batch to the selected calibration file.
Compound Groups
Displays all available groups defined on the Groups page of the Method View. See “Editing
the Groups Page” on page 183.
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 383.
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 389.
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 for Quantitation Methods
In the Data Review view, you can view the data generated by the quantitation master method.
Use Data Review to verify the data for a compound before you generate reports.
 To open the Data Review view
1. Click Analysis in the navigation pane.
The Analysis navigation pane opens.
2. Click Data Review.
The Data Review navigation pane opens.
Choose from a Sample View, Compound View, or Qualitative View in Data Review to
analyze the data generated by the master method.
This section includes the following topics:
• Sample View
• Compound View
• Qualitative View
• Features Common to All Data Review Pages
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Sample View
The Sample View uses three different panes to display a list of all samples in the current batch,
the compound results for all compounds in the method, and peak plots for all compounds
found in the currently selected sample.
These are the default panes and their locations:
Sample Peaks pane
Samples pane
Compound Results pane
When you select a sample in the Samples Pane, the associated Compound Results Pane flags
any compound with errors in the selected sample. The associated Sample Peaks Pane displays
the chromatogram, retention time, area, height, and signal-to-noise ratio for all compounds in
the selected sample. The Sample Peaks pane highlights the compound selected in the
Compound Results pane.
The Sample View display includes the following features:
• Samples Pane
• Compound Results Pane
• Sample Peaks Pane
• Caution Flags
• Viewing Sample View Panes
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Samples Pane
Use the Samples pane to select a specific sample. The associated Compound Results Pane
displays all compounds in the method and flags any compound with errors in the selected
sample.
 To hide or display columns in the Samples pane
1. Click the Field Chooser icon,
, in the upper left corner of the pane.
The Field Chooser displays all available columns of data for the Samples pane.
2. Select the check box for each column that you want to display, or clear the check box for
each column that you want to hide.
The application immediately displays or hides the column in the Samples pane.
3. When you are finished modifying the column display, click
Chooser.
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Figure 93. Samples pane
Compound error in the
selected sample
Selected sample
No compound error in the
selected sample
Table 75. Samples pane columns
Column
Description
Flags
Caution flag displayed when a compound in the sample has an
error. See “Caution Flags” on page 400.
Status
Sample is not acquired.
Sample is acquired but not processed.
Sample is acquired and processed.
Sample is currently acquiring.
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Sample Name
A user-defined name that identifies a sample.
Sample Type
Defines how the TraceFinder application processes the sample
data. Each sample is classified as one of the following sample
types: Specimen, QC, Solvent, Calibrator, Hydrolysis,
Unextracted, or Negative
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Compound Results Pane
Use the Compound Results pane to select a specific compound in the selected sample. The
associated Sample Peaks Pane highlights the selected compound.
 To hide or display columns in the Compound Results pane
1. Click the Field Chooser icon,
, in the upper left corner of the pane.
The Field Chooser displays all available columns of data for the Compound Results pane.
2. Select the check box for each column that you want to display, or clear the check box for
each column that you want to hide.
The application immediately displays or hides the column in the Compound Results
pane.
3. When you are finished modifying the column display, click
Chooser.
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Figure 94. Compound Results pane
Table 76. Compound Results pane columns
Column
Description
Flags
Caution flag displayed when the compound has an error. See
“Caution Flags” on page 400.
Compound
Compound names as identified in the library.
Compound Type
Specified compound type: Target Compound or Internal
Standard.
The remainder of the columns in the results list are common to both the Sample View
Compound Results and the Compound View Sample Results displays. See “Common
Column Parameters” on page 432.
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Sample Peaks Pane
The Sample Peaks pane displays the chromatogram, retention time, area, height, and
signal-to-noise ratio for all compounds in the Compound Results pane. The application
highlights the chromatogram for the compound that is currently selected in the Compound
Results pane.
 To display details for a compound
Double-click the chromatogram in the Sample Peaks pane.
The Compound Details pane opens.
The Compound Details pane displays information about the quan peak, calibration curve,
confirming ion, internal standard, reference peak, ion overlay, and spectra for the compound.
For a detailed description of the available information in the Compound Details pane, see
“Compound Details” on page 437.
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Caution Flags
In the Sample View, the application displays caution flags in both the Samples pane and the
Compound Results pane.
This section includes the following topics:
• Flags in the Samples Pane
• Flags in the Compound Results Pane
• Error Indicators in the Sample Peaks Pane
Flags in the Samples Pane
The Flags column in the Samples pane displays a caution flag if any compound in the sample
is not in compliance with the method criteria.
Click the caution flag icon,
, to display the details. Information in the pop-up box shows
the compound that is in error and describes the exact error condition.
Error condition
Compound name
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Flags in the Compound Results Pane
The Flags column in the Compound Results pane displays a flag if the compound in the
selected sample is not in compliance with the method criteria.
Selected sample
Hold your cursor over the flag icon,
sample.
Status of the Sulfisomidine compound
in the selected sample
, to display details for the compound in the selected
Flags in the Compound Results pane are displayed in these situations:
•
A red flag for compounds that have violated (or are activated by) any of the values
set in the method. See “Editing the QAQC Page” on page 174.
•
A red flag for compounds that are outside the specified ion ratio range.
See Ion ratio failure flag.
•
An orange flag for compounds that are below the LOQ, below the LOD,
or between the LOD and LOQ values specified in the method.
For descriptions of these limits, see “Limits” on page 175.
•
A green flag for “found” compounds that are over the LOR amount specified in the
method. For a description of the LOR limit, see “Limits” on page 175.
•
A yellow flag for compounds that are equal to or below the LOR amount specified
in the method.
•
A yellow flag for compounds that are not found in Calibrator or QC
sample types.
The Compound Results pane does not flag compounds that are not found in
Specimen sample types.
• No flag for compounds that have no errors or where no report options are selected.
Note These criteria for flag states do not apply to Negative sample types when the
compound is an internal standard.
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Error Indicators in the Sample Peaks Pane
In the Sample Peaks pane, peak plots are outlined with the color of their associated error flag.
In the following example, the FENTHION peak plot is highlighted in blue to indicate that
FENTHION is the selected compound, and the Sulfisomidine peak plot is outlined in red to
indicate that the Sulfisomidine compound in the selected sample is outside the specified ion
ratio range.
Figure 95. Ion ratio failure flag
Red flag indicating ion ratio failure
Selected peak
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Peak with ion ratio failure outlined in red
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Viewing Sample View Panes
The Sample View display uses multiple panes to display data: Sample Results, Compound
Results, Sample Peaks, and Compound Details. You can display, hide, or move any of these
panes.
 To display or hide a Sample View pane
From the View menu, choose from the following:
• Compounds with Data: Displays or hides the Compound Results pane.
• Sample View Peaks: Displays or hides the Sample Peaks pane.
• Compound Details: Displays or hides the Compound Details pane.
Note The Sample Results pane is required for the Sample View display. You cannot
hide the Sample Results pane.
Displayed panes are indicated with a check mark.
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Data Review Pane Display Features
The following procedures are common to all Data Review displays.
• To dock a pane
• To make a pane floating or dockable
• To change a pane from a docked pane to a tabbed pane
• To restore the default layout
 To dock a pane
1. Grab the title bar of the pane and begin dragging the pane.
The application displays docking arrows.
2. Drag the pane over one of the arrows.
As you hold the cursor over a docking arrow, the application displays a blue region
indicating where this arrow will place the pane.
3. Drop the pane onto one of the arrows.
 To make a pane floating or dockable
Do one of the following:
• To make a dockable pane floating, right-click the title bar of the pane and choose
Floating.
While a pane is set as floating, you cannot use the docking arrows to dock it or make
it a tabbed pane.
• To make a floating pane dockable, right-click the title bar of the pane and choose
Dockable.
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 To change a pane from a docked pane to a tabbed pane
1. Grab the title bar of the pane and begin dragging the pane.
The application displays docking arrows.
2. Hold the cursor over the center of the docking arrows to display a blue region indicating
the location of the tabbed pane.
3. Drop the pane over the center of the docking arrows.
Note To change a floating pane to a tabbed pane, you must first make the pane a dockable
pane, and then you can make it a tabbed pane.
 To restore the default layout
Choose View > Restore Default Layout.
The Sample View, Compound View, and Qualitative View each have their own defaults
for which panes are displayed and in which location.
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Compound View
The Compound View uses three different panes to display a list of all compounds available in
the method, all samples in the current batch, and the peak plots for all compounds found in
each sample.
These are the default panes and their locations:
Sample Peaks pane
Compounds pane
Sample Results pane
When you select a compound in the Compounds Pane, the Sample Results Pane flags any
sample that contains errors with the selected compound. The Sample Peaks Pane highlights
the selected compound and displays the name of the sample in which the compound was
found and the following information about the compound: chromatogram, retention time,
area, height, and signal-to-noise ratio.
The Compound View includes the following features:
• Compounds Pane
• Sample Results Pane
• Sample Peaks Pane
• Caution Flags
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Compounds Pane
Use the Compounds pane to select a specific compound. The Sample Results Pane displays all
samples in the batch and flags any sample that contains errors with the selected compound.
 To hide or display columns in the Compounds pane
1. Click the Field Chooser icon,
, in the upper left corner of the pane.
The Field Chooser displays all available columns of data for the Compounds pane.
2. Select the check box for each column that you want to display, or clear the check box for
each column that you want to hide.
The application immediately displays or hides the column in the Compounds pane.
3. When you are finished modifying the column display, click
Chooser.
to close the Field
Figure 96. Compounds pane
Selected compound
Error associated with the selected compound
No error associated with the selected compound
Table 77. Compounds pane columns
Thermo Scientific
Column
Description
Flags
Caution flag displayed when a compound has an error in any of the
samples.
Compound
Compound names as identified in the library. If there is no library
selected in the method template, the compound name is identified as
[email protected]
Compound Type
Specified compound type: Target Compound or Internal Standard.
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Sample Results Pane
Use the Sample Results pane to select a specific compound in a specific sample. The Sample
Peaks pane highlights the selected compound and displays the name of the sample in which
the compound was found and the following information about the compound:
chromatogram, retention time, area, height, and signal-to-noise ratio. See Sample Results
pane.
 To hide or display columns in the Sample Results pane
1. Click the Field Chooser icon,
, in the upper left corner of the pane.
The Field Chooser displays all available columns of data for the Sample Results pane.
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2. Select the check box for each column that you want to display, or clear the check box for
each column that you want to hide.
The application immediately displays or hides the column in the Sample Results pane.
3. When you are finished modifying the column display, click
Chooser.
to close the Field
Figure 97. Sample Results pane
Table 78. Sample Results pane columns (Sheet 1 of 2)
Column
Description
Acquisition Order
Sequentially numbers the samples.
Flags
Caution flag displayed when a compound within the sample has
an error.
State
Sample is not acquired.
Sample is acquired but not processed.
Sample is acquired and processed.
Sample is currently acquiring.
Sample Name
Thermo Scientific
A user-defined name that identifies a sample.
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Table 78. Sample Results pane columns (Sheet 2 of 2)
Column
Description
Sample Type
Defines how the TraceFinder application processes the sample
data. Each sample is classified as one of the following sample types:
Specimen, QC, Solvent, Calibrator, Hydrolysis, Unextracted, or
Negative
The remainder of the columns in the Sample Results pane are common to both the Sample
View and the Compound View displays. See “Common Column Parameters” on page 432.
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Sample Peaks Pane
In the Compound View, the Sample Peaks pane displays the compound chromatogram,
retention time, area, height, and signal-to-noise ratio for the selected compound in each of the
samples in the batch. The application highlights the compound chromatogram for the sample
that is currently selected in the Sample Results pane.
 To display details for a compound
1. Double-click the chromatogram in the Sample Peaks pane.
The Compound Details dialog box opens.
The Compound Details dialog box displays information about the quan peak, calibration
curve, confirming ion, internal standard, reference peak, ion overlay, and spectra for the
compound.
For details about the available information in the Compound Details dialog box, see
“Compound Details” on page 437.
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Caution Flags
In the Compound View, the application displays caution flags in both the Compounds pane
and in the Sample Results pane.
This section includes the following topics:
• Flags in the Compounds Pane
• Flags in the Sample Results Pane
• Error Indicators in the Sample Peaks Pane
Flags in the Compounds Pane
The Flags column in the Compounds pane displays a caution flag if the compound in any of
the samples is not in compliance with the method criteria.
Selected Sulfisomidine compound
Status of the Sulfisomidine compound
in each sample
Click the caution flag icon,
, to display the details. Information in the pop-up box shows
the sample where the compound is in error and describes the exact error condition.
Error condition
Sample name
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Flags in the Sample Results Pane
The Flags column in the Sample Results pane displays a flag if the selected compound in the
sample is not in compliance with the method criteria.
Hold your cursor over the flag icon,
the sample.
, to display the details for the selected compound in
Flags in the Sample Results pane are displayed in these situations:
Flag
Description
A green flag for compounds that are over the LOR amount specified in the
method.
A red flag for compounds that have violated (or are activated by) any of the values
set in the method. See “Editing the QAQC Page” on page 174.
A red flag for compounds that are outside the specified ion ratio range. See Ion
ratio failure flag.
An orange flag for compounds that are not found in Calibrator or QC sample
types.
“Not found” compounds are below the LOQ, below the LOD, or between the
LOD and LOQ values specified in the method. The Sample Results pane does
not flag compounds that are not found in Specimen sample types.
No flag for compounds that have no errors or where no report options are
selected.
Note These criteria for flag states do not apply to Negative sample types when the
compound is an internal standard.
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Error Indicators in the Sample Peaks Pane
In the Sample Peaks pane, peak plots are outlined with the color of their associated error flag.
In the following example, the peak plot is highlighted in blue to indicate that Benzo_25557 is
the selected sample and outlined in red to indicate that the FENTHION compound in the
selected sample is outside the specified ion ratio range.
Figure 98. Ion ratio failure flag
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Viewing Compound View Panes
The Compound View display uses multiple panes to display data: Compounds, Sample
Results, Sample Peaks, and Compound Details. You can display, hide, or move any of these
panes.
 To display or hide a Compound View pane
From the View menu, choose from the following:
• Samples with Data: Displays or hides the Sample Results pane.
• Compound View Peaks: Displays or hides the Sample Peaks pane.
• Compound Details: Displays or hides the Compound Details pane.
Note The Compounds pane is required for the Compound View display. You cannot
hide the Compounds pane.
Displayed panes are indicated with a check mark.
For procedures about creating docked, floating, or tabbed panes, see “Data Review Pane
Display Features” on page 404.
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Qualitative View
The Qualitative View uses several different panes to display qualitative information for the
selected sample. If it finds no detected peaks for the selected sample, you can manually add
peaks.
To see processed data for a sample in the Qualitative View, you must select the Qual
Processing parameter for that sample in the Batch View before you process the batch. See
“Batch View Sample List” on page 352.
These are the default panes and their locations:
Samples pane
Sample
Peak Details pane
chromatogram pane
Peaks pane
Spectrum pane
Library Hits pane
The Qualitative View displays data in the following panes:
• Samples Pane
• Peaks Pane
• Sample Chromatogram Pane
• Peak Details Pane
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• Spectrum Pane (Library and Data)
• Library Hits Pane
• Viewing Qualitative View Panes
Samples Pane
Use the Samples pane to select a specific sample. The associated Peaks Pane displays all peaks
found in the selected sample.
 To hide or display columns in the Samples pane
1. Click the Field Chooser icon,
, in the upper left corner of the pane.
The Field Chooser displays all available columns of data for the Samples pane.
2. Select the check box for each column that you want to display, or clear the check box for
each column that you want to hide.
The application immediately displays or hides the column in the Samples pane.
3. When you are finished modifying the column display, click
Chooser.
to close the Field
Figure 99. Samples pane
Table 79. Samples pane columns (Sheet 1 of 2)
Thermo Scientific
Column
Description
Acquisition Order
Sequentially numbers the samples.
Flags
Caution flag displayed when a compound in the sample has an
error. See “Caution Flags” on page 400.
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Table 79. Samples pane columns (Sheet 2 of 2)
Column
Status
Description
Sample is not acquired.
Sample is acquired but not processed.
Sample is acquired and processed.
Sample is currently acquiring.
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Sample Name
A user-defined name that identifies a sample.
Sample Type
Defines how the TraceFinder application processes the sample
data. Each sample is classified as one of the following sample
types: Specimen, QC, Solvent, Calibrator, Hydrolysis,
Unextracted, or Negative
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Peaks Pane
The Peaks pane works with the Samples pane to display graphical values for a unique sample
and peak combination. For detailed descriptions of parameters in the Peaks pane, see “Peaks
pane parameters” on page 422.
 To display peaks for a specific compound
1. From the Samples pane, select a sample.
The Peaks pane displays the retention times for peaks identified in the selected sample,
the values for the best match methods for each peak, and the library match.
The method specifies which technique to use for identifying peaks: peaks within a specific
retention time range, as a minimum percentage of the height or area of the largest peak,
or as a minimum percentage of the nearest internal standard peak. You can change the
method for identifying peaks in the Method Template Editor. See “Creating a Method
Template” on page 224.
2. In the Peaks pane, select a peak in the sample.
The TraceFinder application displays the selected peak in the Peak Details pane, displays
the Qual Data and Qual Library sections in the Spectrum pane, and locates the selected
peak in the Sample Chromatogram pane.
• The Qual Data section shows spectrum data for the peak in the raw data file.
• The Qual Library section shows actual spectrum for the identified library compound.
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Figure 100. Peak Details pane
Note When you select a data-dependent sample, the peak can be from either a full
scan or a QED spectrum of an SRM-filtered chromatogram.
Figure 101. Spectrum pane
Reference
spectrum from
the library
Actual spectrum
data for the
compound
Figure 102. Selected peak in the Sample Chromatogram pane
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 To remove a peak
1. Select a peak in the Sample Chromatogram pane.
2. Right-click the Peak Details pane and choose Remove Qual Peak from the shortcut
menu.
The TraceFinder application removes the selected peak from all Qualitative View panes.
Note There is no undo for this action, but you can manually add a peak to redefine a
removed peak. See “Sample Chromatogram Pane” on page 423.
 To hide or display columns in the Peaks pane
1. Click the Field Chooser icon,
, in the upper left corner of the pane.
The Field Chooser displays all available columns of data for the Peaks pane.
2. Select the check box for each column that you want to display, or clear the check box for
each column that you want to hide.
The application immediately displays or hides the column in the Peaks pane.
3. When you are finished modifying the column display, click
Chooser.
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Figure 103. Peaks pane
Table 80. Peaks pane parameters
Parameter
Description
Filter
Filter used to identify the peaks. Specified in the raw data file or
the master method.
When your raw data file is data-dependent, the filter indicates
this with a “d”.
Data-dependent filter
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Peak RT
Peak retention time. The time after injection when the
compound elutes. The total time that the compound is retained
on the column.
SI
Search index method used to search the NIST library.
RSI
Reverse search index method used to search the NIST library.
MP
Match probability.
Compound
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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Sample Chromatogram Pane
The Sample Chromatogram pane displays all peaks in the selected sample. The peak selected
in the Peaks pane displays a red marker. See “Sample Chromatogram pane” on page 424.
For a description of commands on the shortcut menu, see “Sample chromatogram pane
shortcut menu commands” on page 424.
 To zoom in on a peak
1. In the Sample Chromatogram pane, drag the cursor to delineate a rectangle around the
peak.
The delineated area expands to fill the view.
2. To restore the default view, right-click the Sample Chromatogram pane and choose Reset
Scaling from the shortcut menu.
 To manually add a peak
1. Zoom in to better identify which peak to add to the results set.
2. Right-click the Sample Chromatogram pane, and choose Add Qual Peak from the
shortcut menu.
3. Click to indicate the left and right base points for the peak.
The TraceFinder application marks the peak in the Sample Chromatogram pane.
The TraceFinder application places the peak delimiter tags at the base point locations and
automatically updates the peak values in the Peaks pane and Peak Details pane.
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Figure 104. Peak Details pane with a manually added peak
Manually added
base points
Figure 105. Sample Chromatogram pane
Table 81. Sample chromatogram pane shortcut menu commands
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Command
Description
Add Qual Peak
Select the beginning and ending base points for a new
qual peak. Available only when no peak is detected.
Reset Scaling
Resets the original scaling after a zoom operation.
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Peak Details Pane
The Peak Details pane displays the selected peak. For detailed descriptions of all parameters
on the Peak Details pane, see “Peak Details pane” on page 427.
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 “Peak Details pane shortcut menu
commands” on page 427.
 To zoom in on a peak
1. In the chromatogram plot, drag the cursor to delineate a rectangle around the peak.
The delineated area expands to fill the view.
2. To restore the default view, right-click the chromatogram plot and choose Reset Scaling
from the shortcut menu.
 To manually add a peak
1. Right-click anywhere in the Peak Details pane, and choose Add Qual Peak from the
shortcut menu.
If a peak is already detected, the Add Qual Peak command is not activated.
2. Click to indicate the left and right base points for the peak.
The TraceFinder application places the peak delimiter tags at these locations and
automatically updates the peak values (area, height, and so forth) in the result set.
Manually added base points
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 To remove a peak
Right-click the Peak Details pane, and choose Remove Qual Peak from the shortcut
menu.
The TraceFinder application removes the peak displayed in the Peak Details pane. All data
for this peak are removed from the Qualitative View panes.
 To switch between method and manual integration modes
Right-click the Peak Details pane and choose Method Integration or Manual
Integration from the shortcut menu.
Initially, the method and manual integration settings that are stored for a compound and
file are identical. When you switch modes, the saved result set does not change. However,
when manual data are available, the Peak Details plots and the result set update as you
switch between method and manual modes.
As you switch between modes, each pane reflects the changes. The generated reports for
these data identify the manual modifications.
 To change the displayed information for detected peaks
1. Right-click the Peak Details pane and hold the cursor over Peak Labels.
2. Choose to display labels for the peak retention time (RT), peak height (AH), peak area
(AA), or signal-to-noise (SN).
Label not displayed in chromatogram
Label displayed in chromatogram
3. To remove a label, select the label type again to clear it.
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Figure 106. Peak Details pane
Table 82. Peak Details pane shortcut menu commands
Thermo Scientific
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 Qual Peak
Available only for manually added peaks. Removes the
peak displayed in the Peak Details pane.
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Spectrum Pane (Library and Data)
The Spectrum pane displays the reference spectrum from the library and the spectrum data
for the selected sample. The top pane displays the spectrum for the identified compound
found in the reference library; the bottom pane displays the actual spectrum data for the
selected peak.
Figure 107. Spectrum pane
Reference
spectrum from
the library
Actual spectrum
data for the
compound
 To zoom in on a peak
1. In either spectrum plot, drag the cursor to delineate a rectangle around the peak.
The delineated area expands to fill the view.
2. To restore the default view, right-click the spectrum plot and choose Reset Scaling from
the shortcut menu.
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Library Hits Pane
The Library Hits pane displays the best library matches for the selected peak. Use this pane to
select a different library entry for the peak. See “Library Hits pane.”
When you select a library entry other than the original entry, the TIC Report and TIC
Summary Report indicate this with a “P” flag:
P flag
For detailed descriptions of the Library Hits pane parameters, see “Library Hits pane
parameters.”
 To change the library entry for a selected peak
In the Library Hits pane, select the check box for the library entry that you want to use to
identify the selected peak.
• In the Spectrum pane, the reference spectra change to show the spectra for the
selected library entry.
• In the Peaks pane, the SI, RSI, MP, and Compound values update to reflect the
selected library entry.
Selected library entry
in the Library Hits pane
Reference spectra
for Hexanone
Peak list for
Hexanone
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Figure 108. Library Hits pane
Table 83. Library Hits pane parameters
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Parameter
Description
<Check box column>
Indicates selected library entries for the selected peak.
Rank
Indicates the order of best matches between the selected
peak and library entries.
SI
Search index 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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Viewing Qualitative View Panes
The Qualitative View display uses multiple panes to display data: Samples, Peaks, Sample
Chromatogram, Peak Details, Spectrum, and Library Hits. You can display, hide, or move any
of these panes.
 To display or hide a Qualitative View pane
From the View menu, choose to display or hide the following:
• Peaks
• Sample Chromatogram
• Peak Chromatogram: Displays or hides the Peak Details pane.
• Spectrum
• Library Hits
Note The Samples pane is required for the Qualitative View display. You cannot hide
the Samples pane.
Displayed panes are indicated with a check mark.
For procedures about creating docked, floating, or tabbed panes, see “Data Review Pane
Display Features” on page 404.
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Features Common to All Data Review Pages
The following features are common to all quantitative batch data review pages.
• Common Column Parameters
• Status Indicators
• Inactive and Excluded Compounds
• Compound Details
Common Column Parameters
Table 84. Common parameters for Compound Results and Sample Results tables (Sheet 1 of 2)
Column
Description
Height
The distance from the peak maximum to the peak base, measured perpendicular to the
ordinate. When the Response Ratio is specified as Height, this column displays an asterisk
(*Height).
Area
The area obtained by integrating peak intensities from the start to the end of the peak.
When the Response Ratio is specified as Area, this column displays an asterisk (*Area).
Expected RT
Expected retention time for the compound.
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.
Calculated Amt
The amount present in the sample, as determined using the calibration curve and the
response ratio.
Theoretical Amt
Theoretical amount of the compound expected in the sample.
Sample Amt
The injected volume multiplied by the conversion factor. For example, if you have
1000 ng/mL of a substance that is too concentrated for the mass spectrometer, you can
dilute it by 1000. Then your injection volume is 1, your conversion factor is 1000, and your
sample amount is 1000.
Response Ratio
The ratio of the Response value to the IS Response value. If the Response is specified as Area
in the processing method, the units of both Response and IS Response are counts-sec. If the
Response is specified as Height in the processing method, the units of both Response and IS
Response are counts.
ISTD Amt
Amount of internal standard.
ISTD Response
Response of the internal standard.
Integration Mode
Integration mode specified in the method. See “Quan Peak” on page 439.
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Table 84. Common parameters for Compound Results and Sample Results tables (Sheet 2 of 2)
Column
Description
Active
Displays or hides a compound for a particular sample.
• When a compound is marked inactive, the application does not remove its data and
calculated values from the result set. Instead, the TraceFinder application masks the
appearance of that compound for that particular sample and grays the compound in the
compounds list.
• When a calibration standard is marked inactive, the application no longer uses the data
file’s calibration point for the calibration and removes it from the graphical view of the
calibration curve displayed in the Compound Details pane. It is no longer part of the
result set.
In a Sample View, the Active parameter is in the Compound Results pane.
In a Compound View, the Active parameter is in the Sample Results pane.
Excluded
Turns a compound on or off in the calibration curve in the Compound Details 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 activated multiplexing in the
Application Configuration mode. See “Multiplexing” on page 66.
Final Units
Specifies the calculated amount.
Default: 1
Comment
A user-defined comment for the sample.
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Status Indicators
Status indicators for each sample indicate if the sample is currently acquiring, not acquired,
acquired, or processed.
Sample is not acquired.
Sample is acquired but not processed.
Sample is acquired and processed.
Sample is currently acquiring.
Figure 109. Sample Results
Status indicators
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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 pane.
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.
• When a compound it marked inactive, the application does not remove its data and
calculated values from the result set. Instead, the TraceFinder application masks the
appearance of that compound for that particular sample and grays the compound
name in the compounds list.
• When a calibration standard is marked inactive, the application no longer uses the
data file’s calibration point for the calibration and removes it from the graphical view
of the calibration curve displayed in the Qualification pane. The calibration point is
no longer part of the result set.
3. In the Samples pane, select or clear the Active check box.
Use the horizontal scroll bar at the bottom of the table to scroll to the Active column.
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 To exclude a calibration point
In the sample list, select the Excluded check box for the sample.
Note Only calibration samples have the Excluded check box available.
Use the horizontal scroll bar at the bottom of the table to scroll to the Excluded column.
The application displays a value that is no longer used for calibration as an empty box in
the graphical view of the calibration curve.
Excluded
calibration
point
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Compound Details
Use the Compounds Details pane to display any of the following types of data:
• Quan Peak
• Confirming Ions
• Calibration Curve
• Ion Overlay
• ISTD
• Reference Peak
• Spectra
 To open the Compound Details dialog box
1. Double-click the chromatogram in the Sample Peaks pane.
The Compound Details pane opens.
By default, the first display pane shows the quantitative peak for the selected compound.
In the second pane, select the additional type of data that you want to display. Follow these
procedures to change the display of the peak data in either of the panes:
• To change the peak panes
• To zoom in on a peak
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 To change the peak panes
In any of the peak panes, click
to view a list of commands.
Command
Description
Make All Panels the
Same Size
Evenly divides the area to make all panes the same width.
This command does not change the pane height.
Move Panel Left
Moves the current panel one space to the left. This
command is not available when the current pane is the
leftmost pane.
Move Panel Right
Moves the current panel one space to the right. This
command is not available when the current pane is the
rightmost pane.
Add a Panel
Adds an empty peak pane to the display. You can display a
maximum of four peak panes.
 To zoom in on a peak
1. In any of the views, drag your cursor to delineate a rectangle around the peak or spectra.
The delineated area expands to fill the view.
2. To restore the default view, right-click the chromatogram plot and choose Reset Scaling
from the shortcut menu.
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Quan Peak
A compound can have multiple quantitative peaks. You can switch between quantitative
peaks, but you cannot view multiple quantitative peaks at the same time. The indicator in the
upper right corner of the Quan Peak pane displays which of the multiple quantitative peaks
you are viewing. The Quan Peak pane uses a unique shortcut menu. See “Quan Peak pane
shortcut menu commands” on page 443.
Figure 110. Quantitative peak pane with multiple quantitative peaks
Peak 1 of 2
Peak 2 of 2
Follow these procedures to modify the quantitative or confirming ion peak data:
• To manually add a peak
• To remove a manually created peak
• To switch between method and manual integration modes
• To change the displayed information for detected peaks
• To modify the peak detection settings
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 To manually add a peak
1. Right-click anywhere in the quantitative peak pane, and choose Add Quan Peak from
the shortcut menu.
2. Click the left base of the peak you want to identify.
3. Drag to the right base and release the mouse.
The application places the peak delimiter tags at these locations and automatically
updates the peak values (area, height, and so forth) in the result set.
Manually added right
and left base points
 To remove a manually created peak
Right-click the pane, and choose Cancel Add Peak from the shortcut menu.
The application cancels the Add Peak operation. If you have already completed adding
the peak, select the peak and then choose Remove Quan Peak from the shortcut menu.
 To manually integrate a quantitative peak
1. Hold your cursor over one of the two peak delimiter tags in the peak pane.
When the tag can be selected, the cursor changes to a crosshair-style cursor. You can zoom
in on the baseline to make it easier to select the tag.
Crosshair cursor
2. Drag the peak delimiter tag to another location and automatically update the peak values
(area, height, and so forth) into the result set.
The generated reports for these data identify the manual modifications.
You can store two peak value sets (method and manual integration settings) with each
compound in each file. These settings can result in a different set of stored values. The
application originally calculates the method values based on the processing method
parameters. The manual values are a result of what you have edited.
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 To switch between method and manual integration modes
Right-click the chromatogram view and choose Method Integration Settings or Manual
Integration Settings from the shortcut menu.
Initially, the method and manual integration settings that are stored for a compound and
file are identical. When you switch modes, the saved result set does not change. However,
when manual data are available, the chromatogram plots and the result set update as you
switch between method and manual modes.
As you switch between modes, each pane reflects the changes. The generated reports for
these data identify the manual modifications.
 To change the displayed information for detected peaks
1. Right-click the peak pane and hold the cursor over Peak Labels.
2. Choose to display labels for the peak retention time, peak height, peak area, or signal to
noise.
The label types in the list are selected for displayed labels and are cleared for labels that are
not displayed.
3. To remove a label, select the label type again and clear it.
Label settings are globally applied to quantitative peaks, confirming ion peaks, and
internal standard peaks.
Tip The labels do not always update on all peak displays. To update all labels, select a
different compound, and then reselect the compound whose labels you changed.
 To modify the peak detection settings
1. Right-click the chromatogram view and choose one of the following from the shortcut
menu:
• Peak Detection Settings > Edit Local Method Peak Detection Settings: Makes
changes to the selected compound for all samples in this batch.
• Peak Detection Settings > Edit User Defined Peak Detection Settings: Makes
changes to the selected compound for only the selected sample. The TraceFinder
application saves these changes with the batch and stops applying the local method
detection settings to the compound for this sample only.
The Peak Detection Settings dialog box opens where you can adjust detection settings
that were specified in the method. The title bar of the dialog box lists the selected
compound and indicates whether you are making changes to only the selected sample or
to the local method.
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Figure 111. Peak Detection Settings dialog box
Editing all samples in the batch
Editing only the selected sample
2. Edit any of the detection settings.
For detailed descriptions of all detection settings, see “Detection” on page 119.
3. To save your changes to this compound, click Apply.
• When you are editing a single sample, the application makes changes to the selected
compound for this sample. If the sample is a calibration sample type, this update
changes the calibration curve which, in turn, affects all calculated amounts.
• When you are editing the local method, the application makes changes to the selected
compound for all samples in this batch.
Note The Peak Detection Settings commands are also available on the Confirming Ions
pane.
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Table 85. Quan Peak pane shortcut menu commands (Sheet 1 of 2)
Command
Description
Method Integration Settings
Use Local Method Peak Detection Settings: Applies the
local method integration settings to the selected
compound.
To edit these peak detection settings, use the Peak
Detection Settings > Edit Local Method Peak Detection
Settings command.
Use User Peak Detection Settings: Applies the
user-customized method integration settings to the
selected compound.
To edit these user-customized settings, use the Peak
Detection Settings > Edit User Defined Peak Detection
Settings command.
Thermo Scientific
Manual Integration Settings
Displays manual integration settings.
Add Quan Peak
–or–
Remove Quan Peak
–or–
Cancel Add Peak
Adds a peak, removes a peak, or cancels an add peak
operation in progress.
Confirming Ion List
Select the confirming ions to be viewed. Not available for
analog compounds.
Send RT to Method
Sets the current retention time as the expected retention
time for the compound in the local method.
Peak Labels
Displays or hides the peak labels (Label Area, Label
Retention Time, Label Height, or Label Signal to Noise).
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Table 85. Quan Peak pane shortcut menu commands (Sheet 2 of 2)
Command
Description
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
Edit User Defined Peak Detection Settings: Opens the
Peak Detection Settings dialog box where you can make
changes to the selected compound for this sample.
Edit Local Method Peak Detection Settings: Opens the
Peak Detection Settings dialog box where you can make
changes to the selected compound for all samples in this
batch.
After you apply either of these updates, the application
does not retain manual integration settings.
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Confirming Ions
The Confirming Ions pane displays a graphical view of all qualifying/confirming ions for the
selected compound and displays calculated ion ratios and ion ratio acceptance windows. A red
border indicates that an ion ratio is outside of its window. The Confirming Ions pane uses a
unique shortcut menu. See Confirming Ions pane shortcut menu commands.
Note For compounds with an analog detection type, the application displays “No
Confirming Ions are Enabled” in the Confirming Ions pane.
Figure 112. Quantitative peak with multiple confirming ions
Figure 113. Confirming ion with coelution failure
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 To manually integrate a confirming ion peak
1. Hold your cursor over one of the two peak delimiter tags in the peak pane.
When the tag can be selected, the cursor changes to a crosshair-style cursor. You can zoom
in on the baseline to make it easier to select the tag.
2. Drag the peak delimiter tag to another location and automatically update the peak values
(area, height, and so forth) into the result set.
The generated reports for these data identify the manual modifications.
You can store two peak value sets (method and manual integration settings) with each
compound in each file. These settings can result in a different set of stored values. The
application originally calculates the method values based on the processing method
parameters. The manual values are a result of what you have edited.
Note Because a Blank Report displays only the quantitation mass, when you manually
integrate a confirming ion, the manual integration flag in the report is displayed on
the quantitation mass.
Table 86. Confirming Ions pane shortcut menu commands (Sheet 1 of 2)
Command
Description
Method Integration
Settings
Displays the method integration settings.
Manual Integration
Settings
Displays the manual integration settings.
Add Quan Peak
Adds a quantitation peak, removes a peak, or cancels an add peak
–or–
operation in progress.
Remove Quan Peak
–or–
Cancel Add Quan Peak
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Range Calc Method:
Manual
Selects the method used to calculate the ion ratio range windows:
Manual, Average, Weighted Average, or Level.
Range Calc Level
Displays the range based on the calibration level.
Target Ratio
Specifies the theoretical ratio of the confirming ion's response to
the quantification ion's response.
Window Type
Specifies the Absolute or Relative calculation approach for
determining the acceptable ion ratio range.
Window
Specifies the acceptable ion ratio range as a percentage.
Peak Labels
Displays or hides the peak labels (Label Area, Label Retention
Time, Label Height, or Label Signal to Noise).
Show Peak Info
Displays peak information for the selected compound.
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Table 86. Confirming Ions pane shortcut menu commands (Sheet 2 of 2)
Thermo Scientific
Command
Description
Reset Scaling
Resets the original scaling after a zoom operation.
Peak Detection
Settings
Opens the Peak Detection Settings dialog box for the selected
compound.
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Calibration Curve
The Calibration Curve pane displays a graphical view of the calibration curve for the selected
compound and key statistical values for evaluating the quality of the calibration. The
Calibration Curve pane uses a unique shortcut menu. See Calibration Curve pane shortcut
menu commands.
Figure 114. Quantitative peak with a calibration curve plot
 To manually exclude a calibration point
In the sample list, select the Excluded check box for the sample.
Use the horizontal scroll bar at the bottom of the table to scroll to the Excluded column.
When a value is no longer used for calibration, it is displayed as an empty box in the
graphical view of the calibration curve.
Excluded
calibration
point
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Table 87. Calibration Curve pane shortcut menu commands
Thermo Scientific
Command
Description
Standard Type
Sets the standard type to External or Internal.
Calibration Curve Type
Sets the calibration curve type to one of the following:
• Linear: Allows all settings with this exception: When Origin
is set to Include, all Weighting values are grayed out and
Weighting is set to Equal.
• Quadratic: Allows all settings with this exception: When
Origin is set to Include, all Weighting values are grayed out
and Weighting is set to Equal.
• Average RF: Allows no Weighting or Origin selections. All
Weighting and Origin values are grayed out. Weighting is set
to Equal, and Origin is set to Ignore.
Response Via
Sets the response to Area or to Height.
Weighting
Sets the weighting to equal, 1/X, 1/X^2, 1/Y, or 1/Y^2.
Origin
Sets the origin to Ignore, Force, or Include.
Units
Sets the units.
Done with Settings
Saves the calibration curve settings.
Reset Scaling
Resets the original scale in the calibration curve pane.
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Ion Overlay
The Ion Overlay pane represents an overlay of the entire ion set—quantification and
qualifying/confirming—for the selected compound. Use this pane to graphically review the
peak apex alignment and coeluting peak profiles.
Note For compounds with an analog detection type, the application displays “No Data”
in the Ion Overlay pane.
Figure 115. Quantitative peak with confirming ion overlay
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ISTD
The ISTD pane displays the internal standard specified for the compound in the method. See
“To specify an internal standard for a compound” on page 164.
Figure 116. Quantitative peak with an internal standard
Reference Peak
The Reference Peak pane displays the reference peak as specified in the method.
Figure 117. Quantitative peak with a reference peak
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 To specify a chromatogram reference peak
1. In the Batch View task pane, click Reference Sample.
An empty reference sample table opens.
2. Click the Add Reference Sample icon,
Reference Sample from the shortcut menu.
, or right-click and choose Add
The Open Chromatograph Reference Sample dialog box opens.
Note If you are creating a new method, you will not see any reference samples here.
You must create and save a batch using the current method to see the reference
samples in this list.
3. Select a project from the list of projects.
4. Select a subproject from the list of subprojects.
5. Select a batch from the list of batches.
The TraceFinder application displays only batches that were created using the current
master method.
6. Select a sample from the list of processed samples.
The TraceFinder application displays all the processed samples in the selected batch. To
use a sample as a reference sample, the sample must have been processed with the current
master method.
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7. Click Open.
The selected sample is displayed as the chromatogram reference sample in the Method
View in the Method Development mode.
Tip To clear the reference sample from the master method, select None in the Set
Chromatogram Reference Samples pane.
Spectra
The Spectra pane displays a comparison of the spectra found in the data and the method
reference.
Note For compounds with an analog detection type, the application displays “Not
Available” in the Spectra pane.
Figure 118. Quantitative peak with data and reference spectra
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Working in Data Review for Target Screening Methods
The Data Review view displays the data generated by the target screening master method. Use
Data Review to verify the data for a compound before you generate reports.
 To open the Data Review view
1. Click Analysis in the navigation pane.
The Analysis navigation pane opens.
2. Click Data Review.
The Data Review navigation pane opens.
In the target screening display, the panes show a list of all samples in the current batch, the
compound results for all compounds in the method, and chromatogram and spectrum plots
for all compounds found in the currently selected sample.
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Figure 119. Target Screening panes
Chromatogram pane
Samples pane
Compounds pane
Spectrum pane
When you select a sample in the Samples pane, the associated Compounds pane flags any
compound with errors in the selected sample. The associated Chromatogram pane displays
the chromatogram, retention time, area, height, and signal-to-noise ratio for all compounds in
the selected sample. The Spectrum pane highlights the compound selected in the Compounds
pane. You can display, hide, or move any of these panes.
 To display or hide a Target Screening pane
From the View menu, choose to display or hide the following:
• Samples
• Target Screening Results: Displays or hides the Compounds pane.
• Chromatogram
• Spectrum
Note The Samples pane is required for the Target Screening display. You cannot hide
the Samples pane.
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Displayed panes are indicated with a check mark.
For procedures about creating docked, floating, or tabbed panes, see “Data Review Pane
Display Features” on page 404.
The target screening display includes the following features:
• Samples Pane
• Compounds Pane
• Chromatogram Pane
• Spectrum Pane
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Samples Pane
Use the Samples pane to select a specific sample in the batch. The associated Compounds
Pane displays all compounds in the method and flags any compound with errors in the
selected sample.
Flags in the Samples pane indicate one of the following:
A green circle when the sample/compound/peak combination is identified and fully
confirmed.
A yellow triangle when the sample/compound/peak combination is identified but not
fully confirmed.
A red square when the sample/compound/peak combination is not identified.
Figure 120. Samples pane
Table 88. Samples pane shortcut menu commands
Thermo Scientific
Command
Description
Sort by Alphabetical
Sorts the samples alphabetically by sample name.
Sort by Import Order
Sorts the samples in the order they were processed.
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Compounds Pane
The Compounds pane displays all found peaks in the selected sample and flags any
compound with errors. The Target Screening Results grid reflects the identified compounds
found in the compound database and the results of the method processing criteria.
Color Coding for Measured or Calculated Values
The Compounds pane uses color-coded text to indicate the following:
• Green—Indicates that the measured value of scoring and confirmations pass the criteria
specified in the method.
• Red—Indicates that the measured or calculated value does not pass the criteria specified
in the method.
Displaying Multiple Adducts
When the TraceFinder application finds multiple adducts at the same retention time in a
sample, the Compounds pane displays the adducts on a single row in the table.
The table shows information for the most intense adducts for each retention time for a
compound.
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Exporting Compounds
 To export compounds to an Excel spreadsheet
1. Choose File > Export Data To > Excel from the main menu.
The Export Data to Excel dialog box opens.
2. Locate the folder where you want to save the file.
3. Type a file name for the XLSX file and click Save.
The application saves the specified compound data to an Excel spreadsheet.
You specify the format for the Excel spreadsheet and the types of peaks that are exported in
the Target Screening Report Settings in the master method. See “To specify options for
exporting compounds to an Excel worksheet” on page 209.
 To export compounds to a CSV file
1. Choose File > Export Data To > CSV from the main menu.
The Export Data to CSV dialog box opens.
2. Locate the folder where you want to save the file.
3. Type a file name for the CSV file and click Save.
The application saves the specified compound data to a comma-separated value (.csv) file.
You specify the format for the CSV file and the types of peaks that are exported in the Target
Screening Report Settings in the master method. See “To specify options for exporting
compounds to an Excel worksheet” on page 209.
Figure 121. Compounds pane
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Table 89. Compounds pane parameters
Column
Description
Displays the current compound database. When you have multiple screening databases,
the application lists the results for each database separately.
Expand the list of found compounds in
the screening database.
Flag
Indicates the status of the identification and confirmation criteria.
• A green circle when the sample/compound/peak combination is identified and fully
confirmed.
• A yellow triangle when the sample/compound/peak combination is identified but
not fully confirmed.
• A red square when the sample/compound/peak combination is not identified.
Compound Name
The compound name match in the compound database.
Match Result Name
The compound name match in the compound database and the retention time.
Formula
The formula for the peak as specified in the compound database.
Confirmed
The number of confirmation tests that passed out of the total number specified in the
method.
m/z (Expected)
Mass-to-charge ratio from the compound database. Charge is presumed to be 1.
m/z (Measured)
Mass-to-charge ratio found in the spectra for the peak. Charge is presumed to be 1.
m/z (Delta (ppm))
Difference between the expected and measured mass-to-charge ratio. Charge is presumed
to be 1.
RT (Expected)
The retention time for the peak as specified in the compound database.
RT (Measured)
The found retention time for the peak apex.
RT (Delta)
Difference between the expected and measured retention time for the peak.
Measured Area
The AA value from the chromatogram pane.
Isotopic Pattern Score (%) The percentage of the number of total isotopes to the number of matched isotopes.
Num Isotopes Matched
The number of isotopes matched in the theoretical calculated isotope spectra.
Lib Match Name
The name of the compound match in the library search.
Library Score (%)
The score from the library fit.
S/N
The signal-to-noise ratio calculated for the found peak.
Left RT
The time point of the left leading edge of the integrated peak.
Right RT
The time point of the right leading edge of the integrated peak.
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Chromatogram Pane
Use the Chromatogram pane to display all extracted chromatograms of all adducts of the
selected compound.
The first tab displays the most intense target adduct for the peak result. Additional (optional)
tabs display extracted ion chromatograms for other adducts for the target compound at the
same retention time in order of intensity. If no signal exists for an adduct, it displays the XIC
of the expected m/z within the specified retention and chromatogram windows. When you do
not specify a retention time or window, the application displays the full time range.
Figure 122. Chromatogram pane
Table 90. Chromatogram pane shortcut menu commands
Thermo Scientific
Command
Description
Reset Scaling
Resets the original scaling after a zoom operation.
Copy to Clipboard
Copies the graphic display to the Clipboard.
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Spectrum Pane
Use the Spectrum pane to display the spectrum, isotopes, fragments, and library search
information for the selected adduct in the Chromatogram pane. The Spectrum pane displays
only the identification and confirmation criteria specified in the method. The confirmations
are based only on the most intense adduct. See “To specify identification and confirmation
settings” on page 216.
The Spectrum pane includes the following pages of information (when available) for each
selected sample/compound/peak combination:
• Spectrum
• Isotopes
• Fragments
• Library
Spectrum
The application displays the neutral loss (NL) and compound/peak name information on the
right side of the Spectrum page. When data is available, the plot width is the full mass range
in the raw data file. Otherwise, the application scales the width to the scan range.
Figure 123. Spectrum page
Table 91. Spectrum page shortcut menu commands
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Command
Description
Reset Scaling
Resets the original scaling after a zoom operation.
Copy to Clipboard
Copies the graphic display to the Clipboard.
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Isotopes
The isotopes page displays isotopic pattern results according to the threshold and deviation
parameters defined in the screening method.
To identify or confirm the presence of a compound, the resulting score percentage from
isotopic pattern matching must be higher than the specified fit threshold percentage.
An isotope peak is not found if its intensity, relative to the monoisotopic ion’s intensity, is
more than the specified intensity deviation percentage away from the theoretical relative
intensity of the isotope ion.
An isotope peak is found if its measured m/z is less than the specified mass deviation amount
away from its expected m/z.
To specify threshold and deviation parameters, see “To specify identification and confirmation
settings” on page 216.
Figure 124. Isotopes page with stacked spectra
Theoretical
isotope spectrum
Experimental
spectrum
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Figure 125. Isotopes page with overlaid spectra
Theoretical isotope spectrum displayed in blue.
Experimental spectrum displayed in black.
Table 92. Isotopes page shortcut menu commands
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Command
Description
Reset Scaling
Resets the original scaling after a zoom operation.
Copy to Clipboard
Copies the graphic display to the Clipboard.
Display Overlay Spectra
Display Stack Spectra
Overlays the two spectrum displays, or stacks the simulated
spectrum and the peak apex spectrum.
Show/Hide Noise Label
Adds a noise label to each peak. Theoretical isotope peaks
(displayed in blue) do not display a noise label.
Show/Hide Resolution
Label
Adds a resolution label to each peak. Theoretical isotope peaks
(displayed in blue) do not display a resolution label.
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Fragments
The Fragments page displays the maximum number of fragments as specified in the screening
method. See “To specify identification and confirmation settings” on page 216.
You must define fragments in the screening library. See “To add a fragment to a target peak”
on page 257.
Figure 126. Fragments page
Table 93. Fragments page shortcut menu commands
Thermo Scientific
Command
Description
Reset Scaling
Resets the original scaling after a zoom operation.
Copy to Clipboard
Copies the graphic display to the Clipboard.
Display Overlay Spectra
Display Stack Spectra
Overlays the two spectrum displays, or stacks the simulated
spectrum and the peak apex spectrum.
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Library
The Library page displays the matching library spectrum (in blue) and the experimental
spectrum (in black). The resulting score percentage from a library search match must be
higher than your specified threshold value to identify or confirm the presence of a compound.
See “To specify identification and confirmation settings” on page 216.
The application scales both the matched library spectrum and the highest peak in the
experimental spectra at 100 percent intensity and displays the resulting neutral loss (NL)
value for the matched library entry name on the right of the plot.
Figure 127. Library page with stacked spectra
Figure 128. Library page with overlaid spectra
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Table 94. Library page shortcut menu commands
Thermo Scientific
Command
Description
Reset Scaling
Resets the original scaling after a zoom operation.
Copy to Clipboard
Copies the graphic display to the Clipboard.
Display Overlay Spectra
Display Stack Spectra
Overlays the two spectrum displays, or stacks the simulated
spectrum and the peak apex spectrum.
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Working in the Report View
Use the Report View to display or generate reports for the currently selected batch in the
Analysis mode. See Report View in Analysis mode. You must process each sample in the batch
before you can view or generate a sample-level report for that sample.
 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.
 To refresh the Report View
If you make changes to your reports, click New Data Available - Refresh.
Figure 129. 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.”
–
For quantitative batches, preview reports for all Standard report types are always
available.
–
For target screening batches, preview reports for all Standard and Target Screening
report types are always available.
–
You must generate Custom and ToxID report types before they are available.
The Report View page displays one of the following report outputs:
–
Standard reports as PDF files
–
Custom reports in XLSM format
–
ToxID reports as PDF files
–
Target Screening reports as PDF files (available only for target screening batches)
• Generate Only: Creates all specified report output formats for the selected sample-level
or batch-level report. See “Generating Reports” on page 473.
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This section includes the following topics:
• Viewing Reports
• Generating Reports
• Working with Reports
• Working with the Active View
Viewing Reports
Use the View Only features to view all configured standard or target screening reports and any
custom or ToxID 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. Open the Select a Report list to display all configured report types.
These reports reflect the Displayed Reports selections in the Application Configuration
mode. To change the configured reports that are available in this view, see “Specifying the
Reports Configuration” on page 39.
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 to display in the report list, select any combination of report
filter options in the Filter Reports area.
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Table 95. Filter Reports options
Option
Behavior
Only Show Automated
Batch Reports
Displays only report types that have an output format
specified in the Automated Batch Reports area in the
Batch View. See “Automated Batch Reports Pane” on
page 357.
Standard Reports
Displays Standard report types.
Custom Reports
Displays generated Custom report types. Custom reports
are not available for viewing until you have generated the
report.
ToxID Reports
Displays generated ToxID report types. ToxID reports are
not available for viewing until you have generated the
report.
Target Screening Reports
Displays Target Screening report types.
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 ToxID 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 471.
• When the selected report includes separate reports for each compound, you must
select a compound.
Follow the procedure “To select a compound” on page 471.
• 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 471.
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 To select a sample
1. Open the Sample File list to display all processed samples in the batch.
Note Unprocessed samples are not listed. A message in the sample list reports the
number of unprocessed 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 Quality Control Report, the sample list displays only QC
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 File list closes. The Report View page displays the sample-level report.
 To select a compound
1. Open the Compound list to display 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.
 To select a sample and a compound
1. Open the Sample File list to display 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.
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For example, if you selected the Quality Control Report, the sample list displays only QC
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 File list closes.
4. Open the Compound list to display 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, ToxID, or target screening reports until you generate the report.
When you make changes to either the method in the Local Method view or the peaks in the
Data Review view, you must regenerate the custom, ToxID, 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. Open the Select a Report list to display the available reports.
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 39.
If you have many reports, you can filter the list.
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3. To limit the types of reports 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 “Automated
Batch Reports Pane” on page 357.
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.
ToxID Reports
Displays sample-level ToxID 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. Open the Sample File list to display 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 Quality Control Report, the sample list displays only QC
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 that 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 that 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 469.
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 icons on the Report View page to view, print, or export a report.
• 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 ToxID report, you can create a hardcopy printout or a PDF file.
• For each target screening report, you can create a hardcopy printout, a PDF file, or an
XML file.
Follow these procedures:
• To print a report
• To export a standard report
• To search for text
• To enlarge the report text
 To print a 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 icon,
.
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 that 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 icon,
.
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 icon,
.
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 icon,
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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.
For detailed descriptions of all active view parameters, see “Active View page.”
 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.
Each standard report that uses the Active View displays values that are both common to
all reports and specific to that report. See “Active View Report Contents” on page 485.
 To filter which compounds to display
Click the Showing button to switch the display to either all compounds or only
compounds that are flagged for failing a QAQC test.
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Figure 130. Active View page
Table 96. Active View page parameters (Sheet 1 of 4)
Parameter
Description
View Only
Makes the Active View pane available for reports that support the active view.
Generate Only
Switches the pane to Report View and makes the Active View pane not available.
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 96. Active View page parameters (Sheet 2 of 4)
Parameter
Description
Column headings
Many column headings are specific to individual reports. See “Active View Report Contents”
on page 485.
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 quantitation 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)
Est indicating the estimated compound type for semi-quantitative compounds
Quan flags do not apply to these sample types: Calibrator, QC, or Solvent.
Manual Integration reports do not use the Quan Flag column.
Manual Flags
Indicates manually integrated peaks.
M: Indicates a manually integrated quantitative 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 quantitative peak.
Total Response
The sum of all Quan Peak Response values for the compound.
Quan Peak Response
Response of the quantitative peak.
Quan Peak RT
Retention time for the quantitative peak.
Theoretical Amount
Theoretical amount of the compound. Reports N/A when not applicable.
Concentration
The injected concentration.
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Table 96. Active View page parameters (Sheet 3 of 4)
Parameter
Description
Confirming n Mass
Mass of the confirming peak.
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. Not available for analog compounds.
Confirming n Ion
Ratio
Actual ratio of the confirming ion response to the quantitation 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 164.
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 164.
QIon
Mass range for the quantitative peak. When you select the analog detector in the signal
parameters for the master method, the application displays this value as Analog and reports
with spectra displays show the spectra as Not Available. See “Signal” on page 135.
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 quantitative 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 96. Active View page 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 179.
Maximum Response
Maximum response time as specified on the ISTD page in Method Development mode. See
“ISTD” on page 179.
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 179.
Max RT
Maximum retention time as specified on the ISTD page in Method Development mode. See
“ISTD” on page 179.
Sample RT
Retention time found in the sample.
Graphical data
Quan Peak 1
Displays a graphical view of the quan peak for the selected sample and compound.
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.
For semi-quantitative compounds, the displayed curve is a linked calibration curve and is
indicated with a blue-green background.
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 database 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 486.
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 reports (Report 1 and Report 1 Long) Active View columns
• High Density Sample reports (Report 2 and Report 2 Long) Active View columns
• High Density Sample reports (Report 3 and 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
• Quality Control Report Active View columns
• Quantitation Report Active View columns
• Solvent Blank Report Active View columns
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Table 97. 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 quantitation 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)
Est indicating the estimated compound type for semi-quantitative compounds (Blank,
Quantitation, and High Density reports only)
Quan flags do not apply to these sample types: Calibrator, QC, or Solvent.
The Calibration report does not use the Quan Flags column. The Calibration Curve
report does not use the Quan Flags column.
Manual Flags
Indicates manually integrated peaks.
• M indicates a manually integrated quantitative peak.
• m indicates a manually integrated confirming peak.
Table 98. Blank Report Active View columns (Sheet 1 of 2)
Column
Description
Retention Time
Retention time for the quantitation 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 quantitative peak.
Response
Sum of all Quan Peak Response values for the compound.
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Table 98. Blank Report Active View columns (Sheet 2 of 2)
Column
Description
Inj Conc
Calculated amount as the sample was injected, with no conversion applied.
Inj Units
Injection units specified on the Calibration page in Method Development mode. See
“Calibration” on page 164.
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 164.
Table 99. 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.
Note The Calibration Report does not report semi-quantitative compounds.
Table 100. High Density Sample reports (Report 1 and Report 1 Long) Active View columns (Sheet 1 of 2)
Column
Description
m/z
Mass-to-charge ratio for the quantitative peak.
Total Response
The sum of all Quan Peak Response values for the compound.
Quan Peak Response
Response of the quantitative peak.
Quan Peak RT
Retention time for the quantitative peak.
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Table 100. High Density Sample reports (Report 1 and Report 1 Long) Active View columns (Sheet 2 of 2)
Column
Description
T Amount
Theoretical amount of the compound. Reports N/A when not applicable.
Conc
Calculated (injected) amount.
Table 101. High Density Sample reports (Report 2 and Report 2 Long) Active View columns
Column
Description
m/z
Mass-to-charge ratio for the quantitative peak.
Total Response
Sum of all Quan Peak Response values for the compound.
Quan Peak Response
Response of the quantitative peak.
Quan Peak RT
Retention time for the quantitative 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. Not available for analog compounds.
Confirming 1 Ion Ratio
Actual ratio of the confirming ion response to the quantitation ion response.
Confirming 1 Range
Acceptable range for the confirming ion.
Table 102. High Density Sample reports (Report 3 and Report 3 Long) Active View columns (Sheet 1 of 2)
Column
Description
m/z
Mass-to-charge ratio for the quantitative peak.
Total Response
Sum of all Quan Peak Response values for the compound.
Quan Peak Response
Response of the quantitative peak.
Quan Peak RT
Retention time for the quantitative 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. Not available for analog compounds.
Confirming 1 Ion Ratio
Actual ratio of the confirming ion response to the quantitation ion response.
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Table 102. High Density Sample reports (Report 3 and Report 3 Long) Active View columns (Sheet 2 of 2)
Column
Description
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. Not available for analog compounds.
Confirming 2 Ion Ratio
Actual ratio of the confirming ion response to the quantitation ion response.
Confirming 2 Range
Acceptable range for the confirming ion.
Table 103. 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 179.
Maximum Response
Maximum response time as specified on the ISTD page in Method Development
mode. See “ISTD” on page 179.
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 179.
Max RT
Maximum retention time as specified on the ISTD page in Method Development
mode. See “ISTD” on page 179.
Sample RT
Retention time found in the sample.
Table 104. Ion Ratio Failure Report Active View columns
Column
Description
Quan Ion
The ion for quantitative 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 quantitation ion response.
Range
The acceptable range.
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Table 105. Manual Integration Report Active View columns
Column
Description
m/z
Mass-to-charge ratio for the quantitative 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 106. Quality Control Report Active View columns
Column
Description
Curve Type
L - Linear
A - Average RF
Q - Quadratic
Daily RF
The response factor value for Average RF curve types. For all other curve types, this
column is blank.
Mean RF
The average response factor as found in the calibration file. Displayed for Average RF
curve types. For all other curve types, this column is blank.
Min RF
Minimum QC response factor as found on the QC Check page in the method.
RF % D
Percent difference between daily and average response factor.
Max RF Diff (%)
Maximum QC response factor as found on the QC Check page in the method.
QC Amount
The amount defined by the level for the compound.
Calculated Amount
Reportable amount of concentration.
Amount % Difference
Percentage difference between the calculated amount and the QC amount. Use the
injected concentration to calculate this value.
Max Amount % Difference
Maximum allowed percentage difference between the calculated amount and the QC
amount.
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Table 107. 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 quantitative peak.
When you select the analog detector in the signal parameters for the master method,
the application displays this value as Analog and reports with spectra displays show
the spectra as Not Available. See “Signal” on page 135.
Response
Sum of all quantitative 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 164.
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 164.
Table 108. Solvent Blank Report Active View columns
Column
Description
RT
Retention time for the quantitative 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 quantitative peak.
When you select the analog detector in the signal parameters for the master method, the
application displays this value as Analog and reports that display spectra report the spectra
as Not Available. See “Signal” on page 135.
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 Project Administration View
Working in the Project Administration View
When user security is activated, in either the LabDirector or ITAdmin role, you can create and
manage projects and subprojects on fixed or network drives in the Project Administration
view of the Analysis mode.
This section includes the following topics:
• Working with Drives
• Working with Projects
 To open the Project Administration view
1. Click Analysis in the navigation pane of the current mode.
2. In the Analysis navigation pane, click Project Administration.
The Project Administration view opens.
By default, all projects are created under a main Projects folder on drive C:
C:\Thermo\TraceFinder\3.0\Forensic\Projects
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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 in. disk or a USB drive.
Follow these procedures:
• To choose a drive
• To change the default drive
• To hide a drive from the display
• To refresh the display
 To choose a drive
1. In the Available Drives area, click any drive other than the default drive C.
If you have not created a Projects directory on this drive, you see this message:
2. Click Create Project 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 495.
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 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.
 To hide a drive from the display
Clear the check box in the Show column.
The application does not list the hidden drive in the drive lists. You cannot hide the
default drive.
 To refresh the display
Choose File > Refresh Available Drives from the main menu.
The Available Drives table refreshes to show any drives that have changed (for example, if
you inserted a USB drive). You can now configure any new drives.
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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\3.0\Forensic\Projects
folder.
If you installed the TraceFinder example data, the main Projects folder includes an Example
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 reinstall the
TraceFinder application” on page 10.
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 activates 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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 To delete projects or subprojects
1. Select the project or subproject that 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 activates 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.
There is no undo for this command.
3. At the prompt to remove all empty folders, click OK.
The application removes all folders that have no folders or files.
 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.
Note 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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Using the Analysis Mode
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. 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 83.
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 131. Local Method View of a quantitation method
Figure 132. Local Method View of a screening method
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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. See “Batch Template Editor” on page 506. 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 379.
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 506.
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 506.
 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 and create a new subproject. See “Working in the Project Administration View”
on page 492.
3. To change the current method, click Select Method and select a new method.
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Working in the Batch Template Editor
 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, Specimen 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, Specimen sample.
2. Right-click and choose Insert Sample from the shortcut menu.
The application inserts a new, Specimen sample above the selected sample.
Inserted
sample
 To copy a sample
1. Select the sample that you want to copy.
2. Right-click and choose Insert Copy Sample from the shortcut menu.
The application inserts the copy above the selected sample.
 To remove samples from the list
1. Select the sample that 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.
 To edit sample values
1. For each sample, click the Sample Type column and select a sample type from the list.
Available sample types
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Specimen
QC
Solvent
Calibrator
Unextracted
Negative
Hydrolysis
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2. For each QC or Calibrator 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 Quantitation Master Method” on page 106.
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 that 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.
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.
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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.
Here is an example:
Copying selected report output formats from the first sample
Duplicates the selected report 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 that
you want identified 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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Working in the Batch Template Editor
Figure 133. Batch Template Editor
Table 109. 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 109. 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: Specimen, QC, Solvent, Calibrator, Hydrolysis, Unextracted,
or Negative
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.
Sample 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
Saves reports as XML files.
Available only for standard reports.
Create XLSM
Saves 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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A
Reports
This appendix contains information about standard, custom, ToxID, and target screening
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 standard reports, custom reports, and
reports specific to target screening and ToxID features.
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 Application Configuration mode,
see “Specifying the Reports Configuration” on page 39.
For detailed information about specifying reports when you create a method in the Method
Development mode, see “Editing the Reports Page” on page 189.
For detailed information about viewing reports in the Acquisition mode, see “Selecting and
Reviewing Reports” on page 309.
This section lists all available reports for the following report types:
• “Standard Reports” on page 510
• “Custom Reports” on page 511
• “Target Screening Reports” on page 511
• “ToxID Reports” on page 511
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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) or XLSM (.xlsm) output format. In addition to the report
type, you can specify a report title that appears at the top of each of your reports. The default
report title is the report name.
The TraceFinder application can generate the following types of standard reports:
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Batch Report
Batch Summary Report
Batch Report Rev 1
Calibration Report
Calibration Curve Report
Chromatogram Report
Compound Calibration Report
Compound Calibration Report - Alternate
Confirmation Report
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
Intelligent Sequencing Report
Internal Standard Summary Report
Ion Ratio Failure Report
Manual Integration Report
Method Report
Negative Report
Qualitative Peak Report
Qualitative Summary Report
Quality Control Report
Quantitation Report
Quantitation Report - 2
Sample Report
Sample Report Long
Solvent Blank Report
To view an example of each type of standard report, see “Sample Standard Reports” on
page 513.
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A Reports
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 create a separate report for each sample.
The TraceFinder application can generate the following types of custom reports:
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
AltCalibrationReport
Alternate BatchReport
Alternate CalibrationReport
Alternate ConfirmationReport
Alternate MatrixSpikeReport
Alternate SampleReport
Alternate SummaryReport
BatchReport
BlankReport
CalibrationDensityReport
CalibrationReport
CheckStandardReport
CompoundCalibrationReport
ConfirmationReport
ConfirmationReport2
HighDensitySampleReport1Long
HighDensitySampleReport2Long
HighDensitySampleReport3Long
HighDensitySampleReport4
HighDensitySampleReport5
QuantitationReport
SteroidAnalysisReport
Target Screening Reports
The TraceFinder application can generate the following types of target screening reports:
• Target Screening High Density Sample Report
• Target Screening Summary Report
ToxID Reports
ToxID reports are available only when you install the ToxID™ software and activate the ToxID
features. For a detailed procedure for enabling ToxID features, see “ToxID” on page 64. The
TraceFinder application can generate the following types of ToxID 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 110. 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 111. 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.
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A Reports
Sample Standard Reports
Sample Standard Reports
This section shows samples of the following standard report types:
• Batch Report
• Batch Report Rev 1
• Calibration Report
• Chromatogram Report
• Compound Calibration Report
• Compound Calibration Report - Alternate
•
•
•
•
•
•
•
•
•
•
•
Confirmation Report
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
• Manual Integration Report
• Method Report
• Quality Control Report
• Quantitation Report
• Quantitation Report - 2
• Solvent Blank Report
Tip To easily view reports in landscape format, choose View > Rotate View > Clockwise
from the Adobe Acrobat™ viewer menu.
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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
Theo Conc
% Diff
Min Conc
Max Conc
0.358
0.500
-28.34
0.250
0.750
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0.602
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Cyanazine
Simazine D-10
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Propazine D-14
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542
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295652
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20.45
0.250
0.750
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0.750
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Page 2 of 3
Preview2_EPA536-Triazines
EPA536-Triazines
Cali File: Preview2.calx
Method:
1
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AMER\jamie.humphries
Preview2
Sample ID
SampleID003
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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
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Sample Standard Reports
TraceFinder User Guide
549
A
Reports
Sample Standard Reports
Solvent Blank Report
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550
TraceFinder User Guide
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, Comment, and other columns.
Follow these procedures:
• To automatically copy column values
• To automatically enter sequential column values
• To use Copy Down or Fill Down for a range of samples
 To automatically copy column values
1. Select the cell whose value you want to copy to all cells below it.
Observe the difference between a selected and nonselected cell.
Selected
Not selected
2. Right-click and choose Copy Down from the shortcut menu.
The value is copied to all rows below the selected row.
 To automatically enter sequential column values
1. Enter a value for the first row of the fill down sequence.
This does not have to be the first sample row. You can begin the fill down procedure from
any row in the sequence.
Thermo Scientific
TraceFinder User Guide
551
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 nonselected cell.
Selected
Not selected
3. Right-click and choose Fill Down from the shortcut menu.
The application enters sequential column values starting with the value in the selected
row and ending with the last row in the column.
You can repeatedly use the Fill Down command to create multiple sequences.
When you use the Fill Down command for the Vial Position column with an autosampler
configured, the TraceFinder application knows the number of vial positions configured in
your autosampler and numbers the positions accordingly.
552
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
553
I
Index
Symbols
.cdb, defined 2
.csv, defined 2
.meth, defined 2
.pmd, defined 2
.raw, defined 2
.xml, defined 2
# Background Scans parameter
application configuration 52
method development 147
% Test parameter 169
%CV parameter 433
%Diff parameter 433
%RSD parameter 433
A
Account Number parameter 74
Acquire a New Raw Data File parameter 94
Acquisition command 33
Active parameter
Data Review sample list 433
Identification page 118
Active View page 480
Actual RT parameter 432
Add Compound command 251
Add Compound from Compound Database command 115
Add Group command 184
Add Sample command
Acquisition mode 306
Batch View sample list 355
Batch Wizard 388
Add This Mass as New Confirming Ion command 161
Add This Mass to Existing Quan Mass Ranges command 161
Add User parameter 74
Adduct 1–n parameter 201
Adduct parameter, Compound Database 248
Amount parameter 165
Thermo Scientific
Analysis command 33
Application Configuration command 36
Area Noise Factor parameter
application configuration 54
Detect page 150
Area parameter 432
Area Scan Window parameter
application configuration 55
Detect page 151
Area Tail Extension parameter
application configuration 55
Detect page 151
Area Threshold, event type 58
Assay Type parameter
Batch Wizard 381
Method View 111, 206
Associate a Raw Data File dialog box 97
Auto TSRM Update parameter 320
Autocalc Initial Events parameter, Avalon 153
automated background subtraction options 109
Automatically Create the Master Method parameter 93
Available Methods parameter 381
Available Templates parameter 381
Avalon detection algorithm 46
Avalon Event List dialog box 57
B
background subtraction options 109
Background Subtraction Range Option parameter 112
Barcode Actual parameter 308, 354
Barcode Expected parameter 354
Baseline Window parameter
application configuration 54
Detect page 150
Batch Level parameter
method development 190
report configuration 39
Batch Selection view 290
TraceFinder User Guide
555
Index: C
Batch view 343
batches
Acquisition mode 286
Analysis mode 343
calibration 314
development batch 275
Best Match Method parameter 232
Browse In Raw File command 355
Bunch Factor, event type 58
C
cal1-caln parameter 167
Calculate Concentration As parameter 195
Calculated Amt parameter 432
Calculation Based On parameter 201
Calculation Type parameter 353
Calibration Curve Type command 449
Calibration Levels page, Method View 166
Calibration Method parameter 232
Calibration page
Compounds page 164
QAQC page 176
Calibration parameter 320
Calibrator sample type, defined 337
Cancel Changes parameter 74
Carryover Limit parameter 175
CAS No parameter, Identification page 118
CAS parameter, Compound Database 246
Category parameter, Compound Database 246
caution flags 400, 412
Channel parameter
Batch View 354
Data Review 433
Charge State parameter, Compound Database 248
Collision Energy parameter, Compound Database
confirming peak 250
target peak 249
color codes, Sample Definition view 306
commands
Acquisition 33
Add Compound 251
Add Compound from Compound Database 115
Add Group 184
Add Sample
Acquisition mode 306
Batch View sample list 355
Batch Wizard 388
Add This Mass as New Confirming Ion 161
Add This Mass to Existing Quan Mass Ranges 161
Analysis 33
Application Configuration 36
556
TraceFinder User Guide
Apply to All Peaks in Compound
Avalon 153
Genesis 148
ICIS 151
Apply to All Peaks in Method
Avalon 153
Genesis 147
ICIS 151
Apply to All Peaks with Like Sensitivity Settings
Avalon 153
Genesis 148
ICIS 151
Browse In Raw File 355
Calibration Curve Type 449
Confirming Ion List 443
Copy Down 551
Copy With Headers
Acquisition mode 307
Batch View sample list 308, 355
Create New 392
Delete Compound from Method 181
Display Retention Time Column 181
Export SRM Data 236
Export to CSV File
Acquisition mode 307
Batch View sample list 308, 356
Extend Calibrations 392
Fill Down 551
Import Compounds 262
Import Published Method 235
Import Samples 355
Insert Copy Sample
Acquisition mode 306
Batch View sample list 355
Batch Wizard 388
Insert Sample
Acquisition mode 306
Batch View sample list 355
Batch Wizard 388
Log Off 36
Manual Integration Settings 443
Map Raw Files to Samples 355
Method Integration Settings 443
Methods 33
Modify Columns, Batch View sample list 346
Move Sample Down 388
Move Sample Up 388
New Compound Database
converting legacy data 264
creating new database 241
Open Compound Database 241
Pause Queue 332
Peak Detection Settings 444
Peak Labels 443
Thermo Scientific
Index: D
Reactivate All 332
Real Time Status 36
Reinject Selected Samples
Acquisition mode 306
Batch view sample list 355
Remove Pending Batch 334
Remove Pending Batches 332
Remove Pending Samples 334
Remove Selected Samples
Acquisition mode 307
Batch view sample list 355
Batch Wizard 388
Save Compound Database As 242
Send RT to Method 443
Set This Mass as a New Quan Peak 161
Set This Mass as Quan Mass 161
Show Peak Info 444
Stop Active Batch 332
Stop All Batches 332
Stop Batch 334
Turn Device Off 315
Turn Device On 314
Turn Device Standby 314
Update Confirming Ion Ratios with This Spectrum
161
comma-separated values, defined 2
Comment parameter
Batch View 354
Data Review 433
Company Logo parameter 200
Company Name parameter 200
Compound Database views 243
Compound parameter
Calibration page 176
Compound Database 246
QC levels page 169
Compound Type parameter
Calibration 165
Identification page 117
compound types
internal standards
Detection page 120
Identification page 117
quan
Detection page 120
Identification page 117
target
Detection page 120
Identification page 117
Compounds page, Method View 114
compounds, importing to compound database 262
Confirming Ion List command 443
Confirming n Ion Ratio Flag parameter 483
Thermo Scientific
Confirming n Ion Ratio parameter 483
Confirming n Manual Flag parameter 483
Confirming n Mass parameter 483
Confirming n Range parameter 483
Confirming n Response parameter 483
Constrain Peak Width parameter
Genesis
application configuration 51
Detect page 146
ICIS
application configuration 54
Detect page 150
Conversion Factor parameter 354
Copy Down command 551
Copy With Headers command
Acquisition mode 307
Batch View sample list 308, 355
Create Blank Quantitation Method parameter 97
Create New command 392
Create PDF parameter
Batch Template Editor 507
Method view 190, 210
Create XLSM parameter
Batch Template Editor 507
Method View 190
Create XML parameter
Batch Template Editor 507
Method View 190, 210
Curve Type parameter
Calibration page 165
Method Template Editor 232
custom reports, listed 6
Cutoff parameter 175
CV Test (%) parameter 176–177, 179
D
Data Review view 393, 454
Decimal Places to be Reported parameter 194
Delete Compound from Method command 181
Detection Method parameter
Avalon
application configuration 56
Detect page 152
Genesis
application configuration 50
Detect page 146
ICIS
application configuration 53
Detect page 150
Detection page, Method View 119
Detection Type parameter, Times page 133
TraceFinder User Guide
557
Index: E
Detector parameter, Signal page 142
Development Batch view 275
Device Name parameter
Acquisition mode 318
Batch View 373
dialog boxes
Add Library 17
Associate a Raw Data File 97
Avalon Event List 57
Import an Xcalibur Method 95
Open Chromatograph Reference Sample 305, 378, 452
Open Compound Database 241
Save Compound Database As 242
Save New Compound Database 241, 264
Select Compounds from Database 115
Select Compounds to Add 102
Thermo Library Manager 17
Thermo Xcalibur Instrument Setup 108, 204
Thermo Xcalibur Roadmap 16
Dilution Factor parameter 354
Disable Cluster Off, event type 59
Disable Cluster On, event type 59
Display Compounds Above Set Limit parameter 194
Display Quan Flags and Legend parameter 194
Display Retention Time Column command 181
Displayed Reports parameter 43
E
Edit User parameter 74
Email Address parameter 74
Enable parameter, Ratios page 163
Enable Peak Threshold parameter 232
Enable Tune Time Tracking parameter 195
Enable Valley Detection parameter
application configuration 51
method development 146
Enabled parameter 74
End RT parameter, Times page 134
End Threshold, event type 58
Energy Ramp parameter, Compound Database 249
Estimation Method parameter 165
Event parameter 57
Event types 58
Exact Mass Window parameter 201
Example parameter, Reports page 190
Exclude Matching Quan Peaks parameter 233
Excluded parameter 433
Exclusion Window parameter 233
Expected RT parameter 432
Expected RT parameter, Times page 133
Expected Width parameter
558
TraceFinder User Guide
application configuration 51
method development 146
Experiment parameter, Compound Database 246
Export SRM Data command 236
Export to CSV File command
Acquisition mode 307
Batch View sample list 308, 356
Extend Calibrations command 392
Extracted Ion Chromatogram 260
Extracted Mass parameter, Compound Database
fragment 250
target peak 248
F
feature summary 3
file types, supported 2
Filename parameter, Batch View 308, 353
Fill Down command 551
Filter parameter, Detection 142
Filter parameter, Signal page 141
Final Units parameter
Batch View 354
Data Review 433
Finish view 313
Flag Values Above Carryover parameter 195
Flag Values Above LOR parameter 195
Flag Values Above ULOL parameter 195
Flag Values Below LOD parameter 195
Flag Values Below LOQ parameter 195
Flag Values Between LOD and LOQ parameter 195
Flags parameter 396, 398, 407, 409, 417
Force Cluster Off, event type 59
Force Cluster On, event type 59
Formula parameter, Compound Database 246
Full Name parameter 74
G
General page
Background Subtraction Range Option 112
editing 107
Include Data Dependent Filters parameter 113
Injection Volume parameter
Batch View 353
method development 112, 206
Instrument Method parameter 112, 206
Ion Range Calc Method parameter 112
Library Search Type parameter 207
Mass Precision parameter 112, 206
Mass Tolerance parameter 113, 207
Method View 107
Number of Scans to Subtract parameter 112
Thermo Scientific
Index: H
Qualitative Peak Processing Template parameter 112
Show All Compounds parameter 207
Stepoff Value parameter 112
Generate Only parameter 481
Genesis detection algorithm 46
Groups page, Method View 183
H
Height parameter 432
Hydrolysis page, Master Method View 181
Hydrolysis sample type, defined 337
I
ICIS detection algorithm 46
Identification page, Method View 117
Import an Xcalibur Method dialog box 95
Import Compounds command 262
Import parameter 43
Import Published Method command 235
Import Samples command 355
Include Compound Peak Spectrum as Reference Spectrum
parameter 232
Include Confirming Ions parameter 232
Include Data Dependent Filters parameter 113
Injection Amount parameter 94
Injection Concentration parameter 483
Injection Units parameter 483
Injection Volume parameter
Batch View 353
method development 112, 206
Insert Copy Sample command
Acquisition mode 306
Batch View sample list 355
Batch Wizard 388
Insert Sample command
Acquisition mode 306
Batch View sample list 355
Batch Wizard 388
Installed Reports parameter 43
installing NIST and QED libraries 16
Instrument Method parameter
Batch View 354
General page 112, 206
Method Forge 94
instrument status indicators 315
Instrument view 269
instruments, supported viii
Integration Mode parameter 432
Ion Coelution parameter
Thermo Scientific
application configuration 49
Ratios page 163
Ion Range Calc Method parameter 112
Ion Ratio Window parameter 201
Ionization parameter, Compound Database 246
ISTD Amt parameter 432
ISTD Matching parameter 233
ISTD page, Method View 179
ISTD parameter 165
ISTD Resp parameter 432
IT Administrator role 75
L
Lab Name parameter 111, 206
Laboratory Name parameter 200
Lens parameter, Compound Database 249
Level parameter
Batch View 353
QC Levels page 169
Library Search Type parameter 207
licenses, types of ix
Limit Library Hits parameter 232
Limit the Retention Time Range parameter 232
Limits page, Method View 175
Linked Compound parameter 165
Local Method view 498
LOD (Detection Limit) parameter 175
Log Off command 36
Login parameter 14
LOQ (Quantitation Limit) parameter 175
M
m/z Window parameter 200
Manual Flags parameter 482
Manual Injection parameter 94
Manual Integration Settings command 443
Map Raw Files to Samples command 355
Mass parameter
Compound Database
target peak 247
Mass parameter, Compound Database
confirming peak 249
Mass parameter, Compound Database, confirming peak 250
Mass Precision parameter 112, 206
Mass Tolerance parameter 113, 207
Master Method View
Hydrolysis page 181
Negative page 178
Max Amt Diff (%) parameter 176
TraceFinder User Guide
559
Index: N
Max Conc parameter 178
Max Recovery (%) parameter, ISTD page 179
Max RF Diff (%) parameter 177
Max RSD (%) parameter, Calibration page 176
Max RT (+min) parameter, ISTD page 179
Measurement Unit parameter 201
Method Integration Settings command 443
Method parameter
Matrix Blank page 178
Solvent Blank page 180
Method Template Editor 231
Method View
Calibration Levels page 166
Calibration page
Compounds page 164
QAQC page 176
Compounds page 114
Detection page 119
General page 107
Groups page 183
Identification page 117
ISTD page 179
Limits page 175
QC Levels page 167
Ratios page 162
Real Time Viewer page 170
Reports page 189
Solvent Blank page 180
Spectrum page 157
Suitability page 154
Method view 84
Method View, QAQC page 174
methods
importing Xcalibur 95
instrument 269
local 498
master 83
Method Template Editor 231
update TSQ method 313
Methods command 33
Min Peak Height (S/N) parameter
Genesis
application configuration 51
Detect page 147
ICIS
application configuration 54
Detect page 150
Min Peak Width parameter
application configuration 55
Detect page 151
Min recovery (%) parameter, ISTD page 179
Min RF parameter 177
560
TraceFinder User Guide
Min RT (–min) parameter 179
modes, choosing 33
Modify Calibrations or Active Compounds by Group
parameter 390
Modify Columns command, Batch View sample list 346
Move Sample Down command 388
Move Sample Up command 388
MS Order parameter, Compound Database
confirming peak 250
target peak 248
MS2 Search Library parameter 200
MS3 Search Library parameter 200
Multiplet Resolution parameter
application configuration 55
Detect page 151
Multiplexing Channels parameter 306
N
Name the Master Method parameter 93
Negative page, Master Method View 178
Negative Peaks, event type 58
Negative sample type, defined 337
Neutral Mass parameter, Compound Database 246
New Compound Database command
converting legacy data 264
creating new database 241
NIST library, installing 16
No Specified Retention Time parameter 201
Noise Method parameter
application configuration 55
Detect page 151
Number of Confirming Ions parameter 232
Number of Scans to Subtract parameter 112
O
Only Select Top Peaks parameter 232
Open Chromatograph Reference Sample dialog box 305, 378,
452
Open Compound Database command 241
Open Compound Database dialog box 241
Origin parameter
Calibration 165
Method Template Editor 233
P
parameters
# Background Scans 147
application configuration 52
% Test 169
Thermo Scientific
Index: P
%CV 433
%Diff 433
%RSD 433
Account Number 74
Acquire a New Raw Data File 94
Active
Data Review sample list 433
Identification page 118
Actual RT 432
Add User 74
Adduct 1–n 201
Adduct, Compound Database 248
Amount 165
Area 432
Area Noise Factor
application configuration 54
Detect page 150
Area Scan Window
application configuration 55
Detect page 151
Area Tail Extension
application configuration 55
Detect page 151
Assay Type
Batch Wizard 381
Method View 111, 206
Auto TSRM Update 320
Autocalc Initial Events, Avalon 153
Automatically Create the Master Method 93
Available Methods 381
Available Templates 381
Background Subtraction Range Option 112
Barcode Actual 308, 354
Barcode Expected 354
Baseline Window
application configuration 54
Detect page 150
Batch Level
method development 190
report configuration 39
Best Match Method 232
cal1-caln 167
Calculate Concentration As 195
Calculated Amt 432
Calculation Based On 201
Calculation Type 353
Calibration 320
Calibration Method 232
Cancel Changes 74
Carryover Limit 175
CAS No, Identification page 118
CAS, Compound Database 246
Category, Compound Database 246
Channel
Thermo Scientific
Batch View 354
Data Review 433
Charge State, Compound Database 248
Collision Energy, Compound Database
confirming peak 250
target peak 249
Comment
Batch View 354
Data Review 433
Company Logo 200
Company Name 200
Compound
Calibration page 176
Compound Database 246
QC levels page 169
Compound Type
Calibration 165
Identification page 117
Confirming n Ion Ratio 483
Confirming n Ion Ratio Flag 483
Confirming n Manual Flag 483
Confirming n Mass 483
Confirming n Range 483
Confirming n Response 483
Constrain Peak Width
Genesis
application configuration 51
Detect page 146
ICIS
application configuration 54
Detect page 150
Conversion Factor 354
Create Blank Quantitation Method 97
Create PDF
Batch Template Editor 507
Method view 190, 210
Create XLSM
Batch Template Editor 507
Method View 190
Create XML
Batch Template Editor 507
Method View 190, 210
Curve Type
Calibration page 165
Method Template Editor 232
Cutoff 175
CV Test (%) 176–177, 179
Decimal Places to be Reported 194
Detection Method
Avalon
application configuration 56
Detect page 152
Genesis
application configuration 50
TraceFinder User Guide
561
Index: P
Detect page 146
ICIS
application configuration 53
Detect page 150
Detection Type, Times page 133
Detector 142
Device Name
Acquisition mode 318
Batch View 373
Dilution Factor 354
Display Compounds Above Set Limit 194
Display Quan Flags and Legend 194
Displayed Reports 43
Edit User 74
Email Address 74
Enable Peak Threshold 232
Enable Tune Time Tracking 195
Enable Valley Detection
application configuration 51
method development 146
Enable, Ratios page 163
Enabled 74
End RT, Times page 134
Energy Ramp, Compound Database 249
Estimation Method 165
Event 57
Exact Mass Window 201
Example, Reports page 190
Exclude Matching Quan Peaks 233
Excluded 433
Exclusion Window 233
Expected RT 432
Expected RT, Times page 133
Expected Width
application configuration 51
method development 146
Experiment, Compound Database 246
Extracted Mass, Compound Database
fragment 250
target peak 248
Filename, Batch View 308, 353
Filter 141
Filter, Detection 142
Final Units
Batch View 354
Data Review 433
Flag Values Above Carryover 195
Flag Values Above LOR 195
Flag Values Above ULOL 195
Flag Values Below LOD 195
Flag Values Below LOQ 195
Flag Values Between LOD and LOQ 195
Flags 396, 398, 407, 409, 417
Formula, Compound Database 246
Full Name 74
562
TraceFinder User Guide
Generate Only 481
Height 432
Import 43
Include Compound Peak Spectrum as Reference
Spectrum 232
Include Confirming Ions 232
Include Data Dependent Filters 113
Injection Amount 94
Injection Concentration 483
Injection Units 483
Injection Volume
Batch View 353
method development 112, 206
Installed Reports 43
Instrument Method
Batch View 354
General page 112, 206
Method Forge 94
Integration Mode 432
Ion Coelution
application configuration 49
Ratios page 163
Ion Range Calc Method 112
Ion Ratio Window 201
Ionization, Compound Database 246
ISTD 165
ISTD Amt 432
ISTD Matching 233
ISTD Resp 432
Lab Name 111, 206
Laboratory Name 200
Lens, Compound Database 249
Level
Batch View 353
QC levels page 169
Library Search Type 207
Limit Library Hits 232
Limit the Retention Time Range 232
Linked Compound 165
LOD (Detection Limit) 175
Login 14
LOQ (Quantitation Limit) 175
m/z Window 200
Manual Flags 482
Manual Injection 94
Mass
Compound Database
confirming peak 249
target peak 247
Mass Precision 112, 206
Mass Tolerance 113, 207
Mass, Compound Database, confirming peak 250
Max Amt Diff (%) 176
Max Conc 178
Max Recovery (%), ISTD page 179
Thermo Scientific
Index: P
Max RF Diff (%) 177
Max RSD (%), Calibration page 176
Max RT (+min), ISTD page 179
Measurement Unit 201
Method
Matrix Blank page 178
Solvent Blank page 180
Min Peak Height (S/N)
Genesis
application configuration 51
Detect page 147
ICIS
application configuration 54
Detect page 150
Min Peak Width
application configuration 55
Detect page 151
Min recovery (%)
ISTD page 179
Min RF 177
Min RT (–min) 179
Modify Calibrations or Active Compounds by Group
390
MS Order, Compound Database
confirming peak 250
target peak 248
MS2 Search Library 200
MS3 Search Library 200
Multiplet Resolution
application configuration 55
Detect page 151
Multiplexing Channels 306
Name the Master Method 93
Neutral Mass, Compound Database 246
No Specified Retention Time 201
Noise Method
application configuration 55
Detect page 151
Number of Confirming Ions 232
Number of Scans to Subtract 112
Only Select Top Peaks 232
Origin
Calibration 165
Method Template Editor 233
Password
login screen 14
user administration 74
Path 94
Peak Height (%)
Genesis
application configuration 51
Detect page 146
ICIS
Thermo Scientific
application configuration 54
method development 150
Peak Noise Factor
application configuration 54
method development 150
Peak S/N Cutoff
application configuration 52
Detect page 147
Percentage 178
Phone Number 74
Polarity, Compound Database 248
Post-run System State 318, 373
Precursor Mass, Compound Database, target peak 247
Precursor, Compound Database, confirming peak 249
Priority Sequence 318, 373
Processing Configuration File 200
Product Mass, Compound Database
confirming peak 249
target peak 247
QAQC Flags 482
QC1-QCn 169
QIon 483
Qualitative Peak Processing Template 112
Quan Flags 482
Quan Mass 483
Quan Peak m/z 482
Quan Peak Response 482
Quan Peak RT 482
Quick Mode 381
R^2 Threshold 176
Ranges, compound detection 142
Raw Filename 94
Reference Compound, Identification page 118
Remove User 74
Report All Compounds Listed in Configuration File
201
Report Concentration 194
Report Name 190, 210
Report Noise As
application configuration 52
Detect page 147
Report Semi-Quantitative Result 201
Report Title 190, 210
Report Type 190, 210
Reset Password 74
Response 483
Response Ratio 432
Response Threshold, Compound Database 246
Response Via
Calibration 165
Method Template Editor 233
Retention Time 483
RMS
TraceFinder User Guide
563
Index: P
application configuration 55
Detect page 151
Role 74
RT
Calibration 165
Calibration levels 167
Calibration page 176
Chk Std page 177
Compound Database 249
Hydrolysis page 181
Identification page 117
ISTD page 179
Limits page 175
Matrix Blank page 178
QC levels page 169
Solvent Blank page 180
RT Window 200
S/N Threshold
application configuration 51
method development 146
Sample Amt 432
Sample Comment 94
Sample Concentration 483
Sample File 481
Sample ID, Batch View 308, 353
Sample Name
Batch View 308, 353
Data Review 409
Sample Type
Batch View 353
Data Review 396, 410, 418
Sample Units 483
Sample Volume 354
Sample Weight 354
Save Changes 74
Screening Method 200
Select a Report 481
Sensitivity
Avalon
application configuration 56
Detect page 152
Genesis
application configuration 50
Detect page 146
ICIS
application configuration 53
Detect page 150
Method Template Editor 232
Separate Ion Overlay Display 194
Set Ion Ratio to All Confirming Peaks in Compound
163
Set Ion Ratio to All Confirming Peaks in Method 163
564
TraceFinder User Guide
Set Peak Windows Settings to All Peaks in Compound
134
Set Peak Windows Settings to All Peaks in Method
134
Shade Row when Sample is Outside of Evaluation
Criteria 194
Show All Compounds 207
Show Chromatogram on Quantitation Report 194
Show Quan Peaks Only 170
Showing, Active View 481
Smoothing
Avalon
application configuration 56
Detect page 153
Genesis
application configuration 50
Detect page 146
ICIS
application configuration 54
Detect page 150
Specify Default Ion Ratio Ranges 232
Standard type 165
Start Device 318, 373
Start RT, Times page 134
Start When Ready 318, 373
Starting vial number 381
Status
Active View 482
Batch View 308, 353
Data Review 409
Stepoff Value 112
System Shutdown Method 320
System Startup Method 320
System Status 320
Tailing Factor
Genesis
application configuration 51
method development 146
ICIS
application configuration 54
method development 150
Target Ratio 163
Template Layout 381
Theoretical Amount 482
Theoretical Amt 432
Threshold/Lower Limit 181
Time 57
Time Range Peak, Compound Database 248
Time/Event/Value 56
Total Batch Rows 381
Total Response 482
Total Rows 481
Trace, Detection 142
Thermo Scientific
Index: P
Tune File Lifetime 195
ULOL (Linearity Limit) 175
Units 165
Upper Limit
Hydrolysis page 181
Solvent Blank page 180
Use Alternate Calibration Report Format 194
Use an Existing Raw Data File 93
Use as RT Reference, Identification page 118
Use Autosampler 94
Use Average Scan 201
Use Data Dependent Scans 234
Use Full MS Scan to Confirm 201
Use Genesis Algorithm for Qual Processing 233
Use Method Forge 85, 89, 95
Use Scan at Peak Apex 201
Use These Libraries 232
User Security 64
Username 74
Valley Rise (%)
application configuration 52
Detect page 147
Valley S/N
application configuration 52
method development 147
Value 57
Vial Position
Batch View 308, 353
Method Forge 94
View Only 481
View Width
application configuration 49
Times page 134
Weighting
Calibration 165
Method Template Editor 233
Window
application configuration
ion ratio 49
retention time 49
Compound Database 249
Ratios page 163
Times page 133
Window Type
application configuration 49
Ratios page 163
XIC 141
Password parameter
login screen 14
user administration 74
password, administrator 12
Path parameter 94
Pause Queue command 332
Thermo Scientific
Peak Detection Settings command 444
Peak Height (%) parameter
Genesis
application configuration 51
Detect page 146
ICIS
application configuration 54
method development 150
Peak Labels command 443
Peak Noise Factor parameter
application configuration 54
method development 150
Peak S/N Cutoff parameter
application configuration 52
Detect page 147
Percentage parameter 178
Phone Number parameter 74
Polarity parameter, Compound Database 248
Post-run System State parameter 318, 373
P-P Threshold, event type 58
Precursor Mass parameter, Compound Databasem, target
peak 247
Precursor parameter, Compound Database, confirming peak
249
Priority Sequence parameter 318, 373
procedures
acquisition mode
access real-time display 323
add samples to the sample list 298
assign a specific channel to a sample 303, 305
create a batch template 296–297
export reports to a folder 310
import samples into the sample list 301
insert samples into the sample list 300
pause all batches in a queue 330
preview a standard report 310
re-inject a sample from 302
remove a batch from a queue 334
remove a pending batch from a queue 334
remove a pending sample from a queued batch 333
remove a single batch from a queue 331
remove all batches in a queue 331
remove all pending batches in a queue 331
remove pending samples from a queued batch 333
remove samples from the sample list 302
save a to-be-run batch 315
select a previously acquired batch 295
select a ready-to-acquire batch 294
specify a calibration batch 314
specify device states 314
specify startup or shutdown methods 313
start a new batch 290, 292
start an acquisition 315
TraceFinder User Guide
565
Index: P
update TSRM data 313
view output files 319
analysis mode
access the Analysis mode 340
add samples to the samples list 363
change the displayed information for detected peaks
qualitative peak 426
quantitative peak
Data Review 441
method development 120
change the library entry for a selected peak 429
change the peak panes display 438
copy a sample in the samples list 364
create a new batch 361
customize the column display, Batch View 367
display peaks for a specific compound, qualitative
view 419
edit samples in a batch 370
edit the batch-level output formats 358
edit the sample-level output formats 357
enlarge the report text 479
exclude a calibration point 436
export a report 478
insert samples in the samples list 363
make a compound active or inactive 435
manually add a peak
chromatogram pane 423
qual peak pane 425
quantitation peak 440
manually exclude a calibration point 448
manually integrate a confirming ion peak 446
manually integrate a quantitative peak 440
modify the peak detection settings 441
open a recent batch 370
open a saved batch 369
open the Batch View 343
open the Data Review view 393, 454
open the Local Method View 498
open the Report View 468
print a report 477
reinject a sample 365
reinject a sample from a previously acquired batch
370
remove a manually created peak 440
remove a peak from the peak list 421
remove a peak from the qual peak pane 426
remove samples from the samples list 364
scroll the samples list 346
search for text 479
select a compound 471
select a report
generating reports 473
viewing reports 469
select a sample
566
TraceFinder User Guide
generating reports 475
viewing reports 471
submit all samples in the batch 371
switch between method and manual integration
qual mode 426
quan mode 441
zoom in on a peak
chromatogram navigation 423
qual peak 425
quantitation peak 438
spectra pane 428
application configuration mode
access the Application Configuration mode 37
activate user security 64
add a quantitation peak to a compound 253
change the default drive 494
choose a drive 493
copy the folder hierarchy from another drive 496
create projects or subprojects 495
delete projects or subprojects 496
edit user information 71
hide a drive from display 494
import compounds 262
import new report types 40
open the Defaults page 44
open the Project Administration view 492
open the User Administration view 69
refresh the drives display 494
remove a compound 252
remove a user 73
remove all empty folders 496
specify common detection parameters 46
specify default laboratory and instrument names 44
specify default mass precision and intensity scale 45
configuration mode
add a user 70
getting started
choose a node 33
display a log of instrument errors 34
install the NIST library 16
install the QED library 16
log in to the TraceFinder application 12
monitor the instrument status 34
start the TraceFinder application 11
method development mode 166
access the Method Development mode 79
acquire selected samples 280
acquire the batch 280
add a compound to the database 251
add a mass as a new compound 127
add a mass as a new confirming ion peak 130
add a mass to the existing quan mass ranges 125
add a quan peak 126
add a quan peak to an existing compound 159
Thermo Scientific
Index: Q
add compounds to the method 121
add confirming ions to an existing compound 160
add ions to get an accumulated signal 159
add sample to the development batch 276
automatically select compounds to create a new
method 85
calculate and report semi-quantitative results 197
calibrate the compounds 227
change the compound reference spectrum 124
change the quantitation mass used for a quan peak
specify mass tolerance 110
specify peak criteria 225
specify QC levels and concentrations 167
specify qualitative peak processing 229
specify quantitation flag options 192
specify quantitation limits 191
specify ranges of ions for detection and integration
135
specify standard report types and output formats
190, 208
specify the default parameters 196
specify the exact mass window 198
specify the Exactive parameters 198
specify the ion ratio calculation method 198
specify the maximum concentration as a percentage
157
copy a sample 277
create a blank method 97
create a group 183
create a new instrument method 270
create a new multiplexing instrument method 272
create a target screening method 104
enter a note for the method 110, 230
enter column values 277
export SRM data to an XML file 236
filter the displayed compounds 117, 120
identify the peaks 226
import a master method 235
import an instrument method 274
import an Xcalibur method 95
insert samples into the development batch 276
manually select compounds to create a new method
89
open a compound database 241
open a saved master method 106, 202
open an instrument method 273
open the Compound Database editor 240
open the Development Batch view 275
open the Instrument View 269
open the Qual Browser 281
remove all samples from the samples list 279
remove selected samples from the samples list 278
replace a confirming ion peak 130
replace a quantitation mass 125
replace a quantitative peak with a confirming ion
peak 128
resize or reorganize the columns 278
save the database to a new name 241–242
save the method template 230
save the new method 130
select compounds from the compound database 102
set a confirming ion peak as an additional
quantitative peak 128
set automated background subtraction options 109
specify a chromatogram reference sample 378
specify a location for development batch data 276
specify an internal standard for a compound 164
specify general information for a master method 107
specify ion ratio criteria 162
Thermo Scientific
178
specify user interface options 192
track the use of the tune file 193
update confirming ion ratios 157
zoom in the chromatogram or spectrum displays 160
Processing Configuration File parameter 200
Product Mass parameter, Compound Database
confirming peak 249
target peak 247
Project Administration view 492
projects and subprojects, creating 492
Q
QAQC Flags parameter 482
QAQC page, Method View 174
QAQC role 77
QC Levels page, Method View 167
QC1-QCn parameter 169
QED library, installing 16
QIon parameter 483
Qualitative Peak Processing Template parameter 112
quality check (QC) sample type, defined 337
Quan Flags parameter 482
Quan Mass parameter 483
Quan Peak m/z parameter 482
Quan Peak Response parameter 482
Quan Peak RT parameter 482
quan report settings, specifying 191
Quick Mode parameter 381
R
R^2 Threshold parameter 176
Ranges parameter, compound detection 142
Ratios page, Method View 162
Raw Filename parameter 94
TraceFinder User Guide
567
Index: S
Reactivate All command 332
Real Time Status command 36
Real Time Viewer page, Method View 170
Reference Compound parameter, Identification page 118
reference spectra 428
Reinject Selected Samples command
Acquisition mode 306
Batch view sample list 355
Remove Pending Batch command 334
Remove Pending Batches command 332
Remove Pending Samples command 334
Remove Selected Samples command
Acquisition mode 307
Batch view sample list 355
Batch Wizard 388
Remove User parameter 74
Report All Compounds Listed in Configuration File
parameter 201
Report Concentration parameter 194
report formats, specifying 189
Report Name parameter 190, 210
Report Noise As parameter
application configuration 52
Detect page 147
Report selection view 309
Report Semi-Quantitative Result parameter 201
Report Title parameter 190, 210
Report Type parameter 190, 210
Report View 468
reports
Acquisition mode 309
Analysis mode 468
configuring 39
flags defined 512
listed 5
sample PDFs 513
viewing landscape in PDF 513
Reports page, Method View 189
Reset Password parameter 74
Response parameter 483
Response Ratio parameter 432
Response Threshold parameter, Compound Database 246
Response Via parameter
Calibration 165
Method Template Editor 233
Retention Time parameter 483
RMS parameter
application configuration 55
Detect page 151
Role parameter 74
568
TraceFinder User Guide
RT parameter
Calibration 165
Calibration levels 167
Calibration page 176
Chk Std page 177
Compound Database 249
Hydrolysis page 181
Identification page 117
ISTD page 179
Limits page 175
Matrix Blank page 178
QC levels page 169
Solvent Blank page 180
RT Window parameter 200
S
S/N Threshold parameter
application configuration 51
method development 146
Sample Amt parameter 432
Sample Comment parameter 94
Sample Concentration parameter 483
Sample definition view 298
Sample File parameter 481
Sample ID parameter, Batch View 308, 353
Sample Name parameter
Batch View 308, 353
Data Review 409
Sample Type parameter
Batch View 353
Data Review 396, 410, 418
sample types, defined 337
Sample Units parameter 483
Sample Volume parameter 354
Sample Weight parameter 354
Save Changes parameter 74
Save Compound Database As command 242
Save Compound Database As dialog box 242
Save New Compound Database dialog box 241, 264
Screening Method parameter 200
Select a Report parameter 481
Select Compounds from Database dialog box 115
Select Compounds to Add dialog box 102
Selected Reaction Monitoring 258
Send RT to Method command 443
Sensitivity parameter
Avalon
application configuration 56
Detect page 152
Genesis
Thermo Scientific
Index: T
application configuration 50
Detect page 146
ICIS
application configuration 53
Detect page 150
Method Template Editor 232
Separate Ion Overlay Display parameter 194
Set Ion Ratio to All Confirming Peaks in Compound
parameter 163
Set Ion Ratio to All Confirming Peaks in Method parameter
163
Set Peak Windows Settings to All Peaks in Compound
parameter 134
Set Peak Windows Settings to All Peaks in Method parameter
134
Set This Mass as a New Quan Peak command 161
Set This Mass as Quan Mass command 161
Shade Row when Sample is Outside of Evaluation Criteria
parameter 194
Shoulders On, event type 59
Show All Compounds parameter 207
Show Chromatogram on Quantitation Report parameter
194
Show Peak Info command 444
Show Quan Peaks Only parameter 170
Showing parameter, Active View 481
SIM experiment type 259
Single Ion Monitoring 259
Smoothing parameter
Avalon
application configuration 56
Detect page 153
Genesis
application configuration 50
Detect page 146
ICIS
application configuration 54
Detect page 150
Solvent Blank page, Method View 180
Solvent sample type, defined 337
Specify Default Ion Ratio Ranges parameter 232
Specimen sample type, defined 337
Spectrum page, Method View 157
SRM data, exporting 236
SRM experiment type 258
standard reports, listed 5
Standard type parameter 165
Start Device parameter 318, 373
Start RT parameter, Times page 134
Start Threshold, event type 58–59
Start When Ready parameter 318, 373
Thermo Scientific
Starting vial number parameter 381
status color codes, Sample Definition view 306
Status parameter
Active View 482
Batch View 308, 353
Data Review 409
Stepoff Value parameter 112
Stop Active Batch command 332
Stop All Batches command 332
Stop Batch command 334
Suitability page, Method View 154
Supervisor role 76
supported file types, defined 2
supported software and hardware viii
system requirements viii
System Shutdown Method parameter 320
System Startup Method parameter 320
System Status parameter 320
T
Tailing Factor parameter
Genesis
application configuration 51
method development 146
ICIS
application configuration 54
method development 150
Tangent Skim, event type 59
Target Ratio parameter 163
target screening export settings, specifying 196
target screening reports, listed 7
Technician role 76
Template Layout parameter 381
templates
batch 296–297
method 224
Tension, event type 59
Theoretical Amount parameter 482
Theoretical Amt parameter 432
Thermo Xcalibur Instrument Setup dialog box 108, 204
Threshold/Lower Limit parameter 181
Time parameter 57
Time Range Peak parameter, Compound Database 248
Time/Event/Value parameter 56
Total Batch Rows parameter 381
Total Response parameter 482
Total Rows parameter 481
Trace parameter, Detection 142
Tune File Lifetime parameter 195
Turn Device Off command 315
TraceFinder User Guide
569
Index: U
Turn Device On command 314
Turn Device Standby command 314
Batch Selection 290
Compound Database 243
Data Review 393, 454
Development Batch 275
Finish 313
Instrument 269
Local Method 498
Method 84
Project Administration 492
Report selection 309
Report View 468
Sample definition 298
User Administration 69
U
ULOL (Linearity Limit) parameter 175
Unextracted sample type, defined 337
Units parameter 165
Update Confirming Ion Ratios with This Spectrum
command 161
Upper Limit parameter
Hydrolysis page 181
Solvent Blank page 180
Use Alternate Calibration Report Format parameter 194
Use an Existing Raw Data File parameter 93
Use as RT Reference parameter, Identification page 118
Use Autosampler parameter 94
Use Average Scan parameter 201
Use Data Dependent Scans parameter 234
Use Full MS Scan to Confirm parameter 201
Use Genesis Algorithm for Qual Processing parameter 233
Use Method Forge parameter 85, 89, 95
Use Scan at Peak Apex parameter 201
Use These Libraries parameter 232
user accounts, creating 69
User Administration view 69
user roles and permissions 75
user roles, defined 75
User Security parameter 64
user security, activating 64
Username parameter 74
Weighting parameter
Calibration 165
Method Template Editor 233
Window parameter
application configuration
ion ratio 49
retention time 49
Compound Database 249
Ratios page 163
Times page 133
Window Type parameter
application configuration 49
Ratios page 163
workflow
acquisition mode 288
general 4
X
V
Valley Rise (%) parameter
application configuration 52
Detect page 147
Valley S/N parameter
application configuration 52
method development 147
Value parameter 57
Vial Position parameter
Batch View 308, 353
Method Forge 94
View Only parameter 481
View Width parameter
application configuration 49
Times page 134
views
Batch 343
570
W
TraceFinder User Guide
XIC experiment type 259
XIC parameter, Signal page 141
Thermo Scientific
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