TraceFinder 2.1 User Guide Optimized for Environmental and Food

TraceFinder 2.1 User Guide Optimized for Environmental and Food
Thermo
TraceFinder
Version 2.1
User Guide
Optimized for Environmental and Food Safety
XCALI-97419 Revision A
March 2012
© 2012 Thermo Fisher Scientific Inc. All rights reserved.
Aria, Exactive, FOCUS, LCquan, ToxID, and TriPlus are trademarks, and Accela, Dionex, 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 Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix
System Activation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii
Thermo Scientific
Chapter 1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
About the TraceFinder Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
TraceFinder Summary of Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
TraceFinder Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Reporting Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Standard Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Custom Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Target Screening Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Chapter 2
Getting Started. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Installing the TraceFinder Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Installing the Power Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Installing the NIST and QED Libraries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Launching the NIST Library Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Launching the Qual Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Converting Legacy Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Converting Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Converting Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Converting Method Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Converting Batch Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Choosing a Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Chapter 3
Using the Configuration Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37
User Administration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Editing User Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Choosing User Roles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Project Administration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Working with Drives. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Working with Projects. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
TraceFinder User Guide
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Contents
Compound Datastore . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Opening and Saving a Datastore . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Adding Compounds, Quantitative Peaks, and Confirming Ions to a
Datastore . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Choosing Experiment Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Application Configuration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Specifying the Reports Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Specifying Configuration Defaults. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Specifying Detection Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Enabling Optional Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
iv
Chapter 4
Using the Method Development Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .97
Working with Master Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
Creating a New Master Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Editing a Master Method. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Creating a Method Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
Importing Published Master Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . 226
Exporting SRM Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227
Working with Instrument Methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228
Working with Development Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235
Creating a Development Batch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235
Editing Samples in a Development Batch . . . . . . . . . . . . . . . . . . . . . . . . . . 238
Acquiring Samples in a Development Batch . . . . . . . . . . . . . . . . . . . . . . . . 240
Viewing Raw Data Files in the Qual Browser . . . . . . . . . . . . . . . . . . . . . . . 241
Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243
Chapter 5
Using the Acquisition Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .245
Working with Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 246
Opening and Navigating the Acquisition Mode . . . . . . . . . . . . . . . . . . . . . 246
Creating Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 248
Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
Real-Time Display. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279
Acquisition Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 280
Instrument Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281
Devices Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 282
Queues Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 286
Real-Time Trace Display. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 290
Sample Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 292
TraceFinder User Guide
Thermo Scientific
Contents
Chapter 6
Using the Analysis Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .293
Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295
Working in the Batch View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 297
Batch View Panes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 298
Creating a New Batch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 309
Editing a Batch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 317
Editing Report Output Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 320
Setting Compound Active Status. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 322
Submitting a Batch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 325
Saving a Batch to a New Location . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329
Creating a Batch Using the Batch Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . 331
Working in Data Review View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 345
Data Review Sample List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 346
Quan Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 356
Qual Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 375
Working in the Report View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 387
Viewing Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 388
Generating Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 392
Working with Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 396
Working with the Active View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 399
Working in the Local Method View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 413
Working in the Batch Template Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 415
Appendix A Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .423
Specifying Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 423
Standard Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 424
Custom Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 425
Target Screening Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 425
Report Flags . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 428
Sample Standard Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 430
Batch Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 431
Batch Report Rev 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 432
Blank Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 433
Breakdown Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 434
Calibration Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 435
Calibration Density Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 438
Check Standard Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 439
Chromatogram Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 440
Compound Calibration Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 441
Compound Calibration Report - Alternate . . . . . . . . . . . . . . . . . . . . . . . . . 443
Confirmation Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 445
Confirmation Report 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 446
High Density Calibration Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 447
High Density Internal Standard Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . 448
High Density Internal Standard Report Long . . . . . . . . . . . . . . . . . . . . . . . 449
Thermo Scientific
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Contents
High Density Sample Report 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 450
High Density Sample Report 1 Long. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 451
High Density Sample Report 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 452
High Density Sample Report 2 Long. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 453
High Density Sample Report 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 454
High Density Sample Report 3 Long. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 455
Internal Standard Summary Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 456
Ion Ratio Failure Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 457
LCSLCSD Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 458
Manual Integration Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 459
Method Detection Limit Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 460
Method Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 463
Method Validation Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 466
MSMSD Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 469
Quantitation Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 470
Quantitation Report - 2. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 471
Solvent Blank Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 473
Surrogate Recovery Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 474
TIC Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 475
TIC Summary Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 476
Appendix B Using Copy Down and Fill Down . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .477
Appendix C Using Filter Criteria. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .481
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .483
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TraceFinder User Guide
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P
Preface
The TraceFinder 2.1 application is the newest application in the series of Thermo Scientific
GC/MS and LC/MS analytical software.
Contents
• Related Documentation
• Special Notices
• System Requirements
• System Activation
• Contacting Us
 To suggest changes to documentation or to Help
Complete a brief survey about this document by clicking the 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
vii
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 Help Contents, Index, or Search panes.
• To create your own bookmarks, use the Favorites pane.
2. To view the user guide or quick reference guides, choose Help > Manuals> User Guide
or Quick Reference Guide.
The PDF opens in a new window.
Special Notices
This guide includes the following types of special notices:
IMPORTANT Highlights information necessary to prevent damage to software, loss of
data, or invalid test results; or might contain information that is critical for optimal
performance of the system.
Note Highlights information of general interest.
Tip Highlights helpful information that can make a task easier.
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Preface
System Requirements
Your system must meet these minimum requirements.
System
Computer
Instruments
(supported or
required)
Requirements
•
•
•
•
•
2.33 GHz processor dual core with 4 GB RAM
CD/R-ROM drive
Video card and monitor capable of 1280 × 1024 resolution
75 GB available on drive C
NTFS format
Autosamplers:
• TriPlus™
• AS3000
• Accela™ AS
GC Devices:
• FOCUS™ GC
• Trace GC Ultra™
• Trace 1300 Series
LC Devices:
• Accela 1250 Pump
• Accela Pump
• Dionex™
• TLX-1
• LX2
• Agilent™ 1100
• Agilent 1200
GC/MS and LC/MS mass spectrometers
Software
Thermo Scientific
• Microsoft™ Windows™ XP Professional SP3
or Windows 7 Professional
• Microsoft Office 2007 SP2 or Microsoft Excel™ 2007 SP2
• Microsoft .NET Framework 4.0 Extended
• Thermo Foundation™ 2.0 SP1
• Thermo Xcalibur™ 2.2 SP1
• Adobe™ Reader™ 10.0
• NIST™ 2008
• Thermo LC Devices 2.5 SP2 or Thermo GC Devices 2.2
TraceFinder User Guide
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Preface
System Activation
When you first start the TraceFinder application, a dialog box displays the number of days
remaining in your 60-day free trial. If your free trial has expired, the License Activation
window opens.
Note You can open the License Activation window at any time during your trial period by
choosing Help > License Activation from the TraceFinder menu. If you already have a
permanent license, a message tells you that your product is fully licensed.
Two types of licenses are available:
• 60-Day Evaluation Version (free of charge)
• Full Version Single License
The evaluation version is full-featured and automatically expires 60 days after activation. Any
attempt to set back the system date automatically terminates this version. You can purchase
and then activate the full version of the TraceFinder application at any time, during or after
the free evaluation, without reinstalling the software.
Each activation key is valid only for a single license. Any additional installation generates a
different license and requires a different activation key.
For questions regarding activation, contact Thermo Fisher Scientific Technical Support in
San Jose, CA:
• E-mail: [email protected]
• Fax: 408-965-6120
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Preface
 To request an activation key
1. In the License Activation window, enter your information in the User Info area.
As you type, the License Text box creates an XML text string with your information.
2. In the Barcode box, type the barcode printed on the TraceFinder CD.
The form of the barcode number is either xxxx-xxxx-xxxx or xxxx-xxxx-xxxx-xxxx.
3. When you finish entering all your information, click Copy.
The application copies this XML text to the Clipboard.
If you have not completed all the information, a pop-up box opens, identifying the
missing information.
4. Paste this XML text in the body of an e-mail and send the e-mail to
[email protected]
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Preface
 To use your activation key
Note You must run the TraceFinder application with ITAdmin or LabDirector rights
when entering the activation key.
1. When you receive your activation key, copy it from the e-mail.
2. Choose Help > License Activation from the TraceFinder menu.
The License Activation window opens.
3. Click Paste.
The application pastes the contents of the Clipboard to the License Text box.
4. Click Set.
The application is activated according to the type of authorization your license gives you.
Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need.
 To contact Technical Support
Phone
800-532-4752
Fax
561-688-8736
E-mail
[email protected]
Knowledge base
www.thermokb.com
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.
 To copy manuals from the Internet
Go to mssupport.thermo.com, agree to the Terms and Conditions, and then click
Customer Manuals in the left margin of the window.
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Preface
 To suggest changes to documentation or to Help
• Fill out a reader survey online at www.surveymonkey.com/s/PQM6P62.
• Send an e-mail message to the Technical Publications Editor at
[email protected]
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1
Introduction
This chapter describes general features of the TraceFinder software.
Contents
• About the TraceFinder Application
• TraceFinder Summary of Features
• TraceFinder Workflow
• Reporting Features
About the TraceFinder Application
The TraceFinder application targets the environmental and food safety market, creating the
workflows that laboratories use. It supports a focused workflow for specific nonbioanalytical
laboratory use, instrument control, and method development functionality in a single
software package. TraceFinder is the primary application for the TSQ Quantum™ XLS triple
quadrupole mass spectrometers.
The TraceFinder application can export SRM data in .xml format so that other applications
can import the files into their databases.
The TraceFinder application can import the following file types:
• Sample lists in .csv or .xml format
See “Defining the Sample List” on page 255.
• Processing (.pmd) and instrument (.meth) method files from the Xcalibur data system
See “Working with Master Methods” on page 100 or “Working with Instrument
Methods” on page 228.
• Compounds from files that use the datastore (.xml) format
See “Adding Compounds, Quantitative Peaks, and Confirming Ions to a Datastore” on
page 62.
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Introduction
About the TraceFinder Application
• Batches, methods, or templates from the following applications:
–
TraceFinder 1.0
–
TraceFinder 1.1
–
TraceFinder 2.0
–
QuanLab Forms or EnviroLab Forms 2.5
–
QuanLab Forms or EnviroLab Forms 3.0
See “Converting Legacy Data” on page 19.
The TraceFinder application checks the accuracy and precision of data against systems that
have previously been certified against a standard processing program, such as the Statistical
Analysis System (SAS).
Supported File Types
The TraceFinder application supports the following file types:
• Comma-separated values (.csv): A set of file formats used to store tabular data in which
numbers and text are stored in plain textual form that can be read in a text editor. Lines in
the text file represent rows of a table, and commas in a line separate fields in the tables
row.
• Extensible Markup Language (.xml): A generic framework for storing any amount of text
or any data whose structure can be represented as a tree. The only indispensable
syntactical requirement is that the document has exactly one root element (also called the
document element). This means that the text must be enclosed between a root start-tag
and a corresponding end-tag.
• Instrument method (.meth): A proprietary file format for the Xcalibur software suite with
specific instructions that enable scientific instruments to perform data acquisition.
• Processing method (.pmd): A proprietary file format for the Xcalibur software suite with
specific instructions on processing data that was acquired through the instruments
attached to the system.
• Raw data (.raw): The file type for acquired samples on the system.
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1 Introduction
About the TraceFinder Application
TraceFinder Directory Structure
The TraceFinder application creates folders for projects/subprojects/batches and templates in
the C:\Thermo\TraceFinder\2.1\EFS directory. Within each batch folder, the application
creates folders for data, methods, and reports.
IMPORTANT You cannot rename or move the folders created by the TraceFinder
application.
Figure 1.
Thermo Scientific
Example batch directory structure
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Introduction
TraceFinder Summary of Features
TraceFinder Summary of Features
The TraceFinder system provides a workflow-oriented approach to high-throughput
quantitation. The system uses a batch-centric approach and tools to automate and speed up
the processes of method creation, loading samples, automatically generating data, manually
reviewing and editing results, and finalizing the data review and reporting process.
The TraceFinder software package includes data acquisition, processing, reviewing, and
reporting capabilities designed to assist analysts in environmental 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 user administration, project administration, datastore
administration, and application administration
• Method Development mode for editing instrument methods, setting processing and error
flag parameters, and setting report options
• 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 EnviroLab Forms
application
• Analysis mode with batch views, data review, local method views, and report views
• Database-capable method development
• Quantification workflows, supporting capabilities present in the LCquan™ and
EnviroLab Forms applications
• Standard and customized report formats
Features of the common workflow core include the following:
• Acquisition and processing
• Peak detection
• Quantification to include calibration
• Error analysis and flag setting
• Reporting
• Data persistence
• Raw data file handling
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1 Introduction
TraceFinder Workflow
TraceFinder Workflow
The TraceFinder application is structured with a typical laboratory workflow in mind. You
create a batch, and the system injects samples into the instrument, runs the samples, analyzes
the data, and generates a report. You can set up a master method for specific compound
groups or assays that you expect to run in your laboratory. When you are ready to run a
particular type of sample, select the appropriate method and begin.
When using the TraceFinder application, follow these basic steps:
1. Create and save a master method in the Method Development mode.
A master method combines the instrument method and processing method that define
how the raw data is acquired and processed, how the error checking information evaluates
the results, and how the results appear in reports.
2. Create and submit a batch using one of the batch wizards.
A batch lists samples for processing and reporting using a specified method. Each row of a
batch represents a unique sample.
3. Monitor the status of the batch in the Real Time Status view.
The real-time display is visible from the dashboard and all the TraceFinder modes. You
can begin another batch while you watch the real-time display of the currently acquiring
batch.
Note At any time, you can quickly view the system status by looking in the lower
right corner of the TraceFinder window. This area displays a green, yellow, or red
status light and a description of the number of samples in the queue (if any).
4. Evaluate the data in the Analysis mode.
The Analysis mode includes views where you can review batches, batch data, reports, and
local methods.
5. View and print reports in the Report View of the Analysis mode.
Use the Report View to view or print the reports for the currently selected batch.
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Introduction
Reporting Features
Reporting Features
The report engine can generate several different types of reports designed to meet the needs of
the laboratory, the laboratory's customers, and key regulatory agencies that might review the
results. The following types of reports meet the requirements of various methods and
worldwide regulatory agencies, helping to track the performance of LC and GC systems and
methods. The reports divide into three groups: Standard, Custom, and Target Screening.
For additional information about standard, custom, or target screening reports and examples
of each standard report type, see “Reports” on page 423. Examples of standard reports (as
PDF files) are also located in the C:\Thermo\TraceFinder\2.1\EFS\ExampleReports folder.
Standard Report Types
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
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Batch Report
Batch Report Rev 1
Blank Report
Breakdown Report
Calibration Report
Check Standard Report
Chromatogram Report
Compound Calibration Report
Compound Calibration Report - Alternate
Confirmation Report
Confirmation Report 2
High Density Calibration Report
High Density Internal Standard Report
High Density Internal Standard Report Long
High Density Sample Report 1
High Density Sample Report 1 Long
High Density Sample Report 2
High Density Sample Report 2 Long
High Density Sample Report 3
High Density Sample Report 3 Long
Internal Standard Summary Report
Ion Ratio Failure Report
LCSLCSD Report
Manual Integration Report
Method Detection Limit Report
Method Report
Method Validation Report
MSMSD Report
Quantitation Report
Quantitation Report - 2
Solvent Blank Report
Surrogate Recovery Report
TIC Report
TIC Summary Report
Tune Report
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1 Introduction
Reporting Features
Custom Report Types
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
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 Report Types
Target Screening reports are available only when you install ToxID™ software and enable the
Target Screening features. For a detailed procedure for enabling target screening features, see
“Target Screening” on page 90.
• Target Screening Long Report
• Target Screening Summary Report
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Getting Started
This chapter includes the procedures for getting started with the TraceFinder application.
Contents
• Installing the TraceFinder Application
• Installing the Power Modules
• Installing the NIST and QED Libraries
• Launching the NIST Library Browser
• Launching the Qual Browser
• Converting Legacy Data
• Choosing a Mode
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Getting Started
Installing the TraceFinder Application
Installing the TraceFinder Application
Follow these instructions to install, start, and log in to the TraceFinder application.
 To install the TraceFinder application
1. Insert the TraceFinder CD, open the TraceFinder launcher, and click Next.
The InstallShield Wizard opens.
2. Click TraceFinder 2.1, and follow the instructions in the InstallShield Wizard.
The installer verifies that you have the appropriate versions of the Thermo Foundation
and Thermo Xcalibur applications and updates them if necessary.
IMPORTANT If prompted to install Thermo Foundation, click Yes, and then when
prompted to restart your computer, click OK.
The wizard continues the installation.
3. When prompted, choose to install either the GC or LC version of the software, as
applicable.
4. When the installation completes, do not launch the TraceFinder application.
5. Open the TraceFinder launcher again, and click Next.
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2 Getting Started
Installing the TraceFinder Application
6. Click NIST Library, and follow the instructions to install the NIST library (required for
ToxID).
When the wizard prompts you to select a destination folder, select C:\Program
Files\NISTMS.
7. Install the appropriate device drivers, and configure the instruments in the Thermo
Foundation Instrument Configuration dialog box.
You can now start your TraceFinder application.
 To install example data
(Optional) Click Example Data, and follow the instructions to install an example project
that contains example batch data.
 To start the TraceFinder application
1. Configure your instruments.
You cannot configure your instruments while the TraceFinder application is running.
2. Double-click the TraceFinder icon on your desktop, or go to Start > All Programs >
Thermo TraceFinder > TraceFinder EFS.
By default, user security is not enabled and the application does not require a password.
To enable user security, see “User Security” on page 90.
 To log in to the TraceFinder application (when user security is enabled)
1. Enter your assigned user name in the TraceFinder login screen.
Before you can log in to the TraceFinder application, a system administrator must set up a
user account for you. The administrator assigns you a user name and password and gives
you permission to access specific modes.
IMPORTANT If you are the administrator logging in for the first time with user
security enabled, use Administrator/Password as the username/password.
2. Enter your password.
If your user name or password does not match, the system reports this error:
Correct the user name or password, or contact your system administrator.
3. Click Login.
The TraceFinder dashboard opens. See “TraceFinder Dashboard” on page 35.
4. To exit the TraceFinder application without logging in, click Exit TraceFinder.
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Getting Started
Installing the TraceFinder Application
Figure 2.
TraceFinder login screen
Table 1. Login screen parameters
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TraceFinder User Guide
Parameter
Description
Username
The user’s assigned user name.
Password
The assigned password for the user name.
Login
Verifies the user name and password, and displays the dashboard.
Exit TraceFinder
Closes the TraceFinder application without logging in.
Thermo Scientific
2 Getting Started
Installing the Power Modules
Installing the Power Modules
Follow these instructions to install and enable the TraceFinder power modules for
multiplexing.
 To install the power modules
1. Follow the instructions to install the TraceFinder application.
See “Installing the TraceFinder Application” on page 10.
2. Open the TraceFinder launcher again, and click Next.
3. Click TraceFinder Power Modules, and follow the instructions to install the
multiplexing module.
4. License the power modules.
Licensing for the power modules follows the same procedures as the TraceFinder
application licensing. See “System Activation” on page x.
 To enable the power modules
1. Start the TraceFinder application.
2. Go to the Configuration mode.
3. Click Application Configuration in the navigation pane.
4. Click Optional Features.
5. On the Optional Features page, select the Multiplexing check box.
For detailed instructions, see “Multiplexing” on page 92.
6. Click Apply.
A message prompts you to restart the TraceFinder application so that your changes can
take effect.
7. Click Yes.
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Getting Started
Installing the NIST and QED Libraries
Installing the NIST and QED Libraries
When you are using triple quadrupole instruments, follow these instructions to install the
NIST and QED libraries.
 To install the NIST library
1. 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 library in the NIST
Libraries list.
3. Click Add.
The Add Library dialog box opens.
4. Click Browse, and locate your QED library in the C:\Thermo folder.
5. Click OK.
The Xcalibur application reports that it has added the library to the NIST application.
6. Click Dismiss to close the message box.
The Xcalibur application adds the QED library to the NIST Libraries list in the Library
Manager dialog box.
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Getting Started
Installing the NIST and QED Libraries
7. Click Exit in the Thermo Library Manager dialog box.
8. Start the TraceFinder application.
9. Go to the Method Development mode.
10. Click Method View in the navigation pane.
11. Choose File > New > Method Template from the main menu.
The Method Template Editor displays the QED NIST Library in the Use These Libraries
list.
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2 Getting Started
Launching the NIST Library Browser
Launching the NIST Library Browser
Use the NIST MS Search tool to search the NIST library.
 To open the NIST library browser
Choose Go > Launch Library Browser from the 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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Getting Started
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 Qual Browser Help.
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2 Getting Started
Converting Legacy Data
Converting Legacy Data
Use the TraceFinder Legacy Data Converter to convert methods, batches, method templates,
or batch templates from the source versions of TraceFinder 1.0.1/1.1/2.0, EnviroLab Forms,
QuanLab Forms, or ToxLab Forms to compatible TraceFinder 2.1 target versions.
Table 2. Version compatibility
Source
TraceFinder 2.1 target
General
TraceFinder 2.0 General

TraceFinder 2.0 EFS
EFS
Clinical
Research
















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

EnviroLab Forms 2.5.2
QuanLab Forms 2.5.2
Forensic
Toxicology


ToxLab Forms 2.5.2
 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
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Getting Started
Converting Legacy Data
Converting Methods
Use the data converter to convert legacy methods to TraceFinder 2.1 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 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.
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2 Getting Started
Converting Legacy Data
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 19.
5. In the Target Drive list, select a fixed drive.
You cannot write the converted files to a mapped drive.
6. (Optional) In the New Name column, change the default new name for each 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 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 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 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 Microsoft Notepad text
editor window.
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Getting Started
Converting Legacy Data
Figure 3.
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Sample log file for converting a method
Thermo Scientific
2 Getting Started
Converting Legacy Data
Converting Batches
Use the data converter to convert legacy batches to TraceFinder 2.1 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.
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.
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Converting Legacy Data
When you select a project or subproject folder that contains multiple batch folders, the
application displays all the batches.
4. In the Target Version list, select the version that you are converting to.
The list displays only TraceFinder configurations with compatible data. See “Version
compatibility” on page 19.
5. In the Target Drive list, select a fixed drive.
You cannot write the converted files to a mapped drive.
6. Do one of the following to create a project and subproject for the converted batch:
In the Target Default Project and Subproject boxes, type the name of a project and
subproject.
–or–
Select the Replicate Original Project/Subproject check box.
7. (Optional) In the New Name column, change the default new name for each batch that
you want converted.
When you populate the Batches to be Converted 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 fail. When you manually
enter a new name, you must verify that the name does not already exist.
8. Select the check box for each batch 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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2 Getting Started
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 fails, the Status column displays an error icon. Hold your
cursor over the icon to display the error message.
9. To view a log of the conversion, click View Log.
The application opens a cumulative log file for the session in a Notepad text editor
window.
Figure 4.
Thermo Scientific
Sample log file for converting a batch
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Getting Started
Converting Legacy Data
Converting Method Templates
Use the data converter to convert legacy method templates to TraceFinder 2.1 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.
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2 Getting Started
Converting Legacy Data
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 19.
5. In the Target Drive list, select a fixed drive.
You cannot write the converted files to a mapped drive.
6. (Optional) In the New Name column, change the default new name for each 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
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.
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Converting Legacy Data
Figure 5.
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Sample log file for converting a method template
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2 Getting Started
Converting Legacy Data
Converting Batch Templates
Use the data converter to convert legacy batch templates to TraceFinder 2.1 batch templates.
 To convert a batch template
1. In the Data Type list, select Batch Template.
The TraceFinder Legacy Data Converter displays the interface for converting batch
templates.
2. In the Source Version list, select the version of the batch template 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.
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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 19.
5. In the Target Drive list, select a fixed drive.
You cannot write the converted files to a mapped drive.
6. (Optional) In the New Name column, change the default new name for each batch
template that you want converted.
When you populate the Batch Templates to be Converted 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.
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2 Getting Started
Converting Legacy Data
8. To view a log of the conversion, click View Log.
The application opens a cumulative log file for the session in a Notepad text editor
window.
Figure 6.
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Sample log file for converting a batch template
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Choosing a Mode
Choosing a Mode
When user security is enabled, the dashboard displays the options applicable 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
Configuration




LabDirector

ITAdmin
Supervisor

Technician




QAQC

Note When user security is not enabled, all modes are available to all users.
Follow these procedures:
• To choose a mode
• To display a log of instrument errors
• To monitor instrument status
• To watch the real-time display from the dashboard
 To choose a mode
1. From the dashboard, click the mode where you want to work.
The dashboard shows only the modes that you have permission to use. See “TraceFinder
Dashboard” on page 35.
2. To change modes from within any of the TraceFinder application modes, click a mode
button in the navigation pane.
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Choosing a Mode
 To display a log of instrument errors
1. Right-click the status light in the lower right corner of any mode.
2. Choose Instrument Log.
The Instrument Log dialog box opens.
The Instrument Log displays all instrument errors that have occurred since the
TraceFinder application started or since the last time that you cleared the message log.
3. Do any of the following:
• Click Refresh to display errors that occur after you open the Instrument Log dialog
box.
• Click Clear Messages to remove messages from the Instrument Log display.
The application clears messages only from the Instrument Log display. These
messages remain in the following log file:
C:\Thermo\TraceFinder\2.1\EFS\Logs\TraceFinder.log
• Click OK to dismiss the Instrument Log dialog box.
 To monitor instrument status
Look at the status light in the lower right corner of the TraceFinder window.
Green indicates that the instrument is ready.
Yellow indicates that the instrument is in standby mode.
Red indicates that the instrument is turned off or no device is configured.
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Choosing a Mode
 To watch the real-time display from the dashboard
Click Real Time Status.
The real-time status is displayed at the bottom of the dashboard.
For descriptions of all the features of the real-time display, see “Real-Time Display” on
page 279.
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Choosing a Mode
TraceFinder Dashboard
A dashboard without user security or for a user in the LabDirector role looks like this.
Table 4. TraceFinder dashboard screen parameters (Sheet 1 of 2)
Parameter
Description
Real Time Status
Opens the real-time display for the current acquisition. The acquisition
progress is displayed within the current mode window.
Help
Opens the TraceFinder Help.
Log Off
Logs off the current user and displays the login screen. This function is
available only when user security is enabled. See “User Security” on
page 90.
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 94.
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Choosing a Mode
Table 4. TraceFinder dashboard screen parameters (Sheet 2 of 2)
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Parameter
Description
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.”
Configuration
Opens the Configuration mode where you can set permissions, assign
users to roles, configure available reports and import new reports, and
maintain the various databases, including the Compound Datastore.
See Chapter 3, “Using the Configuration Mode.”
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Using the Configuration Mode
This chapter discusses the configuration tasks assigned to the ITAdmin and LabDirector roles
when user security is enabled. When user security is not enabled, all users have access to all
features in the Configuration mode except the User Administration tasks.
Contents
• User Administration
• Project Administration
• Compound Datastore
• Application Configuration
Users in the ITAdmin or LabDirector role are responsible for the following:
• Handling the databases
• Applying roles to users
• Understanding security, users, and groups
• Creating local users and network groups
• Creating projects and subprojects
• Maintaining compounds in the compounds datastore
 To access the Configuration mode
Click Configuration from the dashboard or the navigation pane.
The Configuration mode navigation pane opens.
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Using the Configuration Mode
Figure 7.
Configuration mode navigation pane
Available only to users in the LabDirector or ITAdmin role.
Available only when you select the Compound Datastore option
in the Application Configuration view.
Available only when you select the Acquisition Batch Wizard as
your wizard style in the Application Configuration view.
Table 5.
Configuration mode navigation pane functions (Sheet 1 of 2)
Function
Description
User Administration
Opens the User Administration view where you can add, remove, or edit user accounts
and permissions. See “User Administration” on page 40.
When user security is not enabled, this task pane is not available. When user security is
enabled, this task pane is available only to users in the LabDirector or ITAdmin role. See
“Application Configuration” on page 67.
Project Administration
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Opens the Project Administration view where you can create and manage projects and
subprojects. See “Project Administration” on page 49.
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Table 5.
Using the Configuration Mode
Configuration mode navigation pane functions (Sheet 2 of 2)
Function
Description
Compound Datastore
Opens the Compound Datastore view where you can manage the definition of
compounds in the current datastore. See “Compound Datastore” on page 55.
This task pane is available only when you have selected the Compound Datastore option
on the Optional Features page of the Application Configuration view. See “Application
Configuration” on page 67.
Application Configuration
Thermo Scientific
Opens the Application Configuration view where you can specify available reports,
application defaults, and detection algorithms. You can also enable the user security,
target screening, compound datastore, multiplexing, and batch wizard features. See
“Application Configuration” on page 67.
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User Administration
User Administration
In the User Administration view of the Configuration mode (when user security is enabled),
users in the LabDirector or ITAdmin role can add, remove, or edit user accounts and
permissions.
For detailed descriptions of each user role and the permissions and responsibilities for each
role, see “Choosing User Roles” on page 46.
 To open the User Administration view
1. Click Configuration from the dashboard or the navigation pane.
The Configuration navigation pane opens.
Note The User Administration view is available only when you enable user security.
Follow the instructions “To turn on user security” on page 90.
2. Click the User Administration task pane.
The User Administration view opens. See “User Administration view” on page 44.
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User Administration
Editing User Information
Follow these procedures:
• To add a user
• To edit user information
• To change a user password
• To remove a user
 To add a user
1. Click the Add User icon,
.
The application enables the parameters in the User area at the bottom of the view.
2. Type a unique name in the Username field.
3. Select a role from the Role list.
A user in the LabDirector or ITAdmin role must assign each user to one of these defined
roles. For detailed information about the permissions allowed for each role, see “Choosing
User Roles” on page 46.
4. Type the user’s password and type it again to confirm it.
Make sure to communicate the password to the user.
5. (Optional) Type the user’s full name, account number, phone number, and e-mail
address.
6. To enable this user login, select the Enabled check box.
You can disable a user login without deleting the user’s information. Follow the
instructions “To edit user information” on page 42.
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User Administration
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.
2. Click the Edit User icon,
.
The application enables the parameters in the User area.
3. Edit any of the parameter values.
If you are editing your own user name, the Enabled check box is unavailable because you
cannot make your own account unavailable.
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User Administration
4. Do one of the following:
When all the user information is correct, click the Save Changes icon,
.
The TraceFinder application adds the new parameter values to the User Listing, and the
parameters in the User area are unavailable.
–or–
To discard all changes and not save the edits, click the Cancel Changes icon,
.
All changes are discarded, and the parameters in the User area are unavailable.
 To change a user password
1. In the User Listing table, select a user.
The user information populates the parameter fields in the User area.
2. Click the Edit User icon,
.
The parameters in the User area are enabled.
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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User Administration
 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 disable a user login without
removing all the user information from the system. Follow the instructions “To edit user
information” on page 42.
Figure 8.
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User Administration view
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User Administration
Table 6. 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 46.
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.
Reset Password
Enables the Password and Confirm Password parameters so that you can change them.
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
Enables the fields in the User area where you can enter information for a new user.
Remove User
Deletes all information for the selected user.
Edit User
Enables the User area where you can edit any of the parameters for the selected user.
Save Changes
Adds the new parameter values to the User Listing table and disables the parameters in
the User area.
Cancel Changes Discards all new or edited information.
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User Administration
Choosing User Roles
This section describes the responsibilities for five different user roles when user security is
enabled: LabDirector, ITAdmin, Supervisor, Technician, and QAQC.
IMPORTANT User roles are in effect only when user security is enabled. When user
security is not enabled, all users have access to all modes.
TraceFinder Mode Access
A laboratory director or an IT administrator assigns you to a role that gives you access to
specific modes of the TraceFinder application. When you log in, the dashboard displays links
to only the modes that you can access.
Table 7. User roles and mode access
User role
Method
Development
Acquisition
Analysis
Configuration




LabDirector

ITAdmin
Supervisor

Technician




QAQC

LabDirector
In the LabDirector role, you review graphically applicable data and manipulate data, batches,
methods, and instruments.
A laboratory director is responsible for these tasks:
• Creating or editing methods for new levels of detection or adding new compounds to the
existing database
• Reviewing data from the mass spectrometer
• Running samples and reviewing data collected by others
• Reporting the data
• Understanding the results and giving final approval of the released data before archiving
ITAdmin
In the ITAdmin role, you set security, manage users into roles, and manipulate the various
databases. You are responsible for adding compounds into the various compound databases.
An IT administrator is responsible for these tasks:
• Handling the databases
• Applying roles to users
• Understanding security, users, and groups
• Creating local users and network groups
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User Administration
Supervisor
In the Supervisor role, you are responsible for setting up the instrument samples and using
previously built sequences and methods for processing and acquiring data. You also develop
and edit methods for processing and acquiring data, review the data, and distinguish between
the need to rerun samples or pass reports up to the lab manager for final review. On a daily
basis, you establish the priority for a list of samples to run and create the sequence of events.
A supervisor is responsible for these tasks:
• Submitting samples
• Creating and submitting batches
• Reporting the data to management
• Creating or editing methods for new levels of detection or adding new compounds to the
existing database
• Reviewing data from the mass spectrometer
• Understanding the results, who ran the batch, and who passed along the results before
giving intermediate approval and sending the data to management
• Modifying new compounds or adjusting methods for specific result sets
Technician
In the Technician role, you are responsible for setting up the instrument samples and using
previously built sequences and methods for processing and acquiring data. You also edit
existing methods for processing and acquiring data, review collected data, and distinguish
between the need to rerun samples or pass reports up to the supervisor. On a daily basis, you
are responsible for gathering the list of samples to run and creating the sequence of events.
A technician is responsible for these tasks:
• Submitting samples
• Creating and submitting batches
• Creating data to be reviewed by management
• Receiving instructions for new sets of samples for the TraceFinder application to analyze
after finishing the current analysis
• Reviewing data from the mass spectrometer
• Understanding the resulting data, making integration changes, and passing those changes
up for further approval
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User Administration
QAQC
In the QAQC role, you review graphically applicable data and interpret the data, but you do
not manipulate the data.
A QAQC technician is responsible for these tasks:
• Reviewing data from the mass spectrometer
• Understanding the results and who ran and passed along the results before giving
intermediate approval and sending the data to management
• Receiving instructions for new sets of samples for the TraceFinder application to analyze
after finishing the current analysis
Note In the QAQC role, you have access only to the Analysis mode.
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Project Administration
Project Administration
When user security is enabled, users in the LabDirector or ITAdmin role can create and
manage projects and subprojects on fixed or network drives in the Project Administration
view of the Configuration mode.
This section includes the following topics:
• Working with Drives
• Working with Projects
 To open the Project Administration view
1. Click Configuration from the dashboard or the navigation pane.
The Configuration navigation pane opens. See “Configuration mode navigation pane” on
page 38.
2. In the Configuration navigation pane, click Project Administration.
The Project Administration view opens.
By default, all projects are created under a main Projects folder on drive C:
C:\Thermo\TraceFinder\2.1\EFS\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-inch 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 C: drive.
If you have not created a Projects directory on this drive, you see this message:
2. Click Create Projects Directory.
The TraceFinder application adds a new Projects directory to the selected drive. To create
projects and subprojects on this drive, see “To create projects or subprojects” on page 52.
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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
Right-click and choose Refresh from the shortcut menu.
The Available Drives table refreshes to show any drives that have changed (for example, if
you inserted a USB drive). You can now configure any new drives.
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Project Administration
Working with Projects
When you create a batch, the application stores the data files, local method, and reports in a
project and subproject that you create in the C:\Thermo\TraceFinder\2.1\EFS\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 install
example data” on page 11.
Follow these procedures:
• To create projects or subprojects
• To delete projects or subprojects
• To remove all empty folders
• To copy the folder hierarchy from another drive
 To create projects or subprojects
1. Select the top-level project.
You can select the main Projects folder and create a new project under it, or you can select
one of the existing projects and create a subproject under it.
When you select a project folder, the application enables the plus sign icon,
indicating that you can create a folder within the selected folder.
,
2. Click the plus sign.
The TraceFinder application creates a new, unnamed project folder under the selected
project.
3. While the new project is still highlighted, type a new name.
Project names are limited to 30 characters and can contain spaces and special characters,
except for the following special characters: \ / : * ? " < > |
Note After you add a subproject to a project, you cannot rename the project.
4. To save the new name, press ENTER or click anywhere in the view.
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Project Administration
 To delete projects or subprojects
1. Select the project or subproject 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 enables the minus sign icon,
.
2. Click the minus sign, or right-click and choose Remove Project from the shortcut menu.
3. At the prompt, click Yes to remove the selected project or subproject.
 To remove all empty folders
1. Select the project or subproject that contains empty folders.
2. Right-click and choose Remove All Empty Child Folders from the shortcut menu.
A dialog box asks if you want to remove all empty folders.
3. Click OK.
The application removes all folders that have no folders or files. There is no undo for this
command.
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Project Administration
 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.
4. Click OK.
To replicate the hierarchy from the specified drive, the application will add new folders to
the current hierarchy, but it will not remove folders.
IMPORTANT The Copy Folder Hierarchy from Drive command copies only the
project and subproject folders; it does not copy batches within the folders.
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Compound Datastore
Compound Datastore
When user security is enabled, users in the LabDirector or ITAdmin role can manage
compound definitions in the current datastore in the Compound Datastore view.
This section includes the following topics:
• Opening and Saving a Datastore
• Adding Compounds, Quantitative Peaks, and Confirming Ions to a Datastore
• Choosing Experiment Types
For a description of all the parameters in the Compound Datastore view, “Compound
Datastore view” on page 59.
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Compound Datastore
Opening and Saving a Datastore
You can use the default datastore or you can create your own datastore. The Compound
Datastore task pane is available only when the Compound Datastore feature is enabled. See
“Enabling Optional Features” on page 88.
Follow these procedures:
• To open the Compound Datastore editor
• To open a compound datastore
• To create a new compound datastore
• To save a datastore
• To save a datastore to a new name
 To open the Compound Datastore editor
1. Click Configuration from the dashboard or the navigation pane.
The Configuration navigation pane opens. See “Configuration mode navigation pane” on
page 38.
2. Click the Compound Datastore task pane.
The current datastore opens in the Compound Datastore view. For a detailed list of all
parameters and functions in the Compound Datastore view, see “Compound Datastore
view” on page 59.
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Compound Datastore
 To open a compound datastore
1. Click Load Compound Datastore in the Compound Datastore task pane.
The Open Compound Datastore dialog box opens.
2. Double-click the name of the datastore that you want to open.
The selected datastore opens in the Compound Datastore view. See “Compound
Datastore view” on page 59.
 To create a new compound datastore
Click New Compound Datastore in the Compound Datastore task pane.
A new, empty datastore opens in the Compound Datastore view.
You can import a file of compounds into the new datastore (by following the instructions,
To import compounds), or you can manually add compounds one at a time (by following
the instructions, To add a compound to the datastore).
 To save a datastore
1. Click Save Compound Datastore in the Compound Datastore task pane.
The application stores the database as
…\Thermo\TraceFinder\2.1\EFS\Databases\filename.xml
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Compound Datastore
If the datastore contains any compounds that do not have associated quantitative peaks,
the Invalid Compound Datastore Not Saved dialog box opens, listing the compounds.
2. To add a quantitative peak row to the listed compounds, click Continue.
The application returns you to the Compound Datastore view.
3. Add quantitative peaks to the incomplete compounds before you save the datastore.
See “To add a quantitative peak to a compound” on page 64.
 To save a datastore to a new name
1. Click Save As Compound Datastore in the Compound Datastore task pane.
The Save Compound Datastore dialog box opens.
2. Type a file name for the new compound datastore.
3. Click OK.
The application stores the database as
…\Thermo\TraceFinder\2.1\EFS\Databases\filename.xml
Table 8. Save Compound Datastore dialog box parameters
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Parameter
Description
Compound Datastore
Name
Lists the file name for the new datastore.
Overwrite
Overwrites the selected datastore.
OK
Writes the new datastore to the Databases folder.
Cancel
Closes the dialog box and makes no changes to the datastore.
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Figure 9.
Using the Configuration Mode
Compound Datastore
Compound Datastore view
Table 9. Compound Datastore view parameters (Sheet 1 of 3)
Parameter
Description
Function icons
Adds a new compound row.
Removes the selected row and all quantitative peak and confirming ion rows within it.
Adds a new quantitative peak row to the compound. Each compound requires at least one
quantitative peak.
Removes the selected row and all confirming ion rows within it.
Adds a new confirming ion row to the quantitative peak.
Removes the selected confirming ion row.
Select Experiment Types Specifies one of these experiment types that each use a different structure for the mass
To Display
filter. See “Choosing Experiment Types” on page 66.
• SRM: Selected Reaction Monitoring
• XIC: Extracted Ion Chromatogram
• SIM: Single Ion Monitoring
Compound parameters
Compound Name
Alphanumeric name assigned to the compound.
Experiment Type
Experiment type: SRM, XIC, or SIM.
Category
(Optional) Alphanumeric identifier.
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Compound Datastore
Table 9. Compound Datastore view parameters (Sheet 2 of 3)
Parameter
Description
Ionization
(Optional) Alphanumeric identifier.
Valid values: None, ESI, APCI, EI, CI, or APPI
Default: None
Chemical Formula
(Optional) Alphanumeric chemical identifier.
Quantitative peak parameters
Precursor Mass
The mass-to-charge ratio (m/z) of a precursor ion. The location of the center of a target
precursor-ion peak in mass-to-charge ratio units.
In confirming ion rows, the precursor mass is a noneditable copy of the quantitative peak
precursor mass.
Available only for SRM experiments.
Default: 0.0
Range: 10.000 to 2999.999
Product Mass
The mass-to-charge ratio of the quantitation ion. The location of the center of a target
quan-ion peak in mass-to-charge ratio (m/z) units.
Available only for SRM experiments.
Default: 0.0
Range: 10.000 to 2999.999
Mass
The mass-to-charge ratio of the quantitation ion. The location of the center of a target
quan-ion peak in mass-to-charge ratio (m/z) units.
Available only for XIC and SIM experiments.
Default: 0.0
Range: 10.000 to 2999.999
Collision Energy
The energy used when ions collide with the collision gas.
Available only for SRM experiments.
Range: –250.00 to 250.00
RT (min)
Retention time. The application uses RT and Window values to determine the start and
stop time for the acquisition.
Range: 0.00 to 999.00
Start time = RT – (Window/2)
Stop time = RT + (Window/2)
Start and stop range: 0.00 to 999.00
Window (sec)
The application uses RT and Window values to determine the start and stop time for the
acquisition.
Range: 0.00 to 499.50
Start time = RT – (Window/2)
Stop time = RT + (Window/2)
Start and stop range: 0.00 to 999.00
Polarity
+ (positive) or – (negative)
Lens
(Optional) Range: –400 to 400
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Compound Datastore
Table 9. Compound Datastore view parameters (Sheet 3 of 3)
Parameter
Description
Energy Ramp
(Optional)
Available only for SRM experiments.
Range: 0.00 to 200.00
Confirming ion parameters
Precursor Mass
The mass-to-charge ratio of a precursor ion. The location of the center of a target
precursor-ion peak in mass-to-charge ratio (m/z) units.
Available as a noneditible field only for SRM experiments.
Default: 0.0
Range: 10.000 to 2999.999
Product Mass
The mass-to-charge ratio of the quantitation ion. The location of the center of a target
quan-ion peak in mass-to-charge ratio (m/z) units.
Available only for SRM experiments.
Default: 0.0
Range: 10.000 to 2999.999
Mass
The mass-to-charge ratio of the quantitation ion. The location of the center of a target
quan-ion peak in mass-to-charge ratio (m/z) units.
Available only for XIC and SIM experiments.
Default: 0.0
Range: 10.000 to 2999.999
Collision Energy
The energy used when ions collide with the collision gas.
Available only for SRM experiments.
Range: –250.00 to 250.00
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Compound Datastore
Adding Compounds, Quantitative Peaks, and Confirming Ions to a Datastore
In the Compound Datastore view, you can import compounds into the datastore, add or
remove compounds from the datastore, add quantitative peaks and confirming ions to a
compound, or remove quantitative peaks or confirming ions from a compound.
Follow these procedures:
• To import compounds
• To add a compound to the datastore
• To remove a compound
• To add a quantitative peak to a compound
• To remove a quantitative peak
• To add a confirming ion to a quantitative peak
• To remove a confirming ion
 To import compounds
1. Click Import Compounds in the Compound Datastore task pane.
2. Browse to a .csv or .xml compounds file and click Open.
The TraceFinder application imports the compounds from the imported file, adds them
to any compounds already in the datastore, and alphabetically sorts them.
When the application imports a compound that contains multiple quantitative peaks and
confirming ions, it lists all the peaks under a single compound name, as in this example
for Monuron:
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 To add a compound to the datastore
1. Click the Add Compound icon,
, or right-click the compounds list
and choose Add Compound from the shortcut menu.
The application adds a new, empty compound row to the end of the compounds table.
2. Click the first table cell, and type the required Compound Name parameter.
3. (Optional) Change the value for the Experiment Type.
The default is SRM. For descriptions of available experiment types, see “Choosing
Experiment Types” on page 66.
After you add a quantitative peak to the compound, you cannot change the experiment
type, even if you cancel the quantitative peak.
4. (Optional) Type a value or select a value from the Category list.
You can use any alphanumeric string. After you type a new Category value, that value is
available from the list.
5. (Optional) Change the values for Ionization.
The default is None.
6. (Optional) Type a value for the Chemical Formula.
You can use any alphanumeric string.
Each compound requires at least one quantitative peak.
 To remove a compound
1. Select the compound row that you want to delete.
2. Click the Remove Compound icon,
, or right-click
and choose Remove Compound from the shortcut menu.
3. If you are sure you want to delete the selected row, at the prompt, click OK.
The application removes the selected row and all quantitative peak and confirming ion
rows within it.
Tip If you add a row of compound information and do not complete all the column
required values, you can right-click and choose Cancel to remove the entire row. You
can cancel only an incomplete compound row.
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Compound Datastore
 To add a quantitative peak to a compound
1. Select the compound.
2. Click the Add Quan Peak icon,
, or right-click
and choose Add Quan Peak from the shortcut menu.
The application adds a new quantitative peak row to the compound. A quantitative peak
includes quantitative values for the compound. Each compound requires at least one
quantitative peak.
Quantitative peak row
3. Enter all required parameters.
For a list of required and optional parameters, see the list of “Compound Datastore view
parameters” on page 59.
Tip You cannot add another new compound or save the compound datastore until
you enter all required quantitative peak parameters or remove incomplete quantitative
peaks from the compound.
4. Repeat steps 2 through 3 to add as many as six quantitative peaks to the compound.
 To remove a quantitative peak
1. Select the row of the quantitative peak that you want to delete.
2. Click the Remove Quan Peak icon,
, or right-click
and choose Remove Quan Peak from the shortcut menu.
3. If you are sure you want to delete the selected row, at the prompt, click OK.
The application removes the selected row and all confirming ion rows within it.
Tip If you add a row of quantitative peak information and do not complete all the
required values, you can right-click and choose Cancel to remove the entire row. You
can cancel only incomplete quantitative peak rows.
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Compound Datastore
 To add a confirming ion to a quantitative peak
1. Click the Add Confirming Ion icon,
, or right-click the quantitative peak row
and choose Add Confirming Ion from the shortcut menu.
The application adds a new confirming ion row to the quantitative peak. A confirming
ion includes a mass value.
Confirming ion row
2. Type the required column values for the confirming ion.
The required confirming ion values differ for each experiment type. See “Choosing
Experiment Types” on page 66.
3. Repeat steps 1 through 2 to add as many as 10 confirming ions to the quantitative peak.
 To remove a confirming ion
1. Select the confirming ion row that you want to delete.
2. Click the Remove Confirming Ion icon,
, or right-click
and choose Remove Confirming Ion from the shortcut menu.
3. If you are sure you want to delete the selected row, at the prompt, click OK.
The application removes the selected confirming ion row.
Tip If you add a row of confirming ion information and do not complete all the
required values, you can right-click and choose Cancel to remove the entire row. You
can cancel only incomplete confirming ion rows.
 To filter a list
Click the funnel icon,
, in the column header.
For each column, the application displays filterable criteria (compound names,
experiment types, categories, or ionization methods) in a list. In all lists, you can choose
to view all criteria or a specific type of criterion for that column.
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Compound Datastore
Choosing Experiment Types
The TraceFinder application uses three experiment types: SRM, XIC, and SIM.
A compound datastore can include multiple experiment types for a single compound;
however, each compound name and experiment type combination must be unique.
SRM: Selected Reaction Monitoring
The SRM experiment type supports triple quadrupole LC/MS. The mass filter includes
precursor mass and narrow mass ranges to identify product masses. Imported compounds
with no experiment type are treated as SRM data.
Confirming ions include values for product mass, collision energy, and a noneditable
precursor mass.
XIC: Extracted Ion Chromatogram
The mass filter is a single, full scan which is post-processed to extract a peak for the ions of
interest.
Confirming ions include a single mass value.
SIM: Single Ion Monitoring
The SIM experiment type supports single quadrupole LC/MS and Exactive™ systems. The
mass filter includes narrow mass ranges to identify product masses.
Confirming ions include a single mass value.
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Application Configuration
Application Configuration
When user security is enabled, users in the LabDirector or ITAdmin role can enable features
such as available reports, user security, compound datastore, reporting defaults, multiplexing,
detection algorithms, and target screening. You can also choose the reports that are available
to users, the application defaults, and the defaults used for peak detection.
This section includes the following tasks:
• Specifying the Reports Configuration
• Specifying Configuration Defaults
• Specifying Detection Parameters
• Enabling Optional Features
 To open the Application Configuration view
1. Click Configuration from the dashboard or the navigation pane.
The Configuration navigation pane opens. See “Configuration mode navigation pane” on
page 38.
2. Click Application Configuration.
The Application Configuration view opens.
Table 10. Application Configuration pages
Page
Reports
See “Specifying the Reports Configuration.”
Defaults
See “Specifying Configuration Defaults” on page 73.
Detection
See “Specifying Detection Parameters” on page 76.
Optional Features
See “Enabling Optional Features” on page 88.
3. In the Application Configuration list, click the type of information that you want to
configure.
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Application Configuration
Specifying the Reports Configuration
When user security is enabled, users in the LabDirector or ITAdmin role can configure a list
of reports that are available to all users when they generate reports from the Method
Development, Analysis, and Acquisition modes. From the Reports page, you can configure
the standard, custom, or target screening reports.
Example PDF files of report formats are located in the following folder:
C:\Thermo\TraceFinder\2.1\EFS\ExampleReports
Follow these procedures:
• To open the Reports page
• To specify which reports are available
• To import new reports
 To open the Reports page
In the Application Configuration view, click Reports.
The Reports page of the Application Configuration view opens. For a list of reports, see
“Reports” on page 70.
 To specify which reports are available
1. Use the directional arrows to move reports from the Installed Reports pane to the
Displayed Reports pane.
Tip Use the CTRL or SHIFT keys to select multiple reports.
In the Method Development, Analysis, and Acquisition modes, users can access all
reports in the Displayed Reports pane.
2. To create a single composite report for an entire batch (rather than 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. Batch-level
reports are prepended with a B to differentiate them.
Note Only reports that can aggregate data at the batch level have the Batch Level
check box enabled. By default, the application selects the Batch Level feature for all
these reports.
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3. Do one of the following:
Apply the current selections as follows:
a. Click Apply.
A message prompts you to restart the TraceFinder application so that a user can access
the reports you selected for the Method Development, Analysis, and Acquisition
modes.
b. To restart the TraceFinder application now, click Yes, or to remain on the Reports
page, click No.
–or–
To return the report selections to their original state (when you first opened this page),
click Undo Changes.
 To import new reports
1. Click Import.
2. In the browser, locate a Crystal Reports .dll or Custom Reports .xltm file and open the
file.
The application writes the imported report to the TraceFinder installation directory and
displays the new report in the Installed Reports pane.
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Application Configuration
Reports
The application uses the following standard, custom, and target screening reports (see
Figure 10, Figure 11, and Figure 12, respectively). For descriptions of the parameters on the
Reports page, see “Reports page parameters” on page 72.
Figure 10. Reports page showing standard reports
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Figure 11. Reports page showing custom reports
Figure 12. Reports page showing target screening reports
Note Target screening reports are available only when you install the ToxID software and
enable the target screening features. See “Enabling Optional Features” on page 88.
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Table 11. Reports page parameters
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Parameter
Description
Installed Reports
All reports listed in this pane are potentially available but are not
selected for use in the application.
Displayed Reports
All reports listed in this pane are selected for use in the
application.
>>
Moves all reports from the Installed Reports list to the Displayed
Reports list.
>
Moves the selected reports from the Installed Reports list to the
Displayed Reports list.
<
Moves the selected reports from the Displayed Reports list to the
Installed Reports list.
<<
Moves all reports from the Displayed Reports list to the Installed
Reports list.
Import
Opens a browser where you can select a report file to add to the
Installed Reports list.
Undo Changes
Returns the report selections to their original state (when you
first opened this page).
Apply
Applies the current selections, and prompts you to restart the
TraceFinder application so that a user can access the reports you
selected for the Method Development, Analysis, and Acquisition
modes.
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Application Configuration
Specifying Configuration Defaults
Use the Application Configuration view of the Configuration mode to specify the default
laboratory and instrument names, the displayed mass precision, and the intensity scale to use
for reporting. When user security is enabled, only users in the LabDirector or ITAdmin role
can access these features.
Follow these procedures:
• To open the Application Defaults page
• To specify a default laboratory name and instrument name
• To specify default mass precision and the intensity scale
 To open the Application Defaults page
In the Application Configuration view, click Defaults.
The Application Defaults page of the Application Configuration view opens.
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Application Configuration
 To specify a default laboratory name and instrument name
1. Type the name of your laboratory in the Lab Name box.
When you create a method, the application uses this default laboratory name for the
Laboratory Name value on the General page of the Master Method View. The application
uses this laboratory name in the report headings.
The application does not apply this default laboratory name to previously created
methods. By default, the laboratory name is Default Laboratory.
2. Type the name of your instrument in the Instrument Name box.
When you create a batch, the application uses this default instrument name for the
Instrument Name value. The application uses this instrument name in the report
headings.
3. In the Application Configuration view, click Apply.
The application does not apply this default instrument name to previously created
batches. By default, the instrument name is Thermo Scientific Instrument.
4. Click Yes.
 To specify default mass precision and the intensity scale
1. In the Display Mass Precision box, set the mass precision decimal places value to an
integer from 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.
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2. Select Relative or Absolute from the Chromatogram Intensity Scale list.
This sets the default display type for both quantitation and qualitative chromatograms
displayed in data review and reports.
3. In the Application Configuration view, click Apply.
4. Click Yes.
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Application Configuration
Specifying Detection Parameters
When user security is enabled, users in the LabDirector or ITAdmin role can specify detection
parameters for the Genesis, ICIS, or Avalon detection algorithms. Use the Peak Detection
Defaults page to specify a peak detection algorithm and its options and to determine the area
under a curve.
This section includes procedures for specifying the following detection algorithms:
• Genesis Detection Method
• ICIS Detection Method
• Avalon Detection Method
 To specify common detection parameters
1. In the Application Configuration view, click Detection.
The Peak Detection Defaults page opens. See “Common peak detection areas.”
2. In the Detector Type list, select a detector type.
3. In the Mass Tolerance area, do the following:
a. Select the unit of measure that you want to use.
b. In the Value box, specify the number of millimass units or parts per million to use as
the upper limit.
The application applies this mass tolerance to the extracted chromatograms. The default
is 500 MMU.
4. In the Retention Time area, do the following:
a. In the Window box, specify the width of the window (in seconds) to indicate how far
around the expected retention time the system will look for a peak apex.
b. In the View Width box, specify the viewable size (in minutes) of the ion
chromatogram display.
5. In the Ion Ratio Parameters area, do the following:
a. In the Window Type box, select Absolute or Relative as the calculation approach for
determining the acceptable ion ratio range.
b. In the Window (+/-%) box, select the acceptable ion ratio range.
c. In the Ion Coelution box, select the maximum difference in retention time between a
confirming ion peak and the quantification ion peak.
6. In the Peak Detection Parameters area, select one of the detection algorithms: Genesis,
ICIS, or Avalon.
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Figure 13. Common peak detection areas
Table 12. Common peak detection parameters
Parameter
Description
Detector Type
Reserved for future releases.
Mass Tolerance
Units
• (Default) MMU (millimass units)
MMU is a static calculation to the extracted mass.
• PPM (parts per million)
PPM is a variable calculation dependent on the actual mass. The smaller the mass, the
narrower the tolerance range. The larger the mass, the wider the tolerance range.
Value
Upper limit of MMU or PPM.
Default: 500
Range: 0.1 through 50 000
Retention Time
Window (sec)
Width of the window (in seconds) to indicate how far around the expected retention time
the system will look for a peak apex.
View Width (min)
Viewable size (in minutes) of the ion chromatogram display. Changing the view width does
not affect the process of peak detection; the TraceFinder application uses it only for
graphical display.
Ion Ratio Parameters
Window Type
The absolute or relative calculation approach for determining the acceptable ion ratio range.
Window (+/-%)
The acceptable ion ratio range.
Ion Coelution (min)
The maximum difference in retention time between a confirming ion peak and the
quantification ion peak.
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Application Configuration
Genesis Detection Method
The TraceFinder application provides the Genesis peak detection algorithm for backward
compatibility with Xcalibur 1.0 studies.
Figure 14. Genesis peak detection page
Table 13. Genesis peak detection page parameters (Sheet 1 of 3)
Parameter
Description
Sensitivity
Specifies the Genesis peak detection algorithm.
Detection Method
Highest peak: Uses the highest peak in the chromatogram for component identification.
Nearest RT: Uses the peak with the nearest retention time in the chromatogram for
component identification.
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Table 13. Genesis peak detection page parameters (Sheet 2 of 3)
Parameter
Description
Smoothing
Determines the degree of data smoothing to be performed on the active component peak
prior to peak detection and integration. The ICIS peak detection algorithm uses this value.
Default: 1
Range: Any odd integer from 1 through 15 points
S/N threshold
Current signal-to-noise threshold for peak integration. Peaks with signal-to-noise values less
than this value are not integrated. Peaks with signal-to-noise values greater than this value
are integrated.
Range: 0.0 to 999.0
Enable Valley
Detection
Uses the valley detection approximation method to detect unresolved peaks. This method
drops a vertical line from the apex of the valley between unresolved peaks to the baseline.
The intersection of the vertical line and the baseline defines the end of the first peak and the
beginning of the second peak.
Expected Width (sec)
The expected peak width parameter (in seconds). This parameter controls the minimum
width that a peak is expected to have if valley detection is enabled.
With valley detection enabled, any valley points nearer than the expected width/2 to the top
of the peak are ignored. If a valley point is found outside the expected peak width, the
TraceFinder application terminates the peak at that point. The application always terminates
a peak when the signal reaches the baseline, independent of the value set for the expected
peak width.
Range: 0.0 to 999.0
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 enables the
Peak Height (%) and Tailing Factor options.
Peak Height (%)
A signal must be above the baseline percentage of the total peak height (100%) before
integration is turned on or off. This text box is active only when you select the Constrain
Peak Width check box.
Range: 0.0 to 100.0%
Tailing Factor
A factor that controls how the TraceFinder application integrates the tail of a peak. This
factor is the maximum ratio of the trailing edge to the leading side of a constrained peak.
This text box is active only when you select the Constrain the Peak Width check box.
Range: 0.5 through 9.0
Min Peak Height (S/N) For the valley detection approximation method to use the Nearest RT Peak Identification
criteria, this peak signal-to-noise value must be equaled or exceeded. For component
identification purposes, the TraceFinder application ignores all chromatogram peaks that
have signal-to-noise values that are less than the S/N Threshold value.
Range: 0.0 (all peaks) through 999.0
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Table 13. Genesis peak detection page parameters (Sheet 3 of 3)
Parameter
Description
Peak S/N Cutoff
The peak edge is set to values below this signal-to-noise ratio.
This test assumes it has found an edge of a peak when the baseline adjusted height of the
edge is less than the ratio of the baseline adjusted apex height and the peak S/N cutoff ratio.
When the S/N at the apex is 500 and the peak S/N cutoff value is 200, the TraceFinder
application defines the right and left edges of the peak when the S/N reaches a value less
than 200.
Range: 50.0 to 10000.0
Valley Rise (%)
The peak trace can rise above the baseline by this percentage after passing through a
minimum (before or after the peak). This criteria is useful for integrating peaks with long
tails.
This method drops a vertical line from the apex of the valley between unresolved peaks to
the baseline. The intersection of the vertical line and the baseline defines the end of the first
peak and the beginning of the second peak.
When the trace exceeds rise percentage, the TraceFinder application applies valley detection
peak integration criteria. This test is applied to both the left and right edges of the peak.
Range: 0.1 to 500.0
Valley S/N
Specifies a value to evaluate the valley bottom. Using this parameter ensures that the
surrounding measurements are higher.
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 15. ICIS peak detection page
Table 14. ICIS peak detection page parameters (Sheet 1 of 3)
Parameter
Description
Sensitivity
Specifies the ICIS peak detection algorithm.
Detection Method
Highest peak: Uses the highest peak in the chromatogram for component identification.
Nearest RT: Uses the peak with the nearest retention time in the chromatogram for
component identification.
Smoothing
Determines the degree of data smoothing to be performed on the active component peak
prior to peak detection and integration. The ICIS peak detection algorithm uses this value.
Range: Any odd integer from 1 through 15 points
Default: 1
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Table 14. ICIS peak detection page parameters (Sheet 2 of 3)
Parameter
Description
Area Noise Factor
The noise level multiplier used to determine the peak edge after the location of the possible
peak. The ICIS peak detection algorithm uses this value.
Range: 1 through 500
Default: 5
Peak Noise Factor
The noise level multiplier used to determine the potential peak signal threshold. The ICIS
peak detection algorithm uses this value.
Range: 1 through 1000
Default: 10
Baseline Window
The TraceFinder application looks for a local minima over this number of scans. The ICIS
peak detection algorithm uses this value.
Range: 1 through 500
Default: 40
Constrain Peak Width
Constrains the peak width of a component during peak integration of a chromatogram. You
can then set values that control when peak integration is turned on and off by specifying a
peak height threshold and a tailing factor. Selecting the Constrain Peak Width check box
enables the Peak Height (%) and Tailing Factor options.
Peak Height (%)
A signal must be above the baseline percentage of the total peak height (100%) before
integration is turned on or off. This text box is active only when you select the Constrain
Peak Width check box.
Range: 0.0 to 100.0%
Tailing Factor
A factor that controls how the TraceFinder application integrates the tail of a peak. This
factor is the maximum ratio of the trailing edge to the leading side of a constrained peak.
This text box is active only when you select the Constrain the Peak Width check box.
Range: 0.5 through 9.0
Min Peak Height (S/N) For the valley detection approximation method to use the Nearest RT Peak Identification
criteria, this peak signal-to-noise value must be equaled or exceeded. For component
identification purposes, the TraceFinder application ignores all chromatogram peaks that
have signal-to-noise values that are less than the S/N Threshold value.
Range: 0.0 (all peaks) through 999.0
Noise Method
The options are INCOS or Repetitive.
INCOS: Uses a single pass algorithm to determine the noise level. The ICIS peak detection
algorithm uses this value.
Repetitive: Uses a multiple pass algorithm to determine the noise level. The ICIS peak
detection algorithm uses this value. In general, this algorithm is more accurate in analyzing
the noise than the INCOS Noise algorithm, but the analysis takes longer.
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Application Configuration
Table 14. ICIS peak detection page parameters (Sheet 3 of 3)
Parameter
Description
Min Peak Width
The minimum number of scans required in a peak. The ICIS peak detection algorithm uses
this value.
Range: 0 to 100 scans
Default: 3
Multiplet Resolution
The minimum separation in scans between the apexes of two potential peaks. This is a
criteria to determine if two peaks are resolved. The ICIS peak detection algorithm uses this
value.
Range: 1 to 500 scans
Default: 10
Area Tail Extension
The number of scans past the peak endpoint to use in averaging the intensity. The ICIS
peak detection algorithm uses this value.
Range: 0 to 100 scans
Default: 5
Area Scan Window
The number of allowable scans on each side of the peak apex. A zero value defines all scans
(peak-start to peak-end) to be included in the area integration.
Range: 0 to 100 scans
Default: 0
RMS
Thermo Scientific
Specifies that the TraceFinder application calculate noise as RMS. By default, the
application uses Peak To Peak for the noise calculation. RMS is automatically selected if you
manually determine the noise region.
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Application Configuration
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 16. Avalon peak detection page
Table 15. Avalon peak detection page parameters
Parameter
Description
Sensitivity
Specifies the Avalon peak detection algorithm.
Detection Method
Highest peak: Uses the highest peak in the chromatogram for component identification.
Nearest RT: Uses the peak with the nearest retention time in the chromatogram for
component identification.
Smoothing
Determines the degree of data smoothing to be performed on the active component peak
prior to peak detection and integration. The ICIS peak detection algorithm uses this value.
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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Application Configuration
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 17. Avalon Event List dialog box
Table 16. Avalon Event List dialog box parameters
Thermo Scientific
Parameter
Description
Time (Min)
Specifies the start time of the event.
Event
Specifies the type of event. For a detailed list of events and value
ranges, see “Event types.”
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 18. Event types
Table 17. 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 17. 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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Application Configuration
Enabling Optional Features
In the Application Configuration view of the Configuration mode, you can enable the
following features:
• User Security
• Target Screening
• Quick Acquisition
• EPA Tune Criteria
• Compound Datastore
• Multiplexing
• Delay Calibration Calculation
• Batch Wizard Style
• Acquisition Submission Options
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Application Configuration
 To open the Optional Features page
In the Application Configuration view, click Optional Features.
The Optional Features page of the Application Configuration view opens.
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User Security
When user security is enabled, all users must log in to the TraceFinder application for access
to only those modes assigned to their user role. See “Choosing User Roles” on page 46.
 To turn on user security
1. Select the User Security check box.
When this check box is selected, all users must log in to the TraceFinder application for
access to the modes assigned to their user role. See “Choosing User Roles” on page 46.
When user security is enabled, only users in the LabDirector or ITAdmin roles can access
the Configuration mode.
When this check box is cleared, users are not required to log in to the TraceFinder
application. When they start the application, the dashboard is the first screen that users
see and all modes are available to them. The User Administration view in the
Configuration mode is hidden from all users except those assigned the LabDirector or
ITAdmin role.
IMPORTANT If you are the administrator logging on with user security enabled, you
can use Administrator/Password as the username/password.
2. Click Apply.
A message prompts you to restart the TraceFinder application so that your changes can
take effect.
3. Click Yes.
Target Screening
You must have the ToxID application installed on your computer before you can generate
Target Screening reports.
 To enable target screening
1. Select the Target Screening (ToxID) check box.
2. Click Apply.
A message prompts you to restart the TraceFinder application so that your changes can
take effect.
3. Click Yes.
For a list of available target screening reports, see “Reports” on page 70.
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Application Configuration
Quick Acquisition
The quick acquisition option enables the Quick Acquisition feature in the Acquisition,
Analysis, or Method Development mode.
Note The Quick Acquisition feature is not available when you enable multiplexing. See
“Multiplexing” on page 92.
 To enable quick acquisition
1. Select the Quick Acquisition (EnviroLab/ToxLab/QuanLab Forms) check box.
2. Click Apply.
A message prompts you to restart the TraceFinder application so that your changes can
take effect.
3. Click Yes.
For a description of the Quick Acquisition features, see “Working with Master Methods” on
page 100.
EPA Tune Criteria
When you select the EPA Tune Criteria option, the application supports Tune, Breakdown,
and Tune/Breakdown sample types and MSTune and Breakdown compound types. This
option changes the Breakdown method to a Tune/Breakdown method on the General page of
the Master Method View and adds the Tune tab to the QAQC page of the Master Method
View.
 To enable the tune criteria
1. Select the EPA Tune Criteria check box.
By default, the EPA Tune Criteria option is selected.
2. Click Apply.
A message prompts you to restart the TraceFinder application so that your changes can
take effect.
3. Click Yes.
For a description of the Tune/Breakdown method on the General page of the Master Method
View, see “Editing the General Page” on page 121.
For a description of the Tune page on the QAQC page of the Master Method View, see
“Editing the QAQC Page” on page 183.
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Compound Datastore
 To enable the compound datastore
1. Select the Compound Datastore check box.
By default, the Compound Datastore option is not selected.
2. In the Application Configuration view, click Apply.
3. Click Yes.
The application implements the following changes:
• Displays the Acquisition List page on the Compounds page in the Master Method
View. See “Editing the Compounds Page” on page 129.
• Displays the Compound Datastore task pane on the Configuration mode navigation
pane. See “Compound Datastore” on page 55.
• Enables the Export SRM Data command in the Method Development mode. See
“Exporting SRM Data” on page 227.
Multiplexing
The Multiplexing options are available only when you have installed the Power Modules. See
“Installing the Power Modules” on page 13.
 To specify multiplexing features
1. Select the Multiplexing check box.
2. Choose 2 Channels or 4 Channels.
3. When you are using 2 channels, select a 1- or 2-arm autosampler configuration.
The 1 arm configuration enables channels 1 and 3; the 2 arm configuration enables
channels 2 and 4.
When you use a 4-channel configuration, autosampler 1 uses channels 1 and 3 and
autosampler 2 uses channels 2 and 4.
4. Click Apply.
A message prompts you to restart the TraceFinder application so that your changes can
take effect.
5. Click Yes.
When you enable multiplexing, the following optional features are not available:
• Quick Acquisition
• Batch Template Wizard
• Single Sample Submission (Intelligent Sequencing)
The application uses multiplexing features in the Acquisition mode when you specify
channels for a sample in a batch (see “Defining the Sample List” on page 255) or monitor an
acquisition (see “Devices Page” on page 282).
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Application Configuration
Delay Calibration Calculation
Use the Delay Calibration Calculation... option to make the application wait until it processes
the last calibration sample in a batch before it calculates the calibration curve (faster) instead
of recalculating the calibration curve after each calibration sample (more responsive).
 To delay calculation of a calibration curve
1. Select the Delay Calibration Calculation... check box.
By default, this option is selected.
2. In the Application Configuration view, click Apply.
3. Click Yes.
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Application Configuration
Batch Wizard Style
Use the Batch Wizard Style option to choose one of two styles for your batch wizard.
 To select a wizard style
1. In the Batch Wizard Style list, select a wizard style:
• Acquisition Batch Wizard: Adds the Acquisition mode to the navigation pane. This
mode is similar to the Acquisition mode in the TraceFinder 1.1 application. See
Chapter 5, “Using the Acquisition Mode.”
When you enable multiplexing, the application automatically enables this wizard
style.
• Batch Template Wizard: The default wizard style that is similar to the acquisition
wizard in the EnviroLab Forms, ToxLab Forms, and QuanLab Forms applications.
See “Creating a Batch Using the Batch Wizard” on page 331.
Note The Batch Template Wizard feature is not available when you enable
multiplexing. See Multiplexing.
2. Click Apply.
A message prompts you to restart the TraceFinder application so that your changes can
take effect.
3. Click Yes.
Acquisition Submission Options
To control acquisitions, you can enable full-sequence or single-sample submission options.
When you submit batches from the Acquisition mode, development batches from the
Method Development mode, or Quick Acquisition batches from any mode, they run in
first-in-last-out order. The last batch submitted is the first batch to run unless you submit a
batch as a priority batch in Acquisition mode.
• When you are using Full Sequence Submission, priority batches always run immediately
after the currently acquiring batch completes.
• When you are using Single Sample Submission, priority batches always run immediately
after the currently acquiring sample completes.
 To specify acquisition submission features
1. Select either the Full Sequence Submission or the Single Sample Submission option:
• Full Sequence Submission: Supports look-ahead features of the autosampler. When
the instrument method specifies the look-ahead feature, the Tracefinder application
functions like a multiplex driver and feeds the autosampler the next vial position.
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When you submit a batch, the autosampler begins preparation for all sample
injections when the pre-run condition begins. All samples in the batch must
complete before other batches (even higher priority batches) can begin.
• Single Sample Submission: Supports intelligent-sequencing features. When you
submit a batch, the autosampler begins preparing for one sample injection at a time.
Higher priority batches can interrupt the sample sequence in the currently acquiring
batch.
Note The Single Sample Submission feature is not available when you enable
multiplexing. See “Multiplexing” on page 92.
2. Click Apply.
A message prompts you to restart the TraceFinder application so that your changes can
take effect.
3. Click Yes.
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Using the Method Development Mode
This chapter includes method development tasks assigned to the Supervisor or LabDirector
role when user security is enabled.
Contents
• Working with Master Methods
• Working with Instrument Methods
• Working with Development Batches
• Using Quick Acquisition
From the Method Development mode, you can create a master method, an instrument
method, or a simple development batch to test your instrument method.
You can also use the Quick Acquisition feature to quickly submit a single sample from any
view in the Method Development mode.
 To access the Method Development mode
Click Method Development from the dashboard or the navigation pane.
The Method Development navigation pane opens. For detailed descriptions of all the
features on the Method Development navigation pane, see “Method Development
navigation pane.”
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Figure 19. Method Development navigation pane
Available only when you enable the Compound
Datastore feature in the Configuration mode.
Available only when you select the Acquisition Batch Wizard
as your wizard style in the Configuration mode.
Table 18. Method Development navigation pane commands (Sheet 1 of 2)
Command
Description
Method View
See “Working with Master Methods” on page 100.
Create Method
Opens the Create Master Method dialog box where you can choose the process that you
want to use to start your master method.
Open Method
Opens the Open Master Method dialog box where you can choose a master method to
open.
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Table 18. Method Development navigation pane commands (Sheet 2 of 2)
Command
Description
Import Published
Method
Opens the Import Published Method dialog box where you can select a published method
to import.
Export SRM Data
Writes the selected reaction monitoring (SRM) table to the following file:
…\Thermo\TraceFinder\2.1\EFS\Methods\methodname.xml
You can use this data in the instrument method editor when you open the TSQ 2.1
application. This command is displayed only when you enable the Compound Datastore
option in the Configuration mode. See “Compound Datastore” on page 92.
The compounds in the Acquisition List must contain at least one SRM experiment type.
Recent Files
Displays recently saved master methods.
Instrument View
See “Working with Instrument Methods” on page 228.
New Instrument
Method
Opens the Instrument View where you can specify instrument settings for your configured
instruments.
If the instrument that you want to use is not configured, close the TraceFinder application,
configure the instrument, and then reopen the application. You cannot configure an
instrument while the TraceFinder application is running.
Open Instrument
Method
Opens a browser where you can choose an instrument method to open.
Development Batch
See “Working with Development Batches” on page 235.
Select Batch Location
Specifies a location to store temporary development batch raw data files.
New Sample List
Removes acquired samples from your development batch so that you can start a new sample
list.
Open Qual Browser
Opens the Thermo Xcalibur Qual Browser where you can view the acquired raw data files.
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Working with Master Methods
The TraceFinder application uses a master method to specify the nature and types of
acquisition, processing, and reporting that occur with a batch of samples. When you are
testing for compounds in an assay, you can create a method designed specifically for that type
of application.
A master method contains a list of compounds and settings for detecting, processing, and
reporting those compounds.
When you create a master method, the TraceFinder application uses the method to determine
how the software works with a set of samples to provide a set of meaningful results. The
application uses an instrument method to define how raw data is acquired. The rest of the
master method defines how the raw data is processed, how the flags information evaluates the
results, and how the reporting functionality defines the output for your data and results.
The TraceFinder application applies your master method to a batch, which is a list of one or
more samples to be processed and reported. Together, the master method and batch provide a
workflow-oriented approach to the data processing and information reporting for batches of
samples.
To speed up the creation of master methods, you can create a method template. Using a
method template helps you to develop methods faster because the TraceFinder application
saves all of your commonly used method settings in a template, such as the number of
confirming ions or the use of data-dependent data.
This section includes instructions for the following tasks:
• Creating a New Master Method
• Editing a Master Method
• Creating a Method Template
• Importing Published Master Methods
• Exporting SRM Data
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Creating a New Master Method
To begin a master method, follow any of four different procedures in the Create Master
Method dialog box:
• Creating a New Method with Method Forge
• Importing an Xcalibur Master Method
• Associating a Raw Data File
• Selecting Compounds from the Compound Datastore
With each procedure, you start the method in a specific way and then use the common
features of the Master Method View to complete and save your master method.
Figure 20. Create Master Method dialog box
Available only when you enable the Compound Datastore feature in the Configuration mode.
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Creating a New Method with Method Forge
With Method Forge, you can create a new master method by manually selecting peaks,
selecting multiple compounds, renaming peaks, or comparing mass spectra from the library
searches. You can also choose to let the TraceFinder application automatically create a master
method for you. For detailed descriptions of all the Method Forge parameters, see “Method
Forge dialog box parameters” on page 108.
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 Method View task pane, click Create Method.
The Create Master Method dialog box opens. See “Create Master Method dialog box” on
page 101.
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 108.
Use Method Forge to create a master method from an existing raw data file or to create a
new raw data file to use for the master method.
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3. In the Method Forge dialog box, do one of the following:
Select the Use the Default Template option.
–or–
Select the Select a Custom Template option and highlight your custom template in the
Method template table.
For detailed instructions on creating a custom method template, see “Creating a Method
Template” on page 216.
4. Select the Name the Master Method check box and type a name for your master method.
You can enter an existing method name and overwrite it when you create the method. If
you do not specify a name, the application names the method for the raw data file used to
create the method.
5. Select the Automatically Create the Master Method check box.
6. Specify a raw data file by doing one of the following:
a. In the Raw File Selection area, choose Use an Existing Raw Data File.
b. Click the browse button and locate a raw data file to use for the method.
c. Go to step 8.
–or–
a. In the Raw File Selection area, choose Acquire a New Raw Data File.
b. From the Instrument method list, select a method (.meth) file to use for acquiring the
data.
c. In the Raw Filename box, type the name of the file where the TraceFinder application
will write the raw data file.
d. In the Path box, type a path or click the browse button and locate a folder where the
application will save the raw data file.
e. (Optional) Type a comment about the acquired sample or the data file.
7. If you chose to acquire a new raw data file, do one of the following:
Choose Manual Injection.
–or–
Specify the autosampler settings:
a. Choose Use Autosampler.
b. In the Vial Position box, type a vial position.
c. In the Injection Volume box, type an injection volume.
The minimum injection volume allowed is 0.1 μL; the maximum injection volume
allowed is 5000 μL.
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8. To automatically create the master method, click OK (or Overwrite).
As the Method Forge creates the method, it displays the following status:
• 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 NIST library and
displays the identified compound names instead of the peak times.
When the acquisition completes, Method Forge performs peak detection, datastore
searching (except for analog peaks), and identification of characteristic ion and reference
spectrum. Method Forge then loads this information into a new master method. This
process occurs immediately if you selected a previously acquired raw data file.
If the compounds in the raw data file that you used to create the method are not in the
current compound datastore, the TraceFinder application displays the compounds in the
Edit Compound Dependent Parameters dialog box.
9. (Optional) Select the compounds that you want to add to the compound datastore and
click Add to CDS.
The selected compounds are added to the current compound datastore.
Note You must click Add to CDS before you continue to the method.
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10. To use these compounds in your method and close the dialog box, click Continue to
Method.
The TraceFinder application uses all compounds found in the raw data file in your
method and displays the General page of the Master Method View. For detailed
descriptions of all the features on the General page, see “General page” on page 126.
11. From the Instrument Method list on the General page, select an instrument method.
12. From the Qualitative Peak Processing Template list, select a method template for
performing peak detection on quantitative samples following target compound analysis.
13. From the Background Subtraction Range Option list, select how you want the
background subtraction range determined from one of these options:
• Before Peak: Averages and subtracts a specified number of scans before the apex of
the peak.
• After Peak: Subtracts a specified number of scans following the apex of the peak.
• Both Sides of Peak: Subtracts a specified number of scans from each side of the apex
of the peak.
14. To save the new method, choose File > Save from the main menu.
For a detailed description of how to modify a master method, see “Editing a Master
Method” on page 119.
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Working with Master Methods
 To manually select compounds to create a new method
1. From the Method View task pane, click Create Method.
The Create Master Method dialog box opens. See “Create Master Method dialog box” on
page 101.
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 110.
3. Do one of the following:
Select the Use the Default Template option.
–or–
Select the Select a Custom Template option and highlight your custom template in the
Method Template table.
For detailed instructions about creating a custom method template, see “Creating a
Method Template” on page 216.
4. Select the Name the Master Method check box and type a name for your master method.
You can enter an existing method name and overwrite it when you create the method. If
you do not specify a name, the method is named for the raw data file used to create the
method.
5. Ensure that the Automatically Create the Master Method check box is not selected.
6. To select a raw data file, click the browse button and locate the file.
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7. To manually create the master method, click OK (or Overwrite).
The Master Method View displays a list of possible matches in the Library Results pane.
The TraceFinder application displays the best match in the Compound Name list and
displays the peak spectrum for that compound.
8. To use a compound other than the compound chosen by the TraceFinder application,
scroll to the spectrum for that compound and select the compound name in the header of
the spectrum pane.
Selected
compound
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9. After you manually select your compound, click Create to create the master method.
The TraceFinder application uses all compounds found in the raw data file in your
method and displays the General page of the Master Method View. For detailed
descriptions of all the features on the General page, see “General page” on page 126.
10. From the Instrument Method list on the General page, select an instrument method.
11. To save the new method, choose File > Save from the main menu.
For a detailed description of how to modify a master method, see “Editing a Master
Method” on page 119.
Figure 21. Method Forge dialog box
Table 19. Method Forge dialog box parameters (Sheet 1 of 2)
Parameter
Description
Method template selection
Use the Default
Template
Creates a new method with the default template.
Select a Custom
Template
Lists all the available method templates.
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Table 19. Method Forge dialog box parameters (Sheet 2 of 2)
Parameter
Description
Name the Master
Method
The name for the new master method.
Automatically Create
the Master Method
When the acquisition completes, Method Forge performs peak detection, library searching,
and identification of characteristic ion and reference spectrum. 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
Enables the Raw Filename box where you can select a raw data file used in creating the
master method.
Acquire a New Raw
Data File
Enables 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.
Function button
Overwrite
Overwrites the specified master method name. This function is enabled only when the
specified master method name already exists.
OK
Creates a master method using the data and parameters 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. From the Method View task pane, click Create Method.
The Create Master Method dialog box opens. See “Create Master Method dialog box” on
page 101.
2. Select the Import Xcalibur Processing Method option and click OK.
The Import an Xcalibur Method dialog box opens.
3. Click the browse button for the Xcalibur Method to Import box, browse to the Xcalibur
processing method file, and open the file.
The TraceFinder application imports the compound information from the Xcalibur
method file.
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4. (Optional) Click the browse button for the Raw Data File to Associate box, 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\2.1\EFS\Methods\MethodName
5. (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.
6. Click OK.
If the compounds in the imported Xcalibur method file are not in the Compound
Datastore, the TraceFinder application displays the compounds in the Edit Compound
Dependent Parameters dialog box.
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7. (Optional) Select the compounds that you want to add to the Compound Datastore and
click Add to CDS.
The selected compounds are added to the current compound datastore.
To add these compounds to the datastore, you must click Add to CDS before you
continue to the method. When you click Continue to Method, the Edit Compound
Dependent Parameters dialog box closes and you cannot return to add the compounds.
8. To add these compounds to your method and close the dialog box, click Continue to
Method.
The TraceFinder application adds all compounds found in the imported Xcalibur method
and displays the General page of the Master Method View. For detailed descriptions of all
the features on the General page, see “General page” on page 126.
9. From the Instrument Method list on the General page, select an instrument method.
10. To save the new method, choose File > Save from the main menu.
For a detailed description of how to modify a master method, see “Editing a Master
Method” on page 119.
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Associating a Raw Data File
You can use the compounds in a previously acquired raw data file to create a new master
method.
Follow these procedures:
• To associate a raw data file with the method
• To add compounds to the method
 To associate a raw data file with the method
1. From the Method View task pane, click Create Method.
The Create Master Method dialog box opens. See “Create Master Method dialog box” on
page 101.
2. Select the Associate a Raw Data File option and click OK.
The Associate a Raw Data File dialog box opens.
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3. 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\2.1\EFS\Methods
4. 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 150.
• 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.
Options that are set to No use the standard values in the method.
5. Click OK.
The TraceFinder application displays the General page of the Master Method View. For
detailed descriptions of all the features on the General page, see “General page” on
page 126.
6. From the Instrument Method list on the General page, select an instrument method.
7. To add compounds to the method, follow the instructions “To add compounds to the
method” on page 115.
To save the method, it must include at least one compound.
8. To save the new method, choose File > Save from the main menu.
For a detailed description of how to modify a master method, see “Editing a Master
Method” on page 119.
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 To add compounds to the method
1. Click the Compounds tab.
The Detection page is selected by default.
Note When the Compound Datastore is enabled, the Compounds page includes an
Acquisition List tab. See “Enabling Optional Features” on page 88.
The Detection page shows an empty Compound list and displays the chromatographic
data for the compounds in the raw data file.
2. Select a filter from the Filter list.
3. Select the peak in the chromatogram that represents the compound that you want to add
to the method.
4. 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.
5. (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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6. 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 129.
For detailed descriptions of how to modify a master method, see “Editing a Master
Method” on page 119.
Selecting Compounds from the Compound Datastore
You can select compounds from the compound datastore to create a new master method. This
method for creating a master method is available only when the compound datastore is
enabled. See “Compound Datastore” on page 92.
 To select compounds from the datastore
1. From the Method View task pane, click Create Method.
The Create Master Method dialog box opens.
2. Select the Select Compounds from CDS option and click OK.
The Select Compounds to Add dialog box opens, listing all the compounds defined in the
compound datastore.
3. Select the check box for each of the compounds that you want to add to the method.
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4. To quickly select multiple compounds, right-click and use any of the commands on the
shortcut menu.
Table 20. Select Compounds to Add shortcut menu commands
Command
Description
Select All
Selects all compounds in the compound datastore.
Deselect All
Clears all compounds in the compound datastore.
Copy Down
Copies the state (checked or cleared) of the currently selected
compound to all compounds below it in the compound list.
5. Click Apply.
The TraceFinder application adds the selected compounds to the method.
Note After you add a compound to a method, the compound is no longer enabled in
the Select Compounds to Add dialog box. You cannot remove the applied compounds
from the method by returning to this dialog box. To remove a compound from a
method, see “Acquisition List” on page 129.
6. From the Instrument Method list on the General page, select an instrument method.
7. To save the new method, choose File > Save from the main menu.
For a detailed description of how to modify a master method, see “Editing a Master
Method.”
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Editing a Master Method
You can open a master method to view or edit the compounds, method instructions, and
reporting options in the method.
This section includes instructions for the following tasks:
• Opening a Master Method
• Editing the General Page
• Editing the Compounds Page
• Editing the QAQC Page
• Editing the Groups Page
• Editing the Reports Page
Opening a Master Method
Use the TraceFinder application to open a master method that was created and saved in the
current TraceFinder application or converted from these legacy applications: TraceFinder,
EnviroLab Forms, QuanLab Forms, or ToxLab Forms. To convert legacy methods, see
“Converting Legacy Data” on page 19.
 To open a saved master method
1. Click Method Development from the dashboard or the navigation pane.
The Method Development navigation pane opens.
2. In the Method View task pane, do one of the following:
Click Open Method.
–or–
Click a method name in the Recent Files list.
When you save a method, the application adds it to the Recent Files list. The Recent Files
list displays a list of your most recently saved master method files.
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The Open Master Method dialog box opens, displaying all available methods.
3. Select a master method and click Open.
The TraceFinder application copies all components of the selected method including its
associated instrument method.
The General page for the selected method opens in the Method View. For detailed
descriptions of all the features on the General page, see “General page” on page 126.
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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 on the General page, see “General page” on page 126.
Follow these procedures:
• To specify general information for a master method
• To edit the instrument method parameters
• To select a qualitative peak processing template
• To set automated background subtraction options
• To specify a chromatogram reference sample
• To specify mass tolerance
 To specify general information for a master method
1. In the Lab Name box, type the name to be displayed on the top of each printed, saved, or
exported report.
The default name is Default Laboratory.
2. In the Assay Type box, type the assay type to be targeted by the method.
3. From the Injection Volume box, select the injection volume (in μL) to be used for sample
injection.
Use the up/down arrows to change the volume in increments/decrements of 1 μL, or use
the keyboard to enter non-integer injection volumes.
IMPORTANT The TraceFinder application uses this injection volume in the master
method, not the injection volume from the instrument method.
4. From the Ion Range Calc Method list, select a method for calculating the ion ratio range
windows.
When you select Level, the TraceFinder application displays a Use Level list where you
can choose a calibration level. To define the calibration levels on the Compounds page,
see “Editing the Compounds Page” on page 129.
5. From the Qualitative Peak Processing Template box, select a template for performing
peak detection on quantitative samples after target compound analysis is complete.
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 To edit the instrument method parameters
1. From the Instrument Method list on the General page, select an instrument method.
2. To edit the instrument method for this master method, click Edit.
The Thermo Xcalibur Instrument Setup dialog box opens. This example of an
instrument setup shows multiple configured instruments.
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” on
page 126.
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5. To update any changes that were made to the instrument method after you created this
master method, click Update.
The Update Instrument Method? dialog box opens.
6. Choose one of the following options:
• Send to Xcalibur Method: Overwrites the instrument method in the
C:\Xcalibur\methods folder with the current instrument method.
• Get From Xcalibur Method: Overwrites the current instrument method with the
instrument method in the C:\Xcalibur\methods folder.
• Cancel: Make no changes to the instrument method in the current master method.
 To select a qualitative peak processing template
In the Qualitative Peak Processing Template list, select the template 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\2.1\EFSTemplates\Methods
 To set automated background subtraction options
1. In the Background Subtraction Range Option list, select how you want the subtraction
range determined from the following options:
• Before Peak: Averages and subtracts a specified number of scans before the apex of
the peak.
• After Peak: Subtracts a specified number of scans 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.
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.
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3. In the Stepoff Value box, enter a number.
The TraceFinder application uses this offset value to average and subtract scans that are
not adjacent to the apex of the peak. For example:
If you 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 a chromatogram reference sample
1. In the Set Chromatogram Reference Sample list, select External.
2. Click Select.
The Open Chromatograph Reference Sample dialog box opens.
Note If you are creating a new method, you will not see any reference samples here.
You must create and save a batch using 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.
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6. Select a sample from the list of processed samples.
The TraceFinder application displays all the processed samples in the selected batch. To
use a sample as a reference sample, the sample must have been processed with the current
master method.
7. Click Open.
The selected sample is displayed as the chromatogram reference sample in the Master
Method View.
Tip To clear the reference sample from the master method, select None in the Set
Chromatogram Reference Sample list.
 To specify mass tolerance
1. Select the units of measure 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.
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Figure 22. General page
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Table 21. 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 Configuration Defaults” on
page 73.
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 through 5000 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 129.
Instrument Method
Instrument method used for acquiring samples.
Tune/Breakdown
Breakdown or tune method used for processing 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
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Table 21. General page parameters (Sheet 2 of 2)
Parameter
Description
Number of Scans to
Subtract
Valid values: Even numbered integers
Default: 0
Stepoff Value
Offset from the selected peak to the first subtracted peak.
Set Chromatogram
Reference Sample
Valid values: None, External
Default: None
Set Reference Sample
This parameter is enabled only when you set Set Chromatogram Reference Sample to
External. Click Select to choose a reference sample from the project folders.
Mass Tolerance
Upper limit of MMU or PPM.
Default: 500
Range: 0.1 through 50 000
• (Default) MMU (millimass units): MMU is a static calculation to the extracted mass.
• PPM (parts per million): PPM is a variable calculation dependent on the actual mass.
The smaller the mass, the narrower the tolerance range. The larger the mass, the wider
the tolerance range.
Notes
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Editing the Compounds Page
Use the Compounds page to set all parameters used to identify, detect, and quantify the target
compound list.
From the Compounds page of the Master Method View, you can access the following pages:
Acquisition List
See also “Acquisition List page parameters” on page 131.
Identification
See also “Identification page parameters” on page 134.
Detection
See also “Detection page panes” on page 147.
Calibration
See also “Calibration page parameters” on page 173.
Calibration Levels
See also “Calibration levels page parameters” on page 176.
QC Levels
See also “QC levels page parameters” on page 178.
Real Time Viewer
See also “Real Time Viewer page parameters” on page 179.
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 181.
Acquisition List
The Acquisition List page displays all compounds defined for the current method. From this
page, you can add or delete compounds from the method. For detailed descriptions of all the
features on the Acquisition List page, see “Acquisition List page parameters” on page 131.
The Acquisition List page is displayed only when you enable the Compound Datastore option
in the Configuration mode. See “Compound Datastore” on page 92.
Follow these procedures:
• To filter the compound list
• To delete a compound from the list
• To add a compound to the list
 To filter the compound list
1. To display a filtered list of compounds, click the funnel icon,
, in the column header.
The application displays a list of filterable criteria. In all lists, you can choose to filter by
All, Blanks, NonBlanks, or by custom filter criteria. Other filter criteria are specific to the
individual columns.
2. To create a custom filter based on compound values in a specific column, choose Custom
from the column list.
For detailed instructions about creating a custom filter, see Appendix C, “Using Filter
Criteria.”
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 To delete a compound from the list
1. Select the compound to remove from the list.
2. Click the Remove Compound icon,
Compound from the shortcut menu.
, or right-click and choose Remove
A confirmation dialog box opens, listing the compound to be removed.
3. To confirm the deletion, click Yes.
The selected compound is removed from the acquisition list, which has no effect on the
compound datastore.
 To add a compound to the list
1. Click the Add Compound icon,
the shortcut menu.
, or right-click and choose Add Compound from
The Select Compounds to Add dialog box opens, listing all the compounds defined in the
compound datastore.
2. Select the check box for each of the compounds that you want to add to the method.
3. To quickly select multiple compounds, right-click and use any of the commands on the
shortcut menu.
Table 22. Select Compounds to Add shortcut menu commands
Command
Description
Select All
Selects all compounds in the compound datastore.
Deselect All
Clears all compounds in the compound datastore.
Copy Down
Copies the state (checked or cleared) of the currently selected
compound to all compounds below it in the compound list.
4. Click Apply.
The TraceFinder application adds the compounds to the Acquisition List page of the
Master Method View. See “Acquisition List page.”
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Figure 23. Acquisition List page
Table 23. Acquisition List page parameters (Sheet 1 of 2)
Parameter
Description
Function Icons
Opens the Select Compounds to Add dialog box that lists all the compounds defined in the
compound datastore.
Deletes the selected compound. The icon is unavailable when no row is selected. If you used
the filters to display a subset of compounds, the selected compound might not be visible on
the Acquisition List page.
Compound parameters
Compound Name
Alphanumeric name assigned to the compound.
Experiment Type
Experiment type: SRM, XIC, or SIM.
Category
(Optional) Alphanumeric identifier.
Ionization
(Optional) Alphanumeric identifier.
Valid values: ESI, APCI, EI, CI, or APPI
Chemical Formula
(Optional) Alphanumeric chemical identifier.
Quantitative peak parameters
Precursor Mass
The mass-to-charge ratio of a precursor ion. The location of the center of a target
precursor-ion peak in mass-to-charge ratio (m/z) units.
Available only for SRM experiments.
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.
Range: 10.000 to 2999.999
Mass
The mass-to-charge ratio of the quantitation ion. The location of the center of a target
quan-ion peak in mass-to-charge ratio (m/z) units.
Available only for XIC and SIM experiments.
Range: 10.000 to 2999.999
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Table 23. Acquisition List page parameters (Sheet 2 of 2)
Parameter
Description
Collision Energy
The energy used when ions collide with the collision gas.
Range: –250 to 250
Lens
(Optional) Range: –400 to 400
Polarity
+ (positive) or – (negative)
RT (min)
Retention time. The time after injection when the compound elutes. The total time that the
compound is retained on the column.
The TraceFinder application uses the RT and Window values to determine the start and stop
time for the acquisition.
Range: 0.00 to 999.00
Start time = RT – (Window/2)
Stop time = RT + (Window/2)
Start and stop range: 0.00 to 999.00
Window (sec)
Acquisition window. The TraceFinder application uses the RT and Window values to
determine the start and stop time for the acquisition.
Range: 0.00 to 499.50
Start time = RT – (Window/2)
Stop time = RT + (Window/2)
Start and stop range: 0.00 to 999.00
Energy Ramp
Available only for SRM experiments.
Range: 0.00 to 200.00
Confirming ion parameters
Precursor Mass
The mass-to-charge ratio of a precursor ion. The location of the center of a target
precursor-ion peak in mass-to-charge ratio (m/z) units.
Available as a read-only field for SRM experiments only.
Range: 10.000 to 2999.999
Product Mass
The mass-to-charge ratio of the 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.
Range: 10.000 to 2999.999
Mass
The mass-to-charge ratio of the quantitation ion. The location of the center of a target
quan-ion peak in mass-to-charge ratio (m/z) units.
Available only for XIC and SIM experiments.
Range: 10.000 to 2999.999
Collision Energy
The energy used when ions collide with the collision gas.
Available only for SRM experiments.
Range: –250.00 to 250.00
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Identification
The Identification page lists the compounds that are targeted for analysis, reporting, and other
compound-specific values. For 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.
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Compound type
Description
Quan Compounds
Displays only quantitation compounds, such as target
compounds, internal standards, and surrogates.
Non Quan Compounds
Displays only non-quantitation compounds, such as
native, breakdown, and tune compounds.
Target Compounds
Displays only target compounds.
Internal Standards
Displays only internal standard compounds.
Surrogates
Displays only surrogate compounds.
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Figure 24. Identification page
Table 24. Identification page parameters
Parameter
Description
RT
Retention time. The time after injection when the compound elutes. The total time that the
compound is retained on the column.
The TraceFinder application uses the RT and Window values to determine the start and
stop time for the acquisition.
Range: 0.00 to 999.00
Start time = RT – (Window/2)
Stop time = RT + (Window/2)
Start and stop range: 0.00 to 999.00
Compound
A list of 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, Internal Standard, Surrogate, MSTune, Native,
and Breakdown. The TraceFinder application uses target compounds, internal standards,
and surrogates in quantitative analysis.
Active
Identifies each compound to be included in data review and reporting. By default, all added
compounds are set to active. This active or inactive setting populates the Batch View and
Data Review view in the Analysis mode.
CAS No
The Chemical Abstract Service (CAS) number that the TraceFinder application matched
with each compound. To change or add a number, click the CAS No cell and enter a new
number.
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
The Identification page uses a right-click shortcut menu. See “Using the Shortcut Menu
Commands” on page 181.
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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 148.
Signal
See also “Signal page parameters” on page 154.
Detect
See also “Detect page parameters for Genesis” on page 158.
See also “Detect page parameters for ICIS” on page 162.
See also “Detect page parameters for Avalon” on page 164.
Spectrum
See also “Spectrum shortcut menu commands” on page 170.
Ratios
See also “Ratios page parameters” on page 172.
On the Detection page (see “Detection page” on page 146), 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 use the cut-and-paste feature on confirming ion peaks
• To add a trace to the real-time viewer
• To replace a confirming ion peak
• To add a mass as a new confirming ion peak
• 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.
Non Quan Compounds
Displays only non-quantitation compounds, such as
native, breakdown, and tune compounds.
Target Compounds
Displays only target compounds.
Internal Standards
Displays only internal standard compounds.
Surrogates
Displays only surrogate compounds.
 To change the displayed information for detected peaks
1. Right-click the chromatogram plot for any of the 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
1. From the main menu, choose Master Method > Associate a Raw Data File.
The Associate a Raw Data File dialog box opens.
2. Browse to a raw data file to associate with the method (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\2.1\EFS\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 Master Method View. See “Editing the General Page” on page 121.
6. Click OK.
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The TraceFinder application displays the chromatographic and spectrum data for the
compounds in the selected raw data file.
7. Select a filter from the Filter list.
8. Click to select the peak in the chromatogram that represents the compound that you
want to add to the method.
9. Right-click and choose Add This Peak as New Compound from the shortcut menu.
The TraceFinder application performs a library search for the selected compound. The
application uses the first match it finds as the compound name, the base peak of the mass
spectrum as the quantitative peak, and the second and third largest ions as the confirming
ion peaks.
If the name of the first match is already in the library, the Add New Compound dialog
box opens.
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Figure 25. Add New Compound dialog box
10. (Optional) To use a compound other than the compound already in the library, scroll to
the spectrum for that compound and select the compound name in the title bar of the
spectrum pane.
Selected
compound
11. In the Type of Compound to Add list, select a compound type.
12. Click OK.
13. Repeat this procedure for each compound that you want to add to the method.
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 To change the compound reference spectrum
1. In the raw data file chromatogram pane, click a peak.
The TraceFinder application displays the spectrum for the selected peak in the spectrum
pane.
2. In the raw data file spectrum pane, right-click and choose Use This Spectrum for
Compound Reference Spectrum from the shortcut menu.
The TraceFinder application replaces the spectrum on the Spectrum page of the
quantitative peak pane with this spectrum.
 To replace a quantitation mass
1. Click the pane for the quantitation mass that you want to replace.
2. In the raw data file spectrum pane, hold the cursor over a peak.
The red box indicates the selected peak.
3. Right-click and choose Set This 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 171.
 To add a mass to the existing quantitation mass ranges
1. In the raw data file spectrum pane, hold the cursor over a peak.
The red box indicates the selected peak.
2. Right-click and choose Add This 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 171.
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 To add a quantitative peak
1. In the raw data file spectrum pane, hold the cursor over a peak.
The red box indicates the selected peak.
2. Right-click and choose Add This 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.
 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. See “Add
New Compound dialog box” on page 142. If the name of the first match is already in the
library, the dialog box opens with the matching compound selected.
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Figure 26. Add New Compound dialog box
3. (Optional) Make any of the following changes:
a. Change the name for the compound in the Name of New Compound box.
b. Use a compound other than the compound chosen by the TraceFinder application by
scrolling to the spectrum for that compound and selecting the compound name in
the title bar of the spectrum pane.
Selected
compound
c. In the Type of Compound to Add list, select a compound type.
4. Click OK.
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 To replace a 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.
 To use the cut-and-paste feature on confirming ion peaks
Right-click the header bar for the confirming ion peak that you want to remove and
choose Cut Confirming Peak from the shortcut menu.
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.
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 To add a trace to the real-time viewer
Right-click the header bar for the quantitative peak or confirming ion peak that you want
to add to the real-time viewer display 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 179.
Trace m/z 465.36 added
to Real Time Viewer
When you acquire samples with this method, the application displays the m/z 465.36
trace in addition to the TIC in the Real Time Status pane.
Trace m/z 465.36 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 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 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 save the new method
1. Choose File > Save.
The Save Master Method dialog box opens.
2. Do one of the following:
Type a new name for the master method and click OK.
–or–
Select a method name to overwrite and click Overwrite.
The TraceFinder application saves the new method data in the following folder:
…\Thermo\TraceFinder\2.1\EFS\Methods
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Figure 27. Detection page
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Table 25. 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 181.
Quan Peak
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.
Trace
Displays a combination of the Detector and Trace values used for the raw data file.
Filter
Displays the filter used for the raw data file.
Reference
Chromatogram
and
Spectra
Displays a reference chromatogram and spectra for the raw data file.
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 the collapse icon,
.
Additional pages
Times
Defines the retention time and window for a quantitative peak.
See “Times” on page 148.
Signal
Defines the detector and detection parameters used to display each chromatogram trace. See
“Signal” on page 150.
Detect
Defines the peak detection algorithm and its options.
See “Detect” on page 156.
Spectrum
Defines a reference mass spectrum for a quantitative peak or compound. See “Spectrum” on
page 166.
Ratios
Defines the criteria for evaluating, confirming, or qualifying ions. See “Ratios” on page 171.
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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 28. Times page
Parameters for single
RT detection types
Parameters for RT
range detection types
Table 26. 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 26. 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.
Method
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Signal
Use the Signal page (see “Signal page” on page 154) 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 154.
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 29. 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.
Figure 30. XIC Filter dialog box
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5. Select an Activation type:
CID
Collision-induced dissociation
MPD
Multiple photo dissociation
ECD
Electron capture dissociation
PQD
Pulsed dissociation
ETD
Electron transfer dissociation
HCD
Higher energy collision-induced dissociation
Any
Allows any activation method.
SAactivation
PTRactivation
NETDactivation Negative electron-transfer dissociation activation
NPTRactivation
6. Select an MS Order:
Any
Allows any MS order.
MS
Single mass spec stage
MS2-MS10
Multiple mass spec stages
Ng
Nano gram
N1
Nano liter
Par
7. Select a value for the polarity.
Valid values: Positive, Negative, or Any.
8. Select a Scan Mode:
Full
Zoom
SIM
Selective ion monitoring
SRM
Selective reaction monitoring
CRM
Consecutive reaction monitoring
Any
Allows any scan mode.
Q1MS
MS using quadrupole 1
Q3MS
MS using quadrupole 3
9. Click OK.
The application updates the chromatogram data using the specified XIC filter options.
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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 This Filter on All Peaks in This Compound: Applies this filter to all other peaks
in the compound.
• Set This Filter on All Compounds: Applies this filter to all peaks in the method.
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Figure 31. Signal page
Table 27. Signal page parameters (Sheet 1 of 2)
Parameter
Description
XIC
Specifies an Extracted Ion Chromatogram experiment type that uses a single, full-scan mass filter
that is post-processed to extract a peak for the ions of interest.
Filter
Select from the list of mass filters to use for processing the compound.
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Table 27. Signal page parameters (Sheet 2 of 2)
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.
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.
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 150.
Start m/z
End m/z
Specifies ranges of ions for detection and integration. The application sums the multiple ions
specified by these ranges.
Ranges specified by a center mass value are listed as a single value in the Start m/z column. The
application uses a range of one amu centered on this value.
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Detect
Use the Detect page to define the peak detection algorithm (sensitivity) and its options and to
determine the area under a curve. There are three sensitivity modes: Genesis, ICIS, and
Avalon. On this page, you can specify how you want each mode to run.
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 158.
• For ICIS sensitivity, see “Detect page parameters for ICIS” on page 162.
• For Avalon sensitivity, see “Detect page parameters for Avalon” on page 164.
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Figure 32. Detect page for Genesis
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Table 28. 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
enables the Peak Height (%) and Tailing Factor options.
Peak Height (%)
A signal must be above the baseline percentage of the total peak height (100%) before
integration is turned on or off. This text box is active only when you select the Constrain
Peak Width check box.
Range: 0.0 to 100.0%
Tailing Factor
A factor that controls how the TraceFinder application integrates the tail of a peak. This
factor is the maximum ratio of the trailing edge to the leading side of a constrained peak.
This text box is active only when you select the Constrain the Peak Width check box.
Range: 0.5 through 9.0
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Table 28. Detect page parameters for Genesis (Sheet 2 of 3)
Parameter
Description
Min Peak Height (S/N) For the valley detection approximation method to use the Nearest RT Peak Identification
criteria, this peak signal-to-noise value must be equaled or exceeded. For component
identification purposes, the TraceFinder application ignores all chromatogram peaks that
have signal-to-noise values that are less than the S/N Threshold value.
Range: 0.0 (all peaks) through 999.0
Peak S/N Cutoff
The peak edge is set to values below this signal-to-noise ratio.
This test identifies an edge of a peak when the baseline adjusted height of the edge is less
than the ratio of the baseline adjusted apex height and the peak S/N cutoff ratio.
When the S/N at the apex is 500 and the peak S/N cutoff value is 200, the TraceFinder
application defines the right and left edges of the peak when the S/N reaches a value less
than 200.
Range: 50.0 to 10000.0
Valley Rise (%)
The peak trace can rise above the baseline by this percentage after passing through a
minimum (before or after the peak).
This method drops a vertical line from the apex of the valley between unresolved peaks to
the baseline. The intersection of the vertical line and the baseline defines the end of the first
peak and the beginning of the second peak.
When the trace exceeds rise percentage, the TraceFinder application applies valley detection
peak integration criteria.
The TraceFinder application applies this test to both the left and right edges of the peak.
The rise percentage criteria is useful for integrating peaks with long tails.
Range: 0.1 to 500.0
Valley S/N
Specifies a value to evaluate the valley bottom. Using this parameter ensures that the
surrounding measurements are higher.
Default: 2.0
Range: 1.0 to 100.0
# Background Scans
Number of background scans performed by the TraceFinder application.
Report Noise As
Determines if the noise used in calculating S/N values is calculated using an RMS
calculation or a peak-to-peak resolution threshold. Options are RMS or Peak to Peak.
Shortcut menu
Apply to All Peaks in
Method
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Updates all compounds in the method with the current settings on the Detect page. These
updates apply to both quantitative and confirming ion peaks.
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Table 28. 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 33. Detect page for ICIS
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Table 29. Detect page parameters for ICIS (Sheet 1 of 2)
Parameter
Description
Sensitivity
Specifies the ICIS peak detection algorithm.
Detection Method
Highest peak: Uses the highest peak in the chromatogram for component identification.
Nearest RT: Uses the peak with the nearest retention time in the chromatogram for
component identification.
Smoothing
Determines the degree of data smoothing to be performed on the active component peak
prior to peak detection and integration.
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
enables the Peak Height (%) and Tailing Factor options.
Peak Height (%)
A signal must be above the baseline percentage of the total peak height (100%) before
integration is turned on or off. This text box is active only when you select the Constrain
Peak Width check box.
Range: 0.0 to 100.0%
Tailing Factor
A factor that controls how the TraceFinder application integrates the tail of a peak. This
factor is the maximum ratio of the trailing edge to the leading side of a constrained peak.
This text box is active only when you select the Constrain the Peak Width check box.
Range: 0.5 through 9.0
Min Peak Height (S/N) For the valley detection approximation method to use the Nearest RT Peak Identification
criteria, this peak signal-to-noise value must be equaled or exceeded. For component
identification purposes, the TraceFinder application ignores all chromatogram peaks that
have signal-to-noise values that are less than the S/N Threshold value.
Range: 0.0 (all peaks) through 999.0
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Table 29. 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 34. Detect page for Avalon
Table 30. Detect page parameters for Avalon (Sheet 1 of 2)
Parameter
Description
Sensitivity
Specifies the Avalon peak detection algorithm.
Detection Method
Highest Peak: Uses the highest peak in the chromatogram for component identification.
Nearest RT: Uses the peak with the nearest retention time in the chromatogram for
component identification.
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Table 30. Detect page parameters for Avalon (Sheet 2 of 2)
Parameter
Description
Smoothing
Determines the degree of data smoothing to be performed on the active component peak
prior to peak detection and integration.
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 85.
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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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 shortcut menu commands” on page 170.
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 35. Original quantitative peak mass example
Original quantitative peak mass
The TraceFinder application replaces the original quantitation mass with the selected
mass.
Figure 36. Updated quantitative peak 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 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 37. Spectrum page
Table 31. Spectrum 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.
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Ratios
Use the Ratios page (see “Ratios page” on page 172) 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 172.
 To specify ion ratio criteria
1. Select the Enable check box to enable the confirming ion.
2. In the Target Ratio box, select the theoretical ratio of the confirming ion’s response to the
quantification ion’s response.
3. In the Window Type list, select Absolute or Relative as the calculation approach for
determining the acceptable ion ratio range.
4. In the Window (+/-%) box, select the acceptable ion ratio range.
5. In the Ion Coelution box, select the maximum difference in retention time between a
confirming ion peak and the quantification ion peak.
In the following example
• The target ratio is expected to be 61.02% and the window is Absolute 20%, so the
acceptable window for this confirming ion 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 38. Ratios page
Table 32. Ratios page parameters
Parameter
Description
Enable
Makes the ion ratio criteria available.
Target Ratio (%)
The theoretical ratio of the confirming ion’s response to the quantification ion’s response.
Window Type
The absolute or relative calculation approach for determining the acceptable ion ratio range.
Window (+/-%)
The acceptable ion ratio range.
Ion Coelution (min)
The maximum difference in retention time between a confirming ion peak and the
quantification ion peak.
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.
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 133.
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 “Peak Display Panes” on
page 358.
Figure 39. Calibration page
Table 33. Calibration page parameters (Sheet 1 of 2)
Parameter
Description
RT
Retention time. The time after injection when the compound elutes. The total time that the
compound is retained on the column.
Compound
The compound name.
Compound Type
Displays the compound type as a Target Compound, Internal Standard, Surrogate,
MSTune, Native, or Breakdown.
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Table 33. Calibration page parameters (Sheet 2 of 2)
Parameter
Description
Standard Type
Specifies Internal or External standards.
Response Via
The use of area or height.
Curve Type
Specifies Linear, Quadratic, or AverageRF curve types.
Origin
The origin treatment as Ignore, Include, or Force. The Origin and Weighting columns are
active only when you are using Linear or Quadratic curve types.
Weighting
Specifies the weighting as Equal, 1/X, 1/X^2, 1/Y, or 1/Y^2.
Units
The units to be displayed with the calculated values.
ISTD
The internal standard (ISTD) for a target compound or surrogate when the standard type is
set to Internal. When you set the standard type to External, this field is inactive. The list
displays all compounds with the compound type of Internal Standard.
Amount
The amount of the internal standard for ISTD compounds.
Shortcut menu
The Calibration page uses a right-click shortcut menu. See “Using the Shortcut Menu
Commands” on page 181.
Calibration Levels
On the Calibration levels page (see “Calibration Levels page” on page 175) 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 176.
 To specify calibration levels and concentrations
1. Select the compound whose calibration levels and concentrations that 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.
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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.
Figure 40. Calibration Levels page
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Table 34. Calibration levels page parameters
Parameter
Description
RT
Retention time. The time after injection when the compound elutes. The total time that
the compound is retained on the column.
Compound
The compound name.
Cal1-Caln
User-defined calibration levels for the compound.
Manage Calibration Levels Defines values for each of the calibration level values for the selected compound.
Shortcut menu
The Calibration Levels page uses a right-click shortcut menu. See “Using the Shortcut
Menu Commands” on page 181.
QC Levels
Use the QC levels page (see “QC Levels page”) for a master method to define the standards
for QC levels. You can edit QC levels for master methods only. The contents of this page are
read-only when you are editing a local method. For detailed descriptions of all the features on
the QC Levels page, see “QC levels page parameters.”
 To specify QC levels and concentrations
1. Select the compound whose QC levels, percentage test values, and concentrations that
you want to define.
2. In the QC Levels area, type a name for the first QC level.
The TraceFinder application adds a new, empty QC level row beneath the edited row.
3. Type a value for the % Test.
The % Test is the acceptable difference (as a percentage) between the known amount and
the calculated (measured) amount of each QC level.
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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 41. QC Levels page
Table 35. QC levels page parameters
Parameter
Description
RT
Retention time. The time after injection when the compound elutes. The total time that the
compound is retained on the column.
Compound
The compound name.
QC1-QCn
User-defined quality control levels for the compound.
QC levels
Level
User-defined quality control level names.
% Test
A value for the acceptable difference (as a percentage) between the known amount and
calculated (measured) amount of each QC level.
Shortcut menu
The QC Levels page uses a right-click shortcut menu. See “Using the Shortcut Menu
Commands” on page 181.
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Real Time Viewer
Use the Real Time Viewer page to specify which traces display in the real-time status pane
when you perform acquisition in the Acquisition mode or when you acquire a development
batch in the Method Development mode. See “Real-Time Display” on page 279.
Figure 42. Real Time Viewer page
Table 36. Real Time Viewer page parameters (Sheet 1 of 2)
Parameter
Description
Show Quan Peaks
Only
Displays only quantitative peaks in the compounds list. Quantitative peaks are indicated
with a black dot in the Quan Peak column.
Displayable Traces
Quan Peak
Checks indicate quantitative peak traces. Unchecked traces indicate confirming ion peaks.
Compound Name
Names of all compounds in the method.
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Table 36. Real Time Viewer page parameters (Sheet 2 of 2)
Parameter
Description
Trace
Lists the simple mass or precursor mass for all traces—both quantitative peak and
confirming ion peak—for each compound.
Moves the selected trace to the Traces to Display in Real Time Viewer pane.
Moves the selected trace to the Displayable Traces pane.
Moves all traces to the Displayable Traces pane.
To move multiple traces to the Traces to Display... pane, hold down the SHIFT key, select
multiple traces, and then click
.
Traces to Display in
Real Time Viewer (0/25)
List the traces to be displayed and the display order in the real-time viewer in the
Acquisition mode. Maximum number of traces is 25.
Move to Top
Moves the selected trace to the top of the Traces to Display... list and the second position in
the real-time display. The TIC is always the first position in the real-time display.
Move Up
Moves the selected trace up one position in the list.
Move Down
Moves the selected trace down one position in the list.
Move to Bottom
Moves the selected trace to the bottom of the list.
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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 37. 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 37. 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 data store. When
CDS
the compound already exists in the compound data store, the
TraceFinder application updates the compound data store with
the current compound information.
This command is available only on the Detection page shortcut
menu when the Compound Datastore is enabled. See “Enabling
Optional Features” on page 88.
Add All Compounds to
CDS
Adds all compounds in the current method to the compound
data store. When any of these compounds already exist in the
compound data store, the TraceFinder application updates the
compound data store with the current compound information.
This command is available only on the Detection page shortcut
menu when the Compound Datastore is enabled. See “Enabling
Optional Features” on page 88.
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Editing the QAQC Page
Use the QAQC page to set limits and ranges so that the TraceFinder application can review
the data and results as an aid to final approval.
From the QAQC page of the Master Method View, you can access these additional pages:
• Limits
• Calibration
• Chk Std
• Breakdown
• Matrix Blank
• ISTD
• Solvent Blank
• Surrogate
• Lab Control
• Meth Val
• Matrix Spike
• Tune
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Limits
Use the Limits page to define levels of review for quantified results. Quantified results appear
on printed and electronic reports. You can also define when a quantified value is reported
instead of reporting less than a particular limit.
Figure 43. Limits page
Table 38. Limits page parameters
Parameter
Description
RT
Retention time. The time after injection when the compound elutes. The total time that the
compound is retained on the column.
Compound
The compound name.
LOD
(Detection Limit)
Limit of detection. The lowest amount that can be detected. Usually derived from a method
detection limit (mdl) study.
LOQ
(Quantitation Limit)
Limit of quantitation. The lowest amount that can be confidently and accurately
quantitated. This is usually the lowest calibration amount.
LOR
Limit of reporting. Also called cutoff in some industries. This is the lowest amount that can
be reported, as determined by each laboratory’s standard operating practices.
ULOL
(Linearity Limit)
Upper limit of linearity. This is usually the highest calibrator amount.
Carryover Limit
The highest amount of a substance that does not leave a residual amount in the instrument.
If a substance has a carryover limit of 5, amounts higher than 5 usually dirty the instrument
and leave residue behind, tainting the following sample. A carryover limit of less than 5 does
not leave any residual amounts of the substance.
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Calibration
Use the Calibration page to define acceptable criteria for initial calibration. The TraceFinder
application 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 44. Calibration page
Table 39. Calibration page parameters
Parameter
Description
RT
Retention time. The time after injection when the compound elutes. The total time that the
compound is retained on the column.
Compound
The compound name.
R^2 Threshold
The minimum correlation coefficient (r2) for an acceptable calibration (when in linear or
quadratic mode).
Max RSD (%)
The maximum relative standard deviation (RSD) for an acceptable calibration (when in
average RF mode).
Min RF
The minimum average response factor (RF) for an acceptable calibration (when in average
RF mode).
Max Amt Diff (%)
The maximum deviation between the calculated and theoretical concentrations of the
calibration curve data points (when in linear or quadratic mode).
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Chk Std
Use the Chk Std page to review the calibration on an ongoing basis. The TraceFinder
application makes the evaluation by comparing the quality check standard results for each
compound in the sample to the initial calibration using values defined on this page.
On the Check Standard report, the TraceFinder application flags the calculated values for
internal standard compounds that exceed these limits.
For linear and quadratic modes, the maximum difference for the calculated concentration in
the Chk Std sample versus the theoretical value is set on the QC Levels page of the
Compounds page.
Figure 45. Chk Std page
Table 40. Chk Std 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.
Max RF Diff (%)
The maximum deviation between the response factor (RF) of the
Chk Std sample and the average response factor from the
calibration (when in average RF mode).
Min RF
The minimum response factor for the Chk Std sample (when in
average RF mode).
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Breakdown
Use the Breakdown page to view and edit values used for the evaluation of breakdown and
degradation reporting. The TraceFinder application makes the evaluation by calculating the
ratio of breakdown compounds to the native compounds.
 To display the list of compounds in a group
Click anywhere in the group row.
 To select a group for breakdown calculation
Select the Active check box in the group row.
You can select any group in the method for breakdown calculation, but the application
calculates and reports only those that contain breakdown and native compounds.
Figure 46. Breakdown page
Table 41. Breakdown page parameters
Parameter
Description
Groups
Lists all groups created on the Groups page. See “Editing the
Groups Page” on page 200.
Active
Specifies which groups are used for analysis.
Max % Breakdown
The maximum allowable percentage of breakdown to native
compounds. This value is calculated by summing the responses of
the breakdown compounds and dividing them by the sum of the
native compounds.
On the Breakdown Report, the application flags the calculated
values for breakdown and native compounds that exceed these
limits.
Compounds for Group Lists all compounds in the selected group.
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Matrix Blank
Use the Matrix Blank page to define acceptable levels of target compounds in blank samples.
The TraceFinder application makes the evaluation by comparing the calculated concentration
for each compound in the sample to the maximum concentration defined on this page. You
can enter the maximum concentration as a percentage of a flag value or as a specified value.
For detailed descriptions of all the features on the Matrix Blank page, see Matrix Blank page
parameters.
On the Matrix Blank report, the application flags the calculated values for target compounds
that exceed these limits.
 To specify the maximum concentration as a percentage
1. From the Method column list, select one of the following methods:
• % of LOD
• % of LOQ
• % of LOR
2. In the Percentage column, type a percentage value.
 To specify the maximum concentration
1. From the Method column list, select Concentration.
2. In the Max Conc column, type an absolute value.
Figure 47. Matrix Blank page
Table 42. Matrix Blank page parameters (Sheet 1 of 2)
Parameter
Description
RT
Retention time. The time after injection when the compound elutes. The total time that the
compound is retained on the column.
Compound
The compound name.
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.
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Table 42. Matrix Blank page parameters (Sheet 2 of 2)
Parameter
Description
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 48. ISTD page
Table 43. 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 (%)
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The minimum and maximum drift (in minutes) for the internal standards to define an
acceptable range. For check standards, the TraceFinder application compares the retention time
of each internal standard in each sample to a range around the average of the retention times of
that compound in all of the calibration standards. For all other samples, the application
calculates the comparison range around the check standard retention times if a check standard
is available in the batch. If no check standard is available, the application tests against the initial
calibration.
Coefficient of Variance test. The coefficient of variance percentage is the standard deviation of
the multiple samples of one level, multiplied by 100, and then divided by the average of the
multiple samples of that level. This calculation is based on the areas of the peaks.
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Solvent Blank
Use the Solvent Blank page to view or edit QC values for solvent reporting. The application
makes the evaluation by comparing the calculated response for each compound in the sample
to the maximum response defined on this page.
On the Solvent Blank report, the TraceFinder application flags the calculated values for target
compounds that exceed these limits.
Figure 49. Solvent Blank page
Table 44. 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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Surrogate
Use the Surrogate page to view or edit values for surrogate recovery reporting. The application
makes the evaluation by comparing the calculated concentration for each compound in the
sample to the theoretical concentration and range defined on this page.
You can use these parameters to evaluate the performance of your method. For this evaluation,
prepare, analyze, and evaluate a number of samples (typically 4 to 10) to document method
accuracy and precision as a comprehensive whole.
On the Surrogate Recovery report, the application flags the calculated values for method
validation compounds that exceed these limits.
Figure 50. Surrogate page
Table 45. Surrogate 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.
Theo Conc
Values for the compounds that represent the expected theoretical
concentration of that compound in the sample.
Min Recovery (%)
A range of the allowable minimum recovery percentage and the
maximum recovery percentage that the application can determine
by comparing the observed calculated concentration in the analysis
to the expected concentration. Each method validation compound
can have its own values for these fields, independent of other
method validation compounds.
Max Recovery (%)
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Lab Control
Use the Lab Control page to view and edit QC values for lab control sample (LCS) and lab
control sample duplicate (LCSD) analyses. The application makes the evaluation by
comparing the calculated concentration for each compound in the sample to the theoretical
concentration and range defined on this page.
You can prepare samples (typically known as clean matrices) as LCS or LCSD. These
represent samples where you have added known concentrations of target analytes. To define
an LCS and its duplicate in a batch, select the appropriate sample type and a common
sample ID.
On the Lab Control report, the application flags the calculated values for spiked compounds
that exceed these limits.
Figure 51. Lab Control page
Table 46. Lab Control 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.
Theo Conc
Values for the lab control compounds that represent the expected theoretical concentration of
that compound in the sample.
Min Recovery (%)
Max Recovery (%)
A range of the allowable minimum recovery percentage and the maximum recovery percentage
that the application can determine by comparing the observed calculated concentration in the
analysis to the expected concentration. Each LCS or LCSD compound can have its own values
for these fields, independent of other LCS or LCSD compounds.
Max RPD
Specifies a maximum value for relative percent difference (RPD) between two spiked samples.
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Meth Val
Use the Meth Val page to view or edit QC values for method validation reporting. The
application makes the evaluation by comparing the calculated concentration for each
compound in the sample to the theoretical concentration and range defined on this page.
You can use these parameters to evaluate the performance of your method. For this evaluation,
prepare, analyze, and evaluate a number of samples (typically four to 10) to document
method accuracy and precision as a comprehensive whole. To define a method validation
sample in the batch, select the appropriate sample type.
On the Method Validation report, the application flags the calculated values for method
validation compounds that exceed these limits.
Figure 52. Meth Val page
Table 47. Meth Val page parameters
Parameter
Description
RT
Compound
Theo Conc
Retention time for the compound.
The compound name.
Values for the compounds that represent the expected theoretical concentration of that
compound in the sample.
A range of the allowable minimum recovery percentage and the maximum recovery
percentage that the application can determine by comparing the observed calculated
concentration in the analysis to the expected concentration. Each method validation
compound can have its own values for these fields, independent of other method validation
compounds.
The maximum relative standard deviation of the set of observed concentrations for a
component across the set of method validation samples.
Min Recovery (%)
Max Recovery (%)
Max RSD (%)
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Matrix Spike
Use the Matrix Spike page to view or edit QC values for matrix spike and matrix spike
duplicate analyses. The application makes the evaluation by comparing the calculated
concentration for each compound in the sample (after subtracting the original sample value)
to the theoretical concentration and range defined on this page.
To evaluate matrix spike or matrix spike duplicate compounds, prepare samples as MS or
MSD. These represent samples where you have added known concentrations of target
analytes. To define a sample, its MS, and its MSD in the batch, select the appropriate Sample
Type and a Sample ID.
Sample IDs must be unique. Duplicating Sample IDs can cause incorrect samples to be
included in reports.
On the MS/MSD report, the application flags the calculated values for spiked compounds
that exceed these limits.
Figure 53. Matrix Spike page
Table 48. Matrix Spike 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.
Theo Conc
Values for the matrix spike compounds that represent the expected theoretical concentration
of that compound in the sample. You can apply or not apply the dilution factor for a sample
to the calculated matrix spike concentrations.
Min Recovery (%)
Max Recovery (%)
A range of the allowable minimum recovery percentage and the maximum recovery
percentage that can be determined by comparing the observed calculated concentration in
the analysis to the expected concentration. Each matrix spike sample can have its own values
for these fields, independent of other matrix spike samples.
Max RPD
Specify a maximum value for relative percent difference (RPD) between two spiked samples.
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Tune
Use the Tune page (see “Tune page” on page 199) to specify mass spectral comparison criteria
according to Environmental Protection Agency (EPA) tune methods. Your master method
must include one (and only one) compound specified as an MSTune compound type. The
QAQC evaluation compares the mass list of the compound to the values in the tune method.
An MSTune sample contains Decafluorotriphenylphosphine (DFTPP) or
bromofluorobenzene (BFB) and is handled differently from other samples in the master
method. The TraceFinder application handles it as a qualitative examination of the mass
spectrum of a specific compound rather than evaluates it on a quantitative basis.
Follow these procedures:
• To select an EPA tune method
• To manually submit a mass spectrum for tune evaluation
 To select an EPA tune method
1. Choose a method from the Method list.
• For some methods, the Use Only Selected Method option is available.
• For some methods, the Perform Background Subtraction option is available.
The application displays the mass spectral reference for the selected method.
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2. (Optional) Select the Use Only Selected Method check box.
The application uses only the specified EPA tune method for tune criteria testing.
If this option is not selected and the tune spectrum fails against the specified tune criteria,
the application performs the comparison against other EPA tune method criteria. The
Tune report displays the pass/fail status of the tune spectra against all methods used for
comparison.
3. (Optional) Select the Perform Background Subtraction check box.
• The 8000 and CLP series methods require background subtraction.
• The 500 and 600 series do not require background subtraction but you can choose to
use it.
The Tune report displays the retention time and scan range of the spectrum.
4. (Optional) Click Max Stepoff to select a number or type a number in the box.
The Max Stepoff field defines the maximum number of scans as the range before and
after the Tune compound peak that is to be used for background subtraction. For
example, a maximum stepoff of 1 means that the background spectrum is taken one scan
before the left edge of the tune peak or one scan after the right edge of the tune peak. If
using the left edge background spectrum fails the tune test, the system automatically tries
the right edge of the spectrum. A maximum stepoff of 2 means trying up to four tests
using four different background spectrum: two scans before the left edge, one scan before
the left edge, one scan after the right edge, and two scans after the right edge. EPA
guidelines assign a maximum stepoff value of 20.
Note This Max Stepoff value is not related to the Stepoff Value parameter on the
General page of the master method. The Stepoff Value on the General page applies
only to the reference spectrum set for the master method and does not affect the Tune
method.
 To manually submit a mass spectrum for tune evaluation
1. Click Select File and Mass Spectrum.
2. In the browser, select a raw data file and click Open.
The Thermo Xcalibur Qual Browser opens.
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Figure 54. Thermo Xcalibur Qual Browser
3. In the Qual Browser, do the following:
a. Select the tune compound peak that you want to use.
b. Select the background subtraction parameters to use, and generate the mass
spectrum.
For detailed instructions, refer to the Qual Browser documentation.
c. When the process is complete, choose View > Spectrum List.
d. Right-click the spectrum list and choose Export > Clipboard.
e. On the TraceFinder Tune page, click Create Tune Report as PDF.
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Figure 55. Tune page
Table 49. Tune page parameters
Parameter
Description
Tune parameter
Tune Compound
Compound specified as a tune compound on the Identification page. See “Identification”
on page 133.
Method
Environmental Protection Agency (EPA) methods used for tuning.
Use Only Selected
Method
Specifies that the application use only the specified EPA tune method for tune criteria
testing.
Perform Background
Subtraction
Specifies that the application average and subtract the mass spectra as specified in the
background subtraction settings on the General page for the master method. See “To set
automated background subtraction options” on page 123.
Max Stepoff
Specifies the maximum number of scans as the range before and after the Tune compound
peak to be used for background subtraction.
Ad Hoc Tune Report
Select File and Mass
Spectrum
Opens a browser where you can select a raw data file to use for the tune report.
Create Tune Report as
PDF
Creates an ad hoc tune report using the mass spectrum data saved to the Clipboard.
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Editing the Groups Page
Use the Groups page of the Master Method View (see “Groups page”) 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 create a group
1. From the Show list, select the type of compounds that you want to view.
2. At the bottom of the Groups area, click Add Group.
The Add a New Group dialog box opens.
3. Type a name for the new group and click OK.
The new group appears in the Groups area.
4. Drag a compound from the Compounds area onto a group name (as if you were moving
files into a folder).
5. To remove all the compounds from a group, rename the group, or delete it, right-click the
group name and choose from the shortcut menu.
6. To remove a single compound, right-click the compound name in the group and choose
Remove from Group from the shortcut menu.
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Figure 56. Groups page
Table 50. Groups page parameters
Parameter
Description
Compounds
Lists all available compounds.
Groups
Lists all available groups.
Add Group
Opens the Add a New Group dialog box where you can create a
new group.
Shortcut menu
Thermo Scientific
Empty Group
Removes all compounds from the selected group.
Rename Group
Changes the name of the selected group.
Delete Group
Removes the selected group and all the compounds in it.
Remove From Group
Removes the selected compound from its group.
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Editing the Reports Page
Use the Reports page to specify how you want to save or print your reports. For detailed
descriptions of the features on the Reports page, see “Reports page parameters.”
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 target screening 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 Settings page.
This section includes instructions for the following tasks:
• Specifying Report Formats
• Specifying Quan Report Settings
• Specifying Target Screening Settings
Specifying Report Formats
• For each standard report, you can create a hardcopy printout, a PDF file, or an XML file.
• For each custom report, you can create a hardcopy printout or an Excel Macro-Enabled
Workbook (.xlsm) file.
• For each target screening report, you can create a hardcopy printout or a PDF file.
In addition to the report type, you can specify a report description for each of your reports.
The default report description is the report name.
 To specify report types and output formats
1. Click the Reports tab.
The Reports page displays the following columns for all configured reports:
• Example: Click the magnifying glass icon to open an example PDF of the report type
• Report Name, Report Description, and Report Type
• For standard report types: Options to create a hardcopy, PDF file, or XML file
• For custom report types: Options to create a hardcopy or Excel Macro-Enabled
Workbook file
• For target screening report types: Options to create a hardcopy or PDF file
• Batch Level: Option that indicates which reports are batch-level reports
For information about configuring which reports are available when you create a master
method or which reports create a batch-level report, see “Specifying the Reports
Configuration” on page 68.
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2. To edit the Report Description, double-click the name and type your new description.
The TraceFinder application uses this description for all reports that use this master
method. You cannot edit the Report Description from other report views.
3. To specify the type of report output to create for each report type, select the check box in
the appropriate column.
4. To duplicate the output type for all reports, click the cell to select it, and then right-click
and choose Copy Down from the shortcut menu.
All check boxes in the column below the selected cell duplicate the selected or cleared
state of the selected cell. This action applies only to reports where this output format is
available.
By default, all report types are cleared.
Figure 57. Reports page
Table 51. Reports page parameters (Sheet 1 of 2)
Parameter
Description
Example
Opens a PDF that displays an example of the report type.
Report Name
The name of a report.
Report Description
The user-defined description to be used on a report.
Report Type
The type of report: Standard, Custom, or Target Screening.
Print
Sends reports to the printer.
Create PDF
Saves reports as PDF files.
Available only for standard and target screening reports.
Create XML
Exports reports in XML format.
Available only for standard reports.
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Table 51. Reports page parameters (Sheet 2 of 2)
Parameter
Description
Create XLSM
Exports reports in Excel Macro-Enabled Workbook (.xlsm) format.
Available only for custom reports.
Batch Level
Rather than creating separate reports for each sample, the application uses a composite of
the data from all the appropriate samples to create a single report for the entire batch.
Batch-level reports are prepended with a B to differentiate them.
You cannot select this option from the Reports page. You must select the Batch Level option
for the report in the report configuration. See “Specifying the Reports Configuration” on
page 68.
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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 correct surrogates
• 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 183.
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.”
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 To correct surrogates
Select the Correct Surrogates check box.
The TraceFinder application applies the conversion factor (specified in the sample row in
the batch) to the sample’s calculated concentrations for surrogates as the conversion factor
is applied to target compounds.
 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 58. Quan Report Settings page
Table 52. Quan Report Settings page parameters (Sheet 1 of 2)
Parameter
Description
Quan Limits Flags
Report Concentration
Reports the concentration at all times or only when the quantified value exceeds either the
limit of detection (LOD), the limit of quantitation (LOQ), or the limit of reporting (LOR).
Report concentration: Always, >LOD, >LOQ, or >LOR.
Decimal Places to be
Reported
Number of decimal places to be included in the report. Maximum value is 6.
Show Chromatogram
on Quantitation
Report
Displays a chromatogram (TIC trace) of the sample on the quantitation report.
Display Compounds
Above Set Limit
Prints only the positive compounds in a sample. If a compound is above the specified Quan
Flag Options limits, the TraceFinder application reports the compound.
User Interface Options
Shade Row When
Sample is Outside of
Evaluation Criteria
Shades a compound row on any of the reports if a value fails one of the criteria used for
evaluation.
Separate Ion Overlay
Display
Separates the ion overlay pane from the confirming ion plots in 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 52. 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.
Surrogate Correction Option
Correct Surrogates
Applies the conversion factor (specified in the sample row in the batch) to the sample’s
calculated concentrations for surrogates as the conversion factor is applied to target
compounds. For example, if you added surrogates to the sample as part of sample
preparation and you require a dilution for analysis, the TraceFinder application dilutes the
surrogates and target compounds and applies a dilution correction to correct for this
dilution. However, if you added surrogates after a dilution has occurred, then you can leave
the option cleared so that, while the target compounds are corrected for the dilution, the
surrogates are reported “as is.”
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 Settings
Use the options on the Target Screening Settings page to set the parameters required to
produce Target Screening reports. For detailed descriptions of the features on the Target
Screening Settings page, see “Target Screening Settings page parameters” on page 213.
The TraceFinder application uses these parameters to process a raw data file and create a
report similar to a ToxID report. See “Example Target Screening Summary Report” on
page 215.
Follow these procedures:
• To specify the default parameters
• To calculate and report semi-quantitative results
• To specify the ion ratio calculation method
• To specify the exact mass window
• To specify the Exactive parameters
 To specify the default parameters
1. Click the Processing Configuration File browse button and select a configuration file
(.csv).
2. From the Screening Method list, select one of these compound screening methods.
• (Default) Auto Detect
• Based on Full MS2 scans
• Based on SRM and MS2 scans
• Based on MS2 and MS3 scans
• Based on MS3 scans
• Based on accurate mass scans
• Based on SRM scans
• Based on Exactive screening method
3. Type the name of the company to print on the report.
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4. Type the name of the laboratory to print on the report.
5. Click the Company Logo browse button and select a graphic file (.jpg, .gif, or .bmp) to
print on the report.
6. In the m/z Window box, enter a value for the window above and below the m/z value for
the compounds.
7. In the RT Window box, enter a value for the window above and below the retention time
value for the compounds.
8. In the MS2 Search Library boxes, type the names of as many as three search libraries for
searching MS/MS spectra.
9. In the MS3 Search Library boxes, type the names of as many as three search libraries for
searching MS3 spectra.
10. Select the Use Full MS Scan to Confirm check box if you want to confirm library search
results with parent ion peak detection in the full scan.
When the application does not detect a peak in the full scan, the compound is not
reported as a hit.
 To calculate and report semi-quantitative results
1. In the Semi Quantitative area, do the following:
a. Select the Report Semi-Quantitative Result check box.
b. Type the measurement units.
The measurement units are used only for labeling purposes.
2. Select either the Scan Intensity or Peak Area option.
• Scan Intensity: The application measures the intensity of the MS/MS peak without
performing background subtraction.
• Peak Area: The application measures the peak area of the reconstructed full-scan
chromatogram peak of the parent ion. When you select Peak Area, the Use Full MS
Scan to Confirm check box is automatically selected.
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 To specify the ion ratio calculation method
1. Select the Use Scan at Peak Apex or Use Average Scan option.
• Use Scan at Peak Apex: The application calculates the ion ratio based on the peak
apex scan spectrum.
• Use Average Scan: The application calculates the ion ratio based on the average scan
spectrum over the range of the peak’s half height. The relative intensity in the
configuration file must use the selected scan method.
2. In the Ion Ratio Window (%) box, type the acceptable percentage of the intensity of the
qualifier ion to the 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.
2. To search the entire raw data file for the specified peak, do the following:
a. Select the No Specified Retention Time check box.
b. Select either the First Peak or Highest Peak option.
When the search finds more than one m/z match in the raw data file, the application
uses the specified peak for processing.
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3. Select the Report All Compounds Listed in Configuration File check box to report all
compounds in the configuration file whether or not matches are found for them.
The default reports on only those compounds where matches are found in the raw data
file. This option applies to the Exactive™ experiment only.
Figure 59. Target Screening Settings page
Table 53. Target Screening Settings page parameters (Sheet 1 of 2)
Parameter
Description
Processing
Configuration File
Specifies a configuration file (.csv).
Screening Method
Specifies one of the following screening methods:
• (Default) Auto Detect
• Based on Full MS2 scans
• Based on SRM and MS2 scans
• Based on MS2 and MS3 scans
• Based on MS3 scans
• Based on accurate mass scans
• Based on SRM scans
• Based on Exactive screening method
Note Using the Auto Detect method, the ToxID application can identify the screening
experiment implemented in the acquired data file.
Company Name
Specifies the name of the company to print on the report.
Laboratory Name
Specifies the name of the laboratory to print on the report.
Company Logo
Specifies a graphic file (.jpg, .gif, or .bmp) to print on the report.
m/z Window (mu)
Specifies a value for the window above and below the m/z value for the compounds.
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Table 53. Target Screening Settings page parameters (Sheet 2 of 2)
Parameter
Description
RT Window (min)
Specifies a value for the window above and below the retention time value for the
compounds.
MS2 Search Library
Specifies the names of as many as three search libraries for searching MS/MS spectra.
MS3 Search Library
Specifies the names of as many as three search libraries for searching MS3 spectra.
Use Full MS Scan to
Confirm
Specifies that the application confirms library search results with parent ion peak detection
in the full scan. When the application does not detect a peak in the full scan, the compound
is not reported as a hit.
Semi Quantitative
Report
Semi-Quantitative
Result
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(%)
Accurate Mass Experiment
Exact Mass Window
Specifies a value in parts per million for the accurate mass experiment.
Exactive
Adduct 1–n
Specifies the adducts listed in and applied throughout the configuration file. Adducts are
polarity sensitive. For negative ionization, enter negative adduct values.
Defaults: Adduct 1: H+, Adduct 2: NH4+, and Adduct 3: Na+
No Specified Retention Specifies either First Peak or Highest Peak to use for processing when the search finds more
Time
than one m/z match in the raw data file.
Report All Compounds Specifies that in an Exactive experiment, the application reports all compounds in the
Listed in Configuration configuration file whether or not matches are found for them.
File
Default: Reports only those compounds where matches are found in the raw data file.
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Figure 60. Example Target Screening Summary Report
Your Company Name
Summary Report
Raw File Name: C:\Xcalibur\examples\ToxID\Exact_Mass\Exact_Mass_Test.RAW
Config File Name: C:\Xcalibur\examples\ToxID\Exact_Mass\ConfigFile_Exact_mass.csv
Sample Name:
Laboratory: Your Lab Name
Acquistion Start Time: 3/24/2008 4:46:43 PM
Screening Conditions: Based on accurate mass scans. Exact mass window (ppm): 30, RT window(min): 0.50.
Peak 1
50
Peak 2
NL: 2.03E5
m/z= 240.15580-240.16300
F: FTMS + c ESI Full ms
[120.00-1000.00]
2.58
2.52
100
1.99 2.39
0
100
2.84 4.16
4.66
NL: 1.26E7
m/z= 250.17665-250.18415
F: FTMS + c ESI Full ms
[120.00-1000.00]
4.69
50
Peak 3
4.82
5.19
4.06
0
100
7.68
9.47
NL: 1.18E7
m/z= 278.18643-278.19477
F: FTMS + c ESI Full ms
[120.00-1000.00]
50
Peak 4
1.53
0
100
4.12
3.57
50
Peak 5
0
100
3.49
3.13
0.87
5.36
10.15
NL: 2.12E6
m/z= 328.14938-328.15922
F: FTMS + c ESI Full ms
[120.00-1000.00]
3.80
4.18
12.50
50
Peak 6
0
100
3.98
4.33
11.50
50
0
Peak
Number
Thermo Scientific
Compound Name
3.72
2
NL: 4.59E6
m/z= 342.16507-342.17533
F: FTMS + c ESI Full ms
[120.00-1000.00]
NL: 9.08E6
m/z= 337.20734-337.21746
F: FTMS + c ESI Full ms
[120.00-1000.00]
4.12
4
6
Time (min)
Expected Detected
m/z
m/z
8
10
Delta
(mDa)
12
Delta
(ppm)
Expected Actual RT
RT
Intensity
1
Albuterol
240.15940 240.15939
-0.0
-0.0
2.58
2.58
199505
2
Alprenolol
250.18040 250.18039
-0.0
-0.0
4.50
4.66
12604499
3
Amitriptyline
278.19060 278.19061
0.0
0.0
5.00
5.19
11769755
4
6-Acetylmorphine
328.15430 328.15433
0.0
0.1
3.30
3.57
2112090
5
6-Acetylcodeine
342.17020 342.17035
0.1
0.4
4.10
4.18
4593306
6
Acebutolol
337.21240 337.21246
0.1
0.2
3.80
3.98
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Creating a Method Template
In the TraceFinder application, you can create a processing method using a method template
that contains common settings.
Follow these procedures:
• To open the Method Template Editor
• To specify peak criteria
• To identify the peaks
• To specify confirming ions
• To calibrate the compounds
• To enter a note for the method
• To save the method template
 To open the Method Template Editor
1. Click Method Development from the dashboard or the navigation pane.
The Method Development navigation pane opens.
2. Click Method View in the navigation pane.
3. From the main menu, choose File > New > Method Template.
The Method Template Editor opens. For a complete description of the Method Template
Editor, see “Method Template Editor dialog box” on page 222.
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 To specify peak criteria
1. In the Find the Peaks area, select a sensitivity level.
In selecting the degree of sensitivity, you define how extensively the peak detector
algorithm searches for low-level peaks.
• The Genesis peak detection algorithm is provided for backward compatibility with
Xcalibur 1.0 studies.
• The ICIS peak detection algorithm is designed for MS data and has superior peak
detection efficiency at low MS signal levels.
• The Avalon peak detection algorithm is designed for integrating UV/Vis and analog
chromatograms.
2. To look for peaks only in a certain range of the entire chromatogram, select the Limit the
Retention Time Range check box and specify a retention time (RT) range.
3. To indicate whether to select peaks by relative height or area and the percentage of the
highest peak that results in compound selection, select the Enable Peak Threshold check
box.
To consider a peak for a processing method, the TraceFinder application uses the Enable
Peak Threshold filter to determine which peaks meet the specified percentage of the
largest peak.
4. To display a specific number of the largest peaks by height or area, select the Only Select
Top Peaks check box and enter the number of peaks to display.
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 To identify the peaks
1. In the Use these Libraries box, select the libraries 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. 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, all weighting values are unavailable except for Equal.
• Quadratic: All other settings are available with this exception: When you select
Include in the Origin list, all weighting values are unavailable except for Equal.
• Average RF: No selections in the Weighting or Origin lists are available. The
Weighting list is set to Equal, and the Origin list is set to Ignore.
3. From the Origin list, select one of the following:
• Ignore: Specifies that the origin is not included as a valid point in the calibration
curve when the curve is generated. When you select Ignore, the calibration curve
might or might not pass through the origin.
• Force: Specifies that the calibration curve passes through the origin of the data point
plot when the calibration curve is generated.
• Include: Specifies that the origin is included as a single data point in the calculation
of the calibration curve. When you select Include, the calibration curve might or
might not pass through the origin.
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4. From the Weighting list, select one of the following:
• Equal: Specifies that the origin is included as a single data point in the calculation of
the calibration curve. When you select Equal, the calibration curve might or might
not pass through the origin.
• 1/X: Specifies a weighting of 1/X for all calibration data points during the
least-squares regression calculation of the calibration curve. Calibrants are weighted
by the inverse of their quantity.
• 1/X^2: Specifies a weighting of 1/X^2 for all calibration data points during the
least-squares regression calculation of the calibration curve. Calibrants are weighted
by the inverse of the square of their quantity.
• 1/Y: Specifies a weighting of 1/Y for all calibration data points during the
least-squares regression calculation of the calibration curve. Calibrants are weighted
by the inverse of their response (or response ratio).
• 1/Y^2: Specifies a weighting of 1/Y^2 for all calibration data points during the
least-squares regression calculation of the calibration curve. Calibrants are weighted
by the inverse of the square of their response (or response ratio).
5. From the Response Via list, select Area or Height.
• Area: Specifies that the TraceFinder application use this area value in response
calculations.
• Height: Specifies that the application use this height value in response calculations.
 To specify qualitative peak processing
1. Select the Use Genesis Algorithm for Qual Processing check box and specify a value for
internal standard matching.
The application uses the Genesis algorithm to match internal standards in a range
plus/minus the value that you specify. For additional information about the Genesis
algorithm, see “Genesis Detection Method” on page 78.
This parameter is available only when the Sensitivity parameter in the Find the Peaks area
is set to ICIS.
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.
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3. To process samples that include data-dependent scans, select the Use Data Dependent
Scans check box.
When you process a sample using this feature, the application uses the TIC trace to find
all data-dependent full scans, lists them, and performs a library search against the
data-dependent MS/MS or MSn scan.
In addition to the peak information, the TIC Report and TIC Summary Report display
information about the data-dependent filtered data. See Appendix A, “Reports.”
 To enter a note for the method
Type in the Notes box, or paste text from another application using CTRL+V.
You can add a note to your method template to explain what makes this template unique.
 To save the method template
1. Choose File > Save from the Method Template Editor menu.
The Save Method Template dialog box opens.
2. Do one of the following:
Type a new name for the master method and click OK.
–or–
Select a method name to overwrite and click Overwrite.
The TraceFinder application saves the new method template in the following folder:
…\Thermo\TraceFinder\2.1\EFS\Templates\Methods
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Figure 61. Method Template Editor dialog box
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Table 54. 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.
Specify Default Ion
Ratio Ranges
Enables the ion ratio range features.
This value defaults to 2 because you typically perform a 3-ion experiment with one
quantitation mass and two confirming ions.
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 54. 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.
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Table 54. Method Template Editor dialog box parameters (Sheet 3 of 3)
Parameter
Description
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
Defines a range plus/minus the Exclusion Window value that you specify.
Use Data Dependent
Scans
Constrains the Qual Mode view in the Data Review to only data-dependent scan spectra.
See “Qual Mode” on page 375. In addition to the peak information, the TIC Report and
TIC Summary report display information about the data-dependent filtered data.
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Importing Published Master Methods
In the TraceFinder application, you can import published methods to use for detecting,
processing, and reporting. The Tracefinder installation provides the following folder of
published methods:
…\Thermo\TraceFinder\2.1\EFS\Published Master Methods
 To import a published master method
1. From the Method View task pane, click Import Published Method.
The Import Published Method dialog box opens.
2. Select a method to import.
3. Click Import.
The application reports that the method successfully imported and saves the method in
the following folder:
…\Thermo\TraceFinder\2.1\EFS\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 your selected reaction monitoring (SRM) data
to an XML file. The Export SRM Data command is displayed only when you enable the
Compound Datastore option in the Configuration mode. See “Compound Datastore” on
page 92.
 To export SRM data to an XML file
1. Open the master method whose SRM data that you want to export.
2. From the Method View task pane, click Export SRM Data.
The TraceFinder application writes the data in the SRM table to the following file:
…\Thermo\TraceFinder\2.1\EFS\Methods\methodname.xml
The data in this file matches the TSQ .xml data, which you can use in the instrument
method editor of the TSQ application.
Figure 62. SRM TSQ Quantum example
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Working with Instrument Methods
An instrument method is a set of experiment parameters that define the operating settings for
an autosampler, mass spectrometer, and so on. Instrument methods are saved as file
type .meth.
IMPORTANT Do not open the Thermo Foundation Instrument Configuration window
while the TraceFinder application is running.
Follow these procedures:
• To open the Instrument View
• To create a new instrument method
• To create a new multiplexing instrument method
• To open an instrument method
• To import an instrument method
 To open the Instrument View
1. Click Method Development from the dashboard or the navigation pane.
The Method Development navigation pane opens.
2. Click the Instrument View task pane.
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 To create a new instrument method
1. Click New Instrument Method in the Instrument View task pane.
The Thermo Xcalibur Instrument Setup window opens.
Figure 63. 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. Click New Instrument Method in the Instrument View task pane.
The Thermo Xcalibur Instrument Setup window opens.
Figure 64. 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
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 To open an instrument method
1. Click Open Instrument Method on the Instrument View task pane.
An instrument method browser opens.
2. In the browser, 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.
Figure 65. Example instrument setup showing multiple configured instruments
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 To import an instrument method
1. From the Instrument View task pane, click Import Published Method.
The Import Published Method dialog box opens. This dialog box lists the master
methods in the Published Master Methods folder. You can import instrument methods
that are associated with these published master methods.
2. Select a method that includes the instrument method that you want to import.
For instructions about importing the master methods, see “Importing Published Master
Methods” on page 226.
3. Click Import.
The Save Instrument Method dialog box opens.
4. Do one of the following:
Type a new name for the instrument method and click OK.
–or–
Select an instrument method name to overwrite and click Overwrite.
The application reports that the method successfully imported.
You can use any of the Open Instrument Method commands to open this method just as you
would an instrument method that you created.
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Working with Development Batches
In the Development Batch view, you can test your instrument method in real time by creating
and acquiring test samples. Development batches let you test different instrument methods
and optimize parameters, such as MS source parameters and autosampler variables, to find the
best conditions for a master method. Development batches are not designed for high
throughput in everyday analysis.
This section includes instructions for the following tasks:
• Creating a Development Batch
• Editing Samples in a Development Batch
• Acquiring Samples in a Development Batch
Creating a Development Batch
You create a development batch to test your instrument method and use it to acquire samples
only once. You cannot save a development batch; you can save only the raw data files created
when you acquire the samples in the batch.
Follow these procedures:
• To open the Development Batch view
• To specify a location for development batch data
• To add samples to the development batch
• To insert samples into the development batch
• To copy a sample
 To open the Development Batch view
1. Click Method Development from the dashboard or the navigation pane.
The Method Development navigation pane opens.
2. In the Method Development navigation pane, click Development Batch.
The Development Batch view opens a new, empty batch.
Note The Channel column is available only when you have enabled multiplexing in
the Configuration mode. See “Multiplexing” on page 92.
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 To specify a location for development batch data
1. To specify a location for the files, click Select Batch Location in the Development Batch
task pane.
By default, the TraceFinder application writes the temporary files, raw data files, and .sld
method file to the following folder:
…\Thermo\TraceFinder\2.1\EFS\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 file name and choose Rename from the shortcut
menu.
d. Type the name for the folder.
e. Click OK.
The TraceFinder application creates all development batch files in the specified folder.
 To add samples to the development batch
Do one of the following:
Right-click and choose Add Sample from the shortcut menu.
–or–
To add multiple sample rows, enter the number of rows and click the Add Sample icon.
The application adds the specified number of new, empty samples to the end of the
sample list.
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 To insert samples into the development batch
1. Select the sample above which you want to insert empty samples.
2. Do one of the following:
Right-click and choose Insert Sample from the shortcut menu.
–or–
To insert multiple sample rows, enter the number of rows and click the Insert Sample
icon.
The TraceFinder application inserts new, empty samples above the selected sample.
Note You cannot insert samples into an empty batch. You must have at least one
sample to select before you can use this icon.
 To copy a sample
1. Select the sample 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.
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Editing Samples in a Development Batch
A development batch requires fewer parameters than a real batch, but the mechanism for
managing the information is the same.
For detailed instructions about using the Copy Down or Fill Down commands to enter
column values, see Appendix B, “Using Copy Down and Fill Down.”
A development batch uses the same shortcut menu features as a batch in the Batch View. For
detailed descriptions of the right-click shortcut menu features, see “Batch View Shortcut
Menu” on page 307.
Follow these procedures:
• To enter column values
• To resize or reorganize the columns
• To remove selected samples from the list
• To remove all samples from the list
 To enter column values
1. Double-click the Filename column and type a file name for the raw data file.
2. (Optional) Enter values for the Sample Name or Sample ID columns.
3. Enter a vial position for each sample.
4. Enter an injection volume for each sample.
The minimum injection volume value allowed is 0.1 μL; the maximum injection volume
value allowed is 5000 μL.
5. To enter an instrument method for each sample, click the down arrow in the Instrument
Method column and select a method from the list.
This list contains all the available instrument methods.
6. To enter a channel for each sample, click the down arrow in the Channel column and
select a channel from the list.
You cannot specify the auto channel selection in a development batch.
Note The Channel column is available only when you have enabled multiplexing in
the Configuration mode. See “Multiplexing” on page 92.
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Figure 66. 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.
 To remove all samples from the list
1. Click New Sample List in the Development Batch task pane.
One of the following happens:
• If the samples in the current batch have all been acquired, the list is cleared.
• If the samples in the current list have not been acquired, a message confirms that you
want to clear them and start a new list.
2. To create a new empty list, click Yes.
Note You cannot save a development batch when you create a new one; you can only
create, acquire, and discard each batch after you use it. The TraceFinder application
saves only the generated raw data files in the specified batch location.
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Acquiring Samples in a Development Batch
In a development batch, you can submit the entire batch for acquisition or submit only
selected samples.
Follow these procedures:
• To acquire selected samples
• To acquire the batch
 To acquire selected samples
1. Select the samples 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:
…\Thermo\TraceFinder\2.1\EFS\Temp
When the acquisition is complete, the application deletes all the temporary working files.
Only the raw data files and a MethodDevelopment.sld file remain in the folder.
If you acquire a sample more than once, the application time-stamps the subsequent raw
data files with the acquisition time.
 To acquire the batch
Right-click and choose Submit Batch from the shortcut menu,
or click the Submit Batch icon,
.
The TraceFinder application creates a raw data file for each sample in the batch and
an .sld method file. The TraceFinder application writes the raw data files, the .sld method
file, and all temporary working files to the specified folder.
When the acquisition is complete, the application deletes all the temporary working files.
Only the raw data files and a MethodDevelopment.sld file remain in the folder.
If a sample is acquired more than once, the subsequent raw data files are time-stamped
with the acquisition time.
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Viewing Raw Data Files in the Qual Browser
You can view the chromatogram and spectra for completed samples in a development batch.
Follow these procedures:
• To open the Qual Browser
• To display the last completed raw data file in the Qual Browser
 To open the Qual Browser
In the Development Batch task pane, click Open Qual Browser.
The Thermo Xcalibur Qual Browser window opens.
For detailed instructions about using the Qual Browser, refer to the Qual Browser Help.
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 To display the last completed raw data file in the Qual Browser
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
You can use the quick acquisition feature to quickly submit a single sample from any view in
the Method Development mode.
Note The Quick Acquisition feature is available only when you enable it in the
Configuration mode. See “Enabling Optional Features” on page 88.
 To run a quick acquisition
1. Choose Go > Quick Acquire Sample from the main menu.
The Quick Acquisition dialog box opens.
2. Select an instrument method.
3. Type a name for the raw data file that you acquire.
4. Click the browse button and locate a folder where you want to write the acquired raw
data file.
5. Select either the manual injection or the autosampler option:
To perform manual injection, do the following:
a. Select the Manual Injection option.
b. Click OK.
The application submits the sample to the Acquisition queue. See “Acquisition Page”
on page 280.
To perform autosampler injection, do the following:
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a. Select the Use Autosampler option.
b. In the Vial Position box, type a vial position.
c. In the Injection Volume box, type an injection volume.
The minimum injection volume allowed is 0.1 μL; the maximum injection volume
allowed is 5000 μL.
d. Click OK.
The Quick Acquisition dialog box opens.
e. Select the Use check box for the device that you want to use for this acquisition.
f.
(Optional) Select the Start Device check box to indicate the device that will initiate
communication with the other instruments.
This is usually the autosampler.
g. (Optional) Select the Start When Ready check box, which starts all instruments
together when they are all ready.
When this is cleared, individual instruments can start at different times and then
must wait for the last instrument to be ready.
h. (Optional) Select the Priority check box to place the sample immediately after any
currently acquiring sample.
i.
(Optional) Select a value for the Post-run System State: Unknown, On (default),
Off, or Standby.
The application sets the system to this state after it acquires the last sample.
j.
Click OK.
The application submits the sample to the Acquisition queue. See “Acquisition Page”
on page 280.
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This chapter describes the tasks associated with the Acquisition mode.
This mode is available only when you select the Acquisition Batch Wizard style in the
Configuration mode. See “Batch Wizard Style” on page 94.
Contents
• Working with Batches
• Using Quick Acquisition
• Real-Time Display
• Sample Types
When you plan to work with multiple samples or use similarly designed batches, use the
Acquisition mode to reduce the amount of data you must enter.
Because the nature and types of batches are often similar (in some cases specified by laboratory
standard practices), you can define a batch template that supplies the basic structure of a
batch.
Note When user security is enabled, only a user in the LabDirector or Supervisor role can
create a batch template.
If you have a master method, you can create a batch and run the samples. Batches represent
one or more samples that are to be acquired, processed, reviewed, and reported as a set. After
you create a batch of samples, you can submit the batch and review the results in the Analysis
mode or you can go directly to viewing and printing reports.
You can set up a calibration batch with known concentrations of the target compounds and
compare the calibration values against samples in future batches.
You can also use the Quick Acquisition feature to quickly submit a single sample from any
page in the Acquisition mode. See “Using Quick Acquisition” on page 277.
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Working with Batches
This section includes instructions for the following tasks:
• Opening and Navigating the Acquisition Mode
• Creating Batches
Opening and Navigating the Acquisition Mode
 To access the Acquisition mode
Click Acquisition from the dashboard or the navigation pane.
The Acquisition mode navigation pane opens.
The TraceFinder application does not use the navigation pane in the Acquisition mode in the
same way it uses the navigation pane in other modes. In the Acquisition mode, this pane
keeps track of your progress as you move through the views to create and submit a batch or a
batch template.
Figure 67. Task pane when you enter the Acquisition mode
The status of each view in the Acquisition mode shows you which tasks are completed and
which tasks are not.
Completed view
Incomplete required view
Current view
Unvisited view
As you complete each view, the task panes display the parameters you specified for your batch.
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Figure 68. Example task pane when you have completed the Acquisition mode
Categories in the Sample Definition list:
QC Samples: Chk Std
Calibration Samples: Cal Std
Blank Samples: Matrix Blank
Unknown Samples: All other samples
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Creating Batches
To create a batch, follow these major steps in Acquisition mode:
1. Selecting a Batch
2. Defining the Sample List
3. Selecting and Reviewing Reports
4. Submitting the Batch
The following workflows show the different Acquisition views required for each batch
creation approach. Depending on your approach to creating a batch, use one of these specific
workflows.
 To create an original batch
Batch and
Method
Samples
Reports
Finish
To create an original batch, start with the instructions “To start a new batch” on
page 250.
 To acquire a previously saved (.tbr) batch
Batch
Finish
Samples
To acquire a previously saved batch, start with the instructions “To select a
ready-to-acquire batch” on page 252.
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 To edit and process a previously acquired batch
Batch
Samples
Finish
To process a previously acquired batch, start with the instructions “To select a previously
acquired batch” on page 253.
 To create a batch template
Template and
Method
Samples
Finish
Note When user security is enabled, this workflow is available only to users in the
LabDirector or Supervisor role.
To create a batch template, start with the instructions “To create a batch template” on
page 254 and then click Save on the Finish page.
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Selecting a Batch
In a Template Selection view of the Acquisition mode, you can choose to create a new batch in
any of your current projects/subprojects.
Follow these procedures:
• To start a new batch
• To start a new batch from a template
• To select a ready-to-acquire batch
• To select a previously acquired batch
• To create a batch template
 To start a new batch
1. Click the New Batch tab.
2. Select the project and subproject where you want to create the new batch.
3. Type a name for the new batch in the Batch Name box.
If the name you enter is not unique, a red warning flashes.
4. Select a method from the Method Selection list.
The Method Compound Data pane displays the compounds in the method. You cannot
edit the compounds list from the Acquisition mode.
5. To continue to the next view, click Next.
The Sample Definition view opens. See “Defining the Sample List” on page 255.
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 To start a new batch from a template
1. Click the New Batch tab.
2. In the Available Templates pane, select the template and method combination that you
want to use.
The system creates a batch name with the selected template name and the date and time
stamp. You can change the default project, subproject, and method associated with this
template.
3. (Optional) Select a different project and subproject where you want to create the new
batch.
4. (Optional) Select a different method to use for the new batch.
5. To continue to the next view, click Next.
The Sample Definition view of the Acquisition mode opens. See “Defining the Sample
List” on page 255.
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 To select a ready-to-acquire batch
1. Click the Ready to Acquire tab.
All your unacquired, saved batches are displayed with the file extension .tbr (to be run).
The TraceFinder application stores all .tbr batches in the following folder:
…\Thermo\TraceFinder\2.1\EFS\Projects\projectname\subprojectname
2. Select the batch you want to acquire.
3. To continue to the next view, click Next.
The Finish view of the Acquisition mode opens. From the Finish view, you can save the
batch, submit the batch for acquisition, or go to the Sample Definition view to edit the
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. Alternatively, you can browse in a
new raw data file to replace the corrupt file.
4. Do one of the following:
• To prepare the batch for acquisition, click Submit.
For detailed instructions, see “Submitting the Batch” on page 269.
–or–
• To edit the sample list, click Previous.
For detailed instructions, see “Defining the Sample List” on page 255.
–or–
• To save the batch to the Ready to Acquire list, click Save.
The TraceFinder application saves your batch as a to-be-run (.tbr) file, closes the
Acquisition mode, and returns you to the application dashboard.
The application saves the .tbr batches in the following folder:
…\Thermo\TraceFinder\2.1\EFS\Projects\projectname\subprojectname
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 To select a previously acquired batch
1. Click the Acquired Batches tab.
From this page, you can resubmit a previously acquired batch, edit the batch, or save it to
be acquired later.
2. In the Project pane, select a project name.
All subprojects included in the selected project are displayed in the Subproject pane.
3. In the Subproject pane, select a subproject name.
The Batch pane displays all previously acquired batches included in the selected
subproject.
4. In the Batch pane, select the batch you want to reacquire.
5. To continue to the next view, click Next.
The Sample Definition view of the Acquisition mode opens. See “Defining the Sample
List” on page 255.
• If the batch is unreadable, the application reports that the batch file is not valid and
cannot be opened.
• If a sample in the batch is unreadable, the application creates a new sample with the
same name and flags the sample. You must complete the missing information such as
Sample Type, Level, and so forth, and then save the batch before you submit it for
acquisition. Alternatively, you can browse in a new raw data file to replace the corrupt
file.
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 To create a batch template
1. Click the Template tab.
Note When user security is enabled, this page is available only to users in the
LabDirector or Supervisor role.
2. Select the project and subproject where you want to create the new batch template.
3. Type a name for the new batch template in the Template Name box.
4. Select a method from the Method Selection list.
5. The Method Compound Data pane displays the compounds in the method. You cannot
edit the compounds list from the Acquisition mode.
6. To continue to the next view, click Next.
7. The Sample Definition view of the Acquisition mode opens. See “Defining the Sample
List.”
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Defining the Sample List
In the Sample Definition view of the Acquisition mode, you can create a list of samples for the
batch. You can add samples, insert samples, import a sample list, or remove samples from the
list. 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 “Sample Definition view parameters” on page 263).
Icons in the toolbar
Remove samples
Add samples
Import samples
Insert samples
Buttons at the bottom of the template selection page
Add samples
Insert samples
Import samples
As you enter sample values, you can use the Copy Down and Fill Down commands to quickly
enter column values. For detailed instructions on using Copy Down and Fill Down to enter
column values, see Appendix B, “Using Copy Down and Fill Down.”
Follow these procedures:
• To add samples to the list
• To insert samples into the list
• To import samples into the list
• To remove samples from the list
• To reinject a sample from a previously acquired batch
• To select channels for the batch
• To assign a specific channel to a sample
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When you finish defining the list of samples, click Next.
• When you are creating a batch from scratch, creating a batch from a template, or
editing a batch template, the Report Selection view opens. See “Selecting and
Reviewing Reports” on page 265.
• When you are editing a previously acquired batch or a .tbr batch, the Finish Selection
view opens. See “Submitting the Batch” on page 269.
 To add samples to the list
1. Select the number of sample rows to add and click Add,
.
2. Type a file name in the Filename column for each sample.
Each file name must be unique.
3. Select a sample type from the Sample Type list for each sample.
Available sample types
Matrix Blank
Solvent
Unknown/TIC
Cal Std
Chk Std
Unknown
LCS
MDL
MS
LCSD
Method Val
MSD
Tune
Tune/Breakdown
Breakdown
For a detailed description of each sample type, see “Sample Types” on page 292.
4. For each Cal Std or Chk Std sample, select a level from the Level list.
The sample levels are defined in the master method. If there is nothing to select in the
Level list, do the following:
a. Return to the Method Development mode.
b. Open the method.
c. Click the Compounds tab.
d. Click the Calibration Levels tab.
e. Add the levels.
f.
Save the method.
g. Return to the Analysis mode, and click Update.
For detailed instructions, see Chapter 4, “Using the Method Development Mode.”
5. Type a vial position in the Vial Position column for each sample.
Tip Use the Fill Down command to make entering vial positions easier.
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6. Type a volume in the Injection Volume column for each sample.
The minimum injection volume value allowed is 0.1 μL; the maximum injection volume
value allowed is 5000 μL.
7. (Optional) Type or edit the values for the remaining columns.
Note When you use the horizontal scroll bar at the bottom of the 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 insert samples into the list
1. Select the sample above which you want to insert new, unknown samples.
You cannot use the Insert command to create the first sample row.
2. Select the number of samples to insert and click Insert,
.
The application inserts the Unknown samples above the selected sample.
Inserted
samples
3. Type a file name in the Filename column for each sample.
Each file name must be unique.
4. Select a sample type from the Sample Type list for each sample.
For a detailed description of each sample type, see “Sample Types” on page 292.
Available sample types
Thermo Scientific
Matrix Blank
Solvent
Unknown/TIC
Cal Std
Chk Std
Unknown
LCS
MDL
MS
LCSD
Method Val
MSD
Tune
Tune/Breakdown
Breakdown
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5. For each Cal Std or Chk Std sample, click the Level cell and select a level from the list.
The sample levels are defined in the master method. If there are no levels to select from
the Level list, ask a user with Supervisor or LabDirector permissions to edit the method
and specify the levels.
For detailed instructions about defining sample levels, see Chapter 4, “Using the Method
Development Mode.”
6. Type a vial position in the Vial Position column for each sample.
Tip Use the Fill Down command to make entering vial positions easier.
7. Type a volume in the Injection Volume column for each sample.
The minimum injection volume value allowed is 0.1 μL; the maximum injection volume
value allowed is 5000 μL.
8. (Optional) Type or edit the values for the remaining columns.
Note When you use the horizontal scroll bar at the bottom of the sample list, the
Status, Filename, Sample Type, and Level columns stay fixed while the other columns
scroll right and left.
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 To import samples into the list
1. Click Import,
.
The Sample Import Tool dialog box opens.
Use this dialog box to import a sample list from a .csv, .xml, or .sld file.
2. Click Browse and select a .csv, .xml, or .sld file that contains the sample definitions you
want to import.
Note The .csv, .xml, or .sld file format must match the TraceFinder file format.
3. From the Imported Samples Will Be list, select either Appended to the End of the List
or Inserted at the Selected Row.
4. Click Import.
The Sample Import Tool dialog box closes, and the specified samples are added to the
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
Matrix Blank
QC
Chk Std
Std Bracket
Cal Std
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5. For each Cal Std or Chk Std sample, click the Level cell and select a level from the list.
The sample levels are defined in the master method. If there are no levels to select from
the Level list, ask a user with Supervisor or LabDirector permissions to edit the method
and specify the levels.
For detailed instructions, see Chapter 4, “Using the Method Development Mode.”
6. Type a vial position in the Vial Position column for each sample.
Tip Use the Fill Down command to make entering vial positions easier.
7. Type a volume in the Injection Volume column for each sample.
The minimum injection volume value allowed is 0.1 μL; the maximum injection volume
value allowed is 5000 μL.
8. (Optional) Type or edit the values for the remaining columns.
Note When you use the horizontal scroll bar at the bottom of the 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.
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 To remove samples from the list
1. Select the samples you want to remove.
Tip Use the CTRL or SHIFT keys to select multiple samples.
2. Right-click and choose Remove Selected Samples from the shortcut menu.
 To reinject a sample from a previously acquired batch
1. In the sample list, select the sample you want to reinject.
2. Right-click and choose Reinject This Sample from the shortcut menu.
The TraceFinder application creates a copy of the selected sample and appends INJ001 to
the file name. Additional reinjections of the same sample are numbered INJ002, INJ003,
and so forth.
The TraceFinder application copies all parameter values from the original sample.
A green status icon indicates previously acquired samples (acquired and processed) and
the sample name is grayed out. A blue status icon indicates samples created for reinjection
(not acquired).
When you submit this batch, the application acquires only the reinjection samples.
 To select channels for the batch
Note These features are available only when you have enabled multiplexing in the
Configuration mode. See “Multiplexing” on page 92.
To disable a configured channel, clear the check box for the channel in the Multiplexing
Channels area at the bottom of the page.
By default, all configured channels are selected. The configured channels are determined
by the multiplexing settings in the Configuration mode. See “Enabling Optional
Features” on page 88.
Disabling a channel in the Multiplexing Channels area does not remove this channel
selection from the Channels list for each sample. When you assign a channel to a sample,
be careful not to assign a channel that you disabled.
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 To assign a specific channel to a sample
1. Scroll to the Channel column.
Note The Channel column is available only when you have enabled multiplexing in
the Configuration mode. See “Multiplexing” on page 92.
All samples default to Auto.
2. Select a channel from the Channel list.
When you submit the batch, samples that are set to Auto run on any of the available
channels and samples that are set to a specific channel run only on that channel.
If you select a channel that is not available for this batch, the application flags the sample
sequence on the Finish page of the Acquisition mode. See the previous procedure, To
select channels for the batch.
3. If you see this error, do the following:
a. Click Previous to return to the Sample Definition view.
The incorrect sample is marked with an error flag.
b. Correct the channel selection.
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Figure 69. Sample Definition view
Table 55. Sample Definition view parameters (Sheet 1 of 2)
Parameter
Definition
Sample Controls
Add
Adds the specified number of empty rows to the sample grid.
Insert
Inserts the specified number of empty rows above the selected row.
Import
Opens the Sample Import Tool where you can import samples defined in a .csv file or
an .xml file.
Multiplexing Channels
These features are available only when you have enabled multiplexing in the Configuration
mode. See “Multiplexing” on page 92.
All Channels
Uses all configured channels to acquire this batch.
Channel 1-n
Uses only the selected channels to acquire this batch.
Previous
Returns you to the previous Acquisition mode view.
Cancel
Confirms that you want to exit the Acquisition mode. When you cancel out of the
Acquisition mode, your edits are not saved.
Save
Saves this batch as a to-be-run (.tbr) batch.
Next
Takes you to the next Acquisition mode view.
Shortcut menu
Add Sample
Adds a single empty row to the sample grid.
Insert Sample
Inserts a single empty row to the sample grid above the selected row.
Insert Copy Sample
Copies the currently selected row and inserts a copy above the row.
Reinject Selected
Samples
Creates a copy of the selected sample and appends INJ001 to the file name. Additional
reinjections of the same sample are numbered INJ002, INJ003, and so forth.
Remove Selected
Samples
Removes selected samples from the sample grid.
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Table 55. Sample Definition view parameters (Sheet 2 of 2)
Parameter
Definition
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 350.
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.
For example
Copy With Headers
from TraceFinder
Paste into Excel spreadsheet
Paste
Pastes a single column of copied data from another application, such as an Excel
spreadsheet, into the selected column.
Undo Last Paste
Removes the last pasted item in the Acquisition mode sample list.
Export to CSV File
Opens the Save As dialog box where you can save the current sample list to a .csv file.
Status Color Codes
Sample is not acquired.
Sample is acquired but not processed.
Sample is acquired and processed.
Sample is currently acquiring.
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Selecting and Reviewing Reports
On the Report Selection view, you can specify the types of reports you want to create. See
“Report Selection view” on page 267. For a complete list of report types and examples of
output files, see Appendix A, “Reports.” In addition to the report type, you can specify a
report description for each of your reports.
For each standard report you generate, you can create a hardcopy printout, a PDF file, or an
XML file.
For each custom report you generate, you can create a hardcopy printout or an XLSM file.
For each target screening report you generate, you can create a hardcopy printout or a PDF
file.
When you finish specifying your report options, click Next to go to the Finish view and
submit your batch. See “Submitting the Batch” on page 269.
The application writes the resulting output files for your reports to the following folder:
…\TraceFinder\2.1\EFS\Projects\projectname\subprojectname\batchname\Reports
Follow these procedures:
• To edit a report description
• To preview a standard report
• To specify a standard report in print format or as a PDF, XML, or XLSM file
• To export reports to a specific folder
 To edit a report description
Select the Report Description column and edit the default description.
The default report description is the same as the report name.
 To preview a standard report
1. Click the magnifying icon,
, to view an example of the report type as a PDF file.
The right pane of the view displays an example PDF report with typical PDF viewer
buttons.
2. To minimize the PDF viewer, click the minimize icon,
.
Note Only Standard report types have preview documents.
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 To specify a standard report in print format or as a PDF, XML, or XLSM file
1. For each type of report you want to create, select the check box in the Print, Create PDF,
Create XML, or Create XLSM columns.
2. To duplicate the output type for all reports, right-click the cell and choose Copy Down
from the shortcut menu.
All check boxes in the column below the selected cell duplicate the selected or cleared
state in the selected cell. This action applies only to report types that make this output
format available.
 To specify a custom report in hardcopy or XLSM format
1. For each custom report that you want to create, select the check box in the Print or Create
XLSM columns.
2. To duplicate the output type for all reports, right-click the cell and choose Copy Down
from the shortcut menu.
All check boxes in the column below the selected cell duplicate the selected or cleared
state in the selected cell. This action applies only to report types that make this output
format available.
 To specify a target screening report in hardcopy format or as a PDF file
1. For each target screening report that you want to create, select the check box in the Print
or Create PDF columns.
2. To duplicate the output type for all reports, right-click the cell and choose Copy Down
from the shortcut menu.
All check boxes in the column below the selected cell duplicate the selected or cleared
state in the selected cell. This action applies only to report types that make this output
format available.
 To export reports to a specific folder
1. Select the Export Results check box at the bottom of the view.
The Browse For Folder dialog box opens.
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2. Locate and select the folder where you want to save the reports.
3. To create a new reports folder within the selected folder, click Make New Folder and type
the new folder name.
4. Click OK.
The application writes all reports to the specified folder in addition to the batch Reports
folder.
Figure 70. Report Selection view
Table 56. Report Selection parameters (Sheet 1 of 2)
Parameter
Description
Displays an example PDF for the report type. This example provides a model of the report
type only; it does not reflect your specific data. This is available for standard reports only.
Report Name
The name of a report.
Report Title
User-editable description to be used on a report.
Report Type
The type of report: Standard, Custom, or Target Screening.
Print
Reports to be sent to the printer.
Create PDF
Reports to be saved as PDF files.
Available only for standard and target screening reports.
Create XML
Reports to be exported in XML format.
Available only for standard reports.
Create XLSM
Reports to be exported in Excel Macro-Enabled Workbook (.xlsm) format.
Available only for custom reports.
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Table 56. Report Selection parameters (Sheet 2 of 2)
Parameter
Description
Batch Level
Rather than creating separate reports for each sample, the application uses a composite of
the data from all the samples to create a single report for the entire batch. Batch-level reports
are prepended with a B to differentiate them.
You cannot select this option from the Report Selection page. You must select the Batch
Level option for the report in the report configuration. See “Specifying the Reports
Configuration” on page 68.
Shortcut menu:
Copy Down
Copies the selected or cleared state to all subsequent reports in the column.
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Submitting the Batch
In the Finish view of the Acquisition mode, you can specify a startup method, a shutdown
method, or a calibration batch. You can save the batch to be acquired later, or you can acquire
and process data and optionally create reports. See “Finish view” on page 275.
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 to-be-run (.tbr) file, closes the
Acquisition mode, and returns you to the application dashboard.
 To start an acquisition
1. Click Submit.
The Submit Options dialog box opens. For detailed descriptions of the parameters, see
“Submit Options dialog box” on page 273.
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 enabled) Select the Priority Sequence check box.
The application acquires the priority batch on the next available channel or the assigned
channel.
7. (Optional without multiplexing enabled) Select the Priority Sequence check box and
then select one of the following priority options to place the batch in the queue:
• Next Available Batch places the batch immediately after the currently acquiring
batch.
• Next Available Sample places the batch immediately after the currently acquiring
sample.
Note When you select Full Sequence Submission in the 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 returns you to the
dashboard and shows the real-time display at the bottom of the dashboard. The real-time
display is visible from the dashboard and all modes. You can begin another batch in the
Acquisition mode while you watch the real-time display of the currently acquiring batch.
–or–
Click Cancel to exit the Acquisition mode without performing any tasks.
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Figure 71. Submit Options dialog box
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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.
Process Data
(Default) Processes the data for the current batch.
Create Reports
Creates reports for the current batch.
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Parameter
Description
Priority Sequence
With multiplexing enabled, places the batch immediately after
the currently acquiring batch.
Without multiplexing enabled, specifies one of the following
priority options to place the batch in the queue:
Next Available Batch: Places the batch immediately after the
currently acquiring batch.
Next Available Sample: Places the batch immediately after
the currently acquiring sample.
Note When you select Full Sequence Submission in the
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 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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 To view the output files
• The TraceFinder application writes saved batches to the subproject folder with the file
extension .tbr (to be run):
…\TraceFinder\2.1\EFS\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
Figure 72. Finish view
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Table 58. 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 to-be-run (.tbr) file.
Submit
Opens the Submit Options dialog box where you can optionally choose to generate reports.
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Using Quick Acquisition
Using Quick Acquisition
The quick acquisition feature lets you quickly submit a single sample from any view of the
Acquisition mode.
Note The quick acquisition feature is available only when you enable it in the
Configuration mode. See “Enabling Optional Features” on page 88.
 To run a quick acquisition
1. Choose Go > Quick Acquire Sample from the main menu.
The Quick Acquisition dialog box opens.
2. Select an instrument method.
3. Type a name for the raw data file that you acquire.
4. Click the browse button and locate a folder where you want to write the acquired raw
data file.
5. Select either the manual injection or the autosampler option:
To perform manual injection, do the following:
a. Select the Manual Injection option.
b. Click OK.
The application submits the sample to the Acquisition queue. See “Acquisition Page”
on page 280.
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To perform autosampler injection, do the following:
a. Select the Use Autosampler option.
b. In the Vial Position box, type a vial position.
c. In the Injection Volume box, type an injection volume.
The minimum injection volume allowed is 0.1 μL; the maximum injection volume
allowed is 5000 μL.
d. Click OK.
The Quick Acquisition dialog box opens.
e. Select the Use check box for the device that you want to use for this acquisition.
f.
(Optional) Select the Start Device check box to indicate the device that will initiate
communication with the other instruments.
This is usually the autosampler.
g. (Optional) Select the Start When Ready check box, which starts all instruments
together when they are all ready.
When this is cleared, individual instruments can start at different times and then
must wait for the last instrument to be ready.
h. (Optional) Select the Priority check box to place the sample immediately after any
currently acquiring sample.
i.
(Optional) Select a value for the Post-run System State: Unknown, On (default),
Off, or Standby.
The application sets the system to this state after it acquires the last sample.
j.
Click OK.
The application submits the sample to the Acquisition queue. See “Acquisition Page”
on page 280.
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Real-Time Display
Real-Time Display
You can access the real-time display from the dashboard and from any mode in the
TraceFinder application.
 To access the real-time display from the dashboard
Click Real Time Status.
The real-time status displays at the bottom of the dashboard.
 To access the real-time display from all modes
Click Real Time Status.
The real-time status displays at the bottom of the current view.
Figure 73. Real Time Status display
The real-time status display has four pages of information and a real-time trace pane:
• Acquisition Page
• Instrument Page
• Devices Page
• Queues Page
• Real-Time Trace Display
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Acquisition Page
Use the Acquisition page to monitor the progress as the application acquires the samples.
 To pause or stop the batches in the queue
Use the Start,
queue.
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, Stop,
, or Pause,
, icons to control batches in the Acquisition
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Instrument Page
Use the Instrument page to monitor the currently acquiring sample.
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Devices Page
Use the Devices page to monitor the status of the instrument. The feedback you see on the
Devices page depends on the instrument you are using. The following examples show an
Accela autosampler and an Aria™ multiplexing device.
Accela Autosampler Feedback
Aria Multiplexing Feedback
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Follow these procedures:
• To pause the autosampler
• To 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 59. 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 287.
Follow these procedures:
• To pause all batches in a queue
• To remove a single batch from a queue
• To remove all batches in a queue
• To remove all pending batches
 To pause all batches in a queue
1. Select a queue (Acquisition, Processing, or Reporting).
Note When multiplexing is enabled, you can have as many as four samples acquiring
at once. Pausing the Acquisition queue does not affect any acquiring samples.
2. Right-click and choose Pause Queue from the shortcut menu.
After the current sample completes, the application pauses all batches and samples in the
specified queue. Only the selected queue is affected.
3. To restart a paused queue, select the queue, right-click, and choose Resume Queue from
the shortcut menu.
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 To remove a single batch from a queue
1. Select a queue (Acquisition, Processing, or Reporting).
2. Right-click and choose Stop Active Batch from the shortcut menu.
Note This command is available only when there are active batches in the queue.
Paused batches and batches that contain only pending samples are not “active.”
The application confirms that you want to remove the active batch from the selected
queue. After the current sample completes, the application removes the batch and all
pending samples from the queue. Only the selected queue is affected.
 To remove all batches in a queue
1. Select a queue (Acquisition, Processing, or Reporting).
2. Right-click and choose Stop All Batches from the shortcut menu.
The application removes all batches with pending samples from the selected queue. The
current sample continues to acquire. Only the selected queue is affected.
 To remove all pending batches
1. Select a queue (Acquisition, Processing, or Reporting).
2. Right-click and choose Remove Pending Batches from the shortcut menu.
Note A pending batch is a batch in which all samples are pending. If any sample in
the batch is active, the batch is not affected by this command.
The application removes all batches that contain only pending samples. Only the selected
queue is affected.
Figure 74. Queue-level shortcut menu
Table 60. Queue-level shortcut menu commands (Sheet 1 of 2)
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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.
Stop Active Batch
Removes all pending samples from the specified queue. The active
sample is not affected.
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Table 60. Queue-level shortcut menu commands (Sheet 2 of 2)
Command
Description
Stop All Batches
Removes all pending samples and batches from the specified
queue. The active sample is not affected.
Remove Pending
Batches
Removes all pending batches from the specified queue. The active
batch is not affected.
Batch-Level Commands
Use the batch-level commands to pause or remove entire batches or samples within batches
from any of the queues on the Queues page. See “Batch-level shortcut menu.”
Follow these procedures:
• To stop a batch
• To remove a pending batch
• To remove pending samples from a batch
• To remove a single pending sample from a batch
 To stop a batch
1. Select an active batch in any of the queues (Acquisition, Processing, or Reporting).
Note The batch must have at least one active sample and one pending sample.
2. Right-click and choose Stop Batch from the shortcut menu.
The application confirms that you want to remove the selected batch from the queue.
After the current sample completes, the application removes the batch and all pending
samples from the queue.
 To remove a pending batch
1. Select a pending batch in any of the queues (Acquisition, Processing, or Reporting).
Note A pending batch is a batch in which all samples are pending. If any sample in
the batch is active, this command is not available.
2. Right-click and choose Remove Pending Batch from the shortcut menu.
The application confirms that you want to remove the selected batch from the queue and
then removes the batch from the queue.
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 To remove pending samples from a batch
1. Select a batch in any of the queues (Acquisition, Processing, or Reporting).
The batch must have at least one pending sample.
2. Right-click and choose Remove Pending Samples from the shortcut menu.
The application confirms that you want to remove all pending samples from the batch
and then removes the samples. If the batch includes only pending samples, the
application removes the batch from the queue.
 To remove a single pending sample from a batch
1. Select a pending sample.
2. Right-click and choose Remove Sample from the shortcut menu.
The application confirms that you want to remove the selected sample from the batch and
then removes the sample.
Figure 75. Batch-level shortcut menu
Table 61. 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 display shows only the TIC trace as each sample acquires. To observe
specific traces, such as the internal standard, use the RTV Display Traces function to display
multiple traces.
When you create your method, you can specify additional traces to display in the real-time
viewer and in which order the traces are displayed. The application always displays the TIC
trace in the top pane. See “Real Time Viewer” on page 179.
 To display multiple traces
Right-click the chromatogram pane and choose the number of traces you want to display.
The chromatogram pane displays real-time chromatograms for the selected number of
traces.
The TIC is always displayed at the top. When there are more traces than can fit in the
pane, you can scroll through the traces.
For each trace, the application displays the mass or precursor mass.
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Real-Time Display
Figure 76. Real-time display with multiple traces
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Sample Types
Sample Types
The TraceFinder application uses the following sample types in all sample definitions and
reports. To view example standard reports specific to a sample type, see Appendix A,
“Reports.”
Table 62. Sample type definitions
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Sample type
Definition
Matrix Blank
Contains no target compounds but might contain an ISTD when you
use the internal standard quantitative analysis technique. By analyzing a
blank sample, you can confirm that there are no residual compounds in
the solvent system that can cause erroneous results.
Cal Std
(Calibration standard) Contains known amounts of all target
compounds. The purpose of a standard is to measure the response of the
instrument to the target compounds so that the processing software can
generate a calibration curve for each compound.
Chk Std
(Check standard) Contains a known amount of one or more specific
target compounds. The application places check standard samples in the
sequence so that it can test quantitative analysis results for quality
assurance purposes. After the application analyzes the Chk Std sample, it
compares the measured quantity with the expected value and an
acceptability range. The quantitative analysis of a Chk Std sample is
classified as passed if the difference between the observed and expected
quantities is within the user-defined tolerance. A Chk Std sample is
classified as failed if the difference between the observed and expected
quantities is outside the user-defined tolerance.
Solvent
Contains only solvent.
Unknown
Used for quantitative analysis of samples.
Unknown/TIC
Used for quantitative and qualitative analysis of samples.
LCS
Lab control sample.
LCSD
Lab control sample duplicate.
MDL
Method detection limits sample.
Method Val
Method validation sample.
MS
Matrix spike sample.
MSD
Matrix spike duplicate sample.
Tune
Verifies the tune of the system according to EPA guidelines.
Tune/Breakdown
Verifies the tune of the system according to EPA guidelines, allowing for
the degradation of compounds.
Breakdown
Checks the degradation of compounds.
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Using the Analysis Mode
This chapter includes instructions for using the features of the Analysis mode.
Contents
• Using Quick Acquisition
• Working in the Batch View
• Creating a Batch Using the Batch Wizard
• Working in Data Review View
• Working in the Report View
• Working in the Local Method View
• Working in the Batch Template Editor
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 from the dashboard or the navigation pane.
The Analysis navigation pane opens.
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Using Quick Acquisition
Using Quick Acquisition
With the quick acquisition feature, you can quickly submit a single sample from any view of
the Analysis mode.
Note The quick acquisition feature is available only when you enable it in the
Configuration mode. See “Enabling Optional Features” on page 88.
 To run a quick acquisition
1. Choose Go > Quick Acquire Sample from the main menu.
The Quick Acquisition dialog box opens.
2. Select an instrument method.
3. Type a name for the raw data file that you acquire.
4. Click the browse button and locate a folder where you want to save the acquired raw data
file.
5. Select either the manual injection or the autosampler option:
To perform manual injection, do the following:
a. Select the Manual Injection option.
b. Click OK.
The application submits the sample to the Acquisition queue. See “Acquisition Page”
on page 280.
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Using Quick Acquisition
To perform autosampler injection, do the following:
a. Select the Use Autosampler option.
b. In the Vial Position box, type a vial position.
c. In the Injection Volume box, type an injection volume.
The minimum injection volume allowed is 0.1 μL; the maximum injection volume
allowed is 5000 μL.
d. Click OK.
The Quick Acquisition dialog box opens.
e. Select the Use check box for the device that you want to use for this acquisition.
f.
(Optional) Select the Start Device check box to indicate the device that will initiate
communication with the other instruments.
This is usually the autosampler.
g. (Optional) Select the Start When Ready check box, which starts all instruments
together when they are all ready.
When this is cleared, individual instruments can start at different times and then
must wait for the last instrument to be ready.
h. (Optional) Select the Priority check box to place the sample immediately after any
currently acquiring sample.
i.
(Optional) Select a value for the Post-run System State: Unknown, On (default),
Off, or Standby.
The application sets the system to this state after it acquires the last sample.
j.
Click OK.
The application submits the sample to the Acquisition queue. See “Acquisition Page”
on page 280.
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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.
 To open the Batch View
1. Do one of the following:
From the dashboard, click Analysis.
–or–
Click Analysis in the navigation pane of the current mode.
2. In the Analysis navigation pane, click Batch View.
The Batch View opens for the currently selected batch.
This section contains information about the following topics:
• Batch View Panes
• Creating a New Batch
• Editing a Batch
• Editing Report Output Formats
• Submitting a Batch
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Batch View Panes
The Batch View is divided into three panes:
• Sample List
Use the sample list pane to create a batch. See “Creating a New Batch” on page 309.
• Automated Batch Reports
Use the Automated Batch Reports pane to select the type of output formats that you want
to generate for the reports. See “Editing Report Output Formats” on page 320.
• Compound Active Status
Use the Compound Active Status pane to make specific compounds active or inactive. See
“Setting Compound Active Status” on page 322.
Use the Batch View toolbar or shortcut menu to create the sample list and submit samples for
acquisition. See “Batch View Toolbar” on page 304 or “Batch View Shortcut Menu” on
page 307.
Sample list
Automated Batch Reports pane
Compound Active Status pane
Tip To resize the panes, drag the separators that divide the panes.
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Sample List
The sample list includes the following features:
• Column Display
• Status Indicators
• Sample Weight Calculation
Column Display
The sample list can contain many columns of information. You can scroll to see all the
columns of information, and you can customize which columns to display and their display
order.
Follow these procedures:
• To scroll the sample list
• To customize the column display
 To scroll the sample list
Use the horizontal scroll bar at the bottom of the sample list to view all the information.
When you use the scroll bar at the bottom of the sample list, the Status, Filename, Sample
Type, 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.
All the columns you select 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.
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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.
Figure 77. Modify Columns dialog box
Table 63. Modify Columns function buttons (Sheet 1 of 2)
Function
Description
Moves all columns to the Displayed Columns pane.
Moves the selected column to the Displayed Columns pane.
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Table 63. Modify Columns function buttons (Sheet 2 of 2)
Function
Description
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.
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
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Sample Weight Calculation
Use the features for calculating sample weight 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 Weight, Sample Volume, Calculation Type, Dilution
Factor, 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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Batch View Toolbar
The Batch View includes this toolbar for creating and submitting a batch.
Icon
Description
Adds the specified number of new, empty samples to the end of the
sample list. See the instructions “To add samples to the list” on
page 310.
Inserts a new, empty sample or samples above the selected sample. See
the instructions “To insert samples into the list” on page 311.
Removes the selected samples from the sample list. See the
instructions “To remove samples from the list” on page 312.
Adds imported samples from a .csv, .xml, or .sld file to the sample list.
See the instructions “To import samples into the list” on page 311.
Submits only the selected samples for acquisition, processing, or
report generation. See the instructions “To submit selected samples”
on page 326.
Submits the batch for acquisition, processing, or report generation.
See the instructions “To submit all samples in the batch” on page 325.
Closes/Opens the Analysis navigation pane.
Opens the Quick Acquisition dialog box where you can quickly
submit a single sample. See “Using Quick Acquisition” on page 295.
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.
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The sample list includes the following columns of information:
Figure 78. Batch View sample list
Cells in the sample list that are not editable, such as Barcode Actual, are shaded and empty.
Table 64. 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:
Matrix Blank, Solvent, Cal Std, Chk Std, Unknown, Unknown/TIC, LCS, LCSD, MDL,
MS, MSD, Method Val, Tune, Tune/Breakdown, or Breakdown
Default: Unknown
Level
The level defined for a calibration sample or quality control sample.
Sample ID
A user-defined, alphanumeric string that identifies a sample.
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Table 64. Batch View sample list columns (Sheet 2 of 2)
Column
Description
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.
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 enabled multiplexing in the
Configuration mode. See “Multiplexing” on page 92.
Barcode Expected
Barcode Actual
Comment
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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 65. 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 311.
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 350.
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 65. 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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Creating a New Batch
In the Batch View, you can create a new batch.
Follow these procedures:
• To create a new batch
• To add samples to the list
• To insert samples into the list
• To import samples into the list
• To remove samples from the list
• To copy a sample
• To reinject a sample
• To edit sample values
• To browse in raw data files
• To customize the column display
 To create a new batch
1. Click New Batch in the Batch View task pane or choose File > New > Batch.
The Create a New Batch dialog box opens.
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2. Select a master method from the Method list.
3. Select a drive from the Storage Location list.
The project list displays all projects, subprojects, and batches on the selected drive.
Tip The application does not display drives that do not have a project and subproject.
You cannot use network drives to acquire data. For more information about network
drives, see “Working with Drives” on page 50.
4. Select a project and a subproject and type a name for your new batch.
Tip To enable the Save button, you must select a subproject and enter a unique batch
name. If the Save button is not enabled, either you have entered a name that is already
used or you have not selected a subproject.
5. Click Save.
A new, unnamed batch opens with one Unknown sample.
 To add samples to the list
1. To add a single sample row, right-click the sample list and choose Add Sample from the
shortcut menu.
2. To add multiple sample rows, select the number of rows and then click the Add Sample
icon,
.
The application adds the specified number of new, empty samples to the end of the
sample list.
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 To insert samples into the list
Select the sample above which you will insert new, Unknown samples, and then do one of
the following:
• To insert a single sample row, right-click and choose Insert Sample from the shortcut
menu.
• To insert multiple sample rows, select the number of rows and then click the Insert
Sample icon
.
The application inserts the Unknown samples above the selected sample.
Inserted
samples
 To import samples into the list
1. Choose Batch > Import Samples from the main menu, or click the Import Samples
icon,
.
The Sample Import Tool dialog box opens.
From this dialog box, you can import samples from a .csv, .xml, or .sld file.
2. Click Browse and select a .csv, .xml, or .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.
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4. Click Import.
The Sample Import Tool dialog box closes, and the application adds the specified samples
to the sample list.
When you import samples from an Xcalibur sequence file (.sld), the TraceFinder
application makes the following column name substitutions:
Xcalibur column
TraceFinder column
Position
Vial Position
Inj Vol
Injection Volume
Dil Factor
Conversion Factor
When you import samples from an Xcalibur sequence file (.sld), the TraceFinder
application makes the following sample type substitutions:
Xcalibur sample type
TraceFinder sample type
Blank
Matrix Blank
QC
Chk Std
Std Bracket
Cal Std
5. (Optional) When using multiplexing, select a channel for each imported sample.
Imported samples default to Auto.
Note The Channel column is available only when you have enabled multiplexing in
the Configuration mode. See “Multiplexing” on page 92.
 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
Matrix Blank
Solvent
Unknown/TIC
Cal Std
Chk Std
Unknown
LCS
MDL
MS
LCSD
Method Val
MSD
Tune
Tune/Breakdown
Breakdown
3. For each Cal Std or Chk Std sample, select a level from the Level list.
The sample levels are defined in the master method. If there is nothing to select in the
Level list, do the following:
a. Return to the Method Development mode.
b. Open the method.
c. Click the Compounds tab.
d. Click the Calibration Levels tab.
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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.”
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 inserts any additional browsed in files above the selected sample.
For all browsed in raw data files, the application sets the Status to Acquired,
the Sample Type to Unknown.
, and sets
Note You cannot overwrite an acquired sample. When you select a sample that is
acquired, the application inserts all browsed in files above the selected sample.
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 To customize the column display
1. Right-click the Batch View sample list and choose Modify Columns from the shortcut
menu.
The Modify Columns dialog box opens.
Table 66. 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.
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2. Use the arrow buttons to move all the columns that you want displayed to the Displayed
Columns pane.
All the columns you select are displayed after the Status, Filename, Sample Type, or 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 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 to-be-run (.tbr) batch.
Follow these procedures:
• To open a saved batch
• To open a recent batch
• To edit samples in a batch
• To reinject a sample from a previously acquired batch
• To submit all samples in the batch
• To submit selected samples
 To open a saved batch
1. From the Batch View task pane, click Open Batch.
The Open Batch dialog box opens.
2. Select a drive from the Storage Location list.
The project list displays all projects, subprojects, and batches on the selected drive.
3. Select a project, subproject, and batch.
4. Click Open.
The selected batch opens in the Batch View.
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 To open a recent batch
Click a batch name in the Recent Files list.
The selected batch opens in the Batch View.
Tip To view the drive, project, and subproject for a recent batch, hold your cursor
over the batch name.
 To edit samples in a batch
Use the commands described in “Working in the Batch View” on page 297.
You can edit samples, add new samples, reinject acquired samples, or delete samples.
 To reinject a sample from a previously acquired batch
1. In the sample list, select the sample 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).
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3. To save this batch with the new samples for reinjection, choose File > Save > Batch from
the main menu.
The batch is saved as a .tbr batch. You can open this batch from the Ready to Acquire
page in the Acquisition mode and submit the batch. The application acquires all
submitted samples—both the reinjection samples and the previously acquired samples.
The application appends a timestamp to the acquired raw data files to differentiate each
acquisition.
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Editing Report Output Formats
In the Automated Batch Reports pane, you can view the reports that are selected for this batch
and modify which output formats are generated for each report.
 To edit the sample-level output formats
1. Click the Sample Level tab.
The application displays reports and the output formats as they were specified in the
method.
For detailed instructions for specifying which reports and output formats are generated,
see “Specifying the Reports Configuration” on page 68.
2. Select or clear any of the check boxes for your reports.
3. To duplicate an output format for all reports for this sample, right-click the cell and
choose Copy Down from the shortcut menu.
All check boxes in the column below the selected cell duplicate the selected or cleared
state in the selected cell. You can duplicate the output type only for reports that have this
output format available.
4. To duplicate the output format for all samples in the batch, right-click the cell and choose
Apply Selection to All Samples from the shortcut menu.
Tip In the Batch View, you can change the output formats but you cannot change
which reports are available.
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 To edit the batch-level output formats
1. Click the Batch Level tab.
The application displays the reports and the output formats as they were specified in the
method.
For detailed instructions for specifying which reports and output formats are generated
and which reports are batch-level, see “Specifying the Reports Configuration” on page 68.
2. Select or clear any of the check boxes for your reports.
3. To duplicate the output format for all reports, right-click the cell and choose Copy Down
from the shortcut menu.
All check boxes in the column below the selected cell duplicate the selected or cleared
state in the selected cell. You can duplicate the output type only for reports that have this
output format available.
Tip In the Batch View, you can change the output formats but you cannot change
which reports are available.
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Setting Compound Active Status
In the Compound Active Status pane, you can choose specific compounds to be active or
inactive.
 To set a compound as active or inactive
1. In the 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 133.
• 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.
When you specify a compound as inactive in this pane, it becomes inactive in the
Compounds pane in the Data Review view. Inactive compounds are grayed out:
For instructions for changing the active/inactive status in the Data Review view, see
“Inactive and Excluded Compounds” on page 354.
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Compound Active/Inactive Status
You can specify which compounds are active or inactive in the Local Method View, the Batch
View, or the Data Review view.
Figure 79. Active and inactive compounds in the Local Method View
For details about setting the status on the Identification page, see “Identification” on
page 133.
Figure 80. Active and inactive compounds in the Batch View
For details about setting the status in the Batch View, see “Setting Compound Active Status”
on page 322.
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Figure 81. Active and inactive compounds in the Data Review view
Inactive
For details about setting the status in the Data Review view, see “Inactive and Excluded
Compounds” on page 354.
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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 327.
Follow these procedures:
• To submit all samples in the batch
• To submit selected samples
For a description of commands on the shortcut menu, see “Batch View shortcut menu
commands” on page 307.
 To submit all samples in the batch
1. Click the Submit Batch icon,
.
The Submit Options dialog box opens. See “Submit Options dialog box” on page 327.
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 enabled) Select the Priority Sequence check box.
The application acquires the priority batch on the next available channel or the assigned
channel.
8. (Optional without multiplexing enabled) Select the Priority Sequence check box and
then select one of the following priority options to place the batch in the queue:
• Next Available Batch places the batch immediately after the currently acquiring
batch.
• Next Available Sample places the batch immediately after the currently acquiring
sample.
9. To start the selected processes, click OK.
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 To submit selected samples
1. Select the samples to submit.
2. Click the Submit Selected Samples icon,
.
The Submit Options dialog box opens. See “Submit Options dialog box.”
3. Select the tasks that you want to perform: acquire data, process data, or create reports.
4. Select the Use check box for the device that you want to use for this acquisition.
5. (Optional) Click Show Details to display additional Acquisition parameters.
6. (Optional) Select the Start Device check box to indicate the device that will initiate
communication with the other instruments.
This is usually the autosampler.
7. (Optional) Select the Start When Ready check box to have all instruments start together
when they are all ready.
When this is cleared, individual instruments can start at different times and then must
wait for the last instrument to be ready.
8. (Optional with multiplexing enabled) Select the Priority Sequence check box.
The application acquires the priority batch on the next available channel or the assigned
channel.
9. (Optional without multiplexing enabled) Select the Priority Sequence check box and
then select one of the following priority options to place the batch in the queue:
• Next Available Batch places the batch immediately after the currently acquiring
batch.
• Next Available Sample places the batch immediately after the currently acquiring
sample.
10. To start the selected processes, click OK.
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Figure 82. Submit Options dialog box
Table 67. 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.
Process Data
(Default) Processes the data for the current batch.
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Table 67. Submit Options dialog box parameters (Sheet 2 of 2)
Parameter
Description
Create Reports
Creates reports for the current batch.
Priority Sequence
With multiplexing enabled, places the batch immediately after the
currently acquiring batch.
Without multiplexing enabled, specifies one of the following
priority options to place the batch in the queue:
• Next Available Batch places the batch immediately after the
currently acquiring batch.
• Next Available Sample places the batch immediately after the
currently acquiring sample.
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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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 101 and “Working in the Batch Template Editor” on page 415.
Note This batch wizard is available only when you select the Batch Template Wizard
(EnviroLab/ToxLab/QuanLab forms) style in the Configuration mode. See “Application
Configuration” on page 67.
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 415.
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 333.
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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 83. Batch Template Selection page
Table 68. Batch Template Selection parameters (Sheet 1 of 2)
Parameter
Description
Starting Vial Position
The vial position where you want to begin acquiring samples.
Default: 1
Total Batch Rows
The number of sample rows in the batch template.
Assay Type
The assay type specified in the master method used to create the batch template.
Quick Mode
Limits the columns of information on the Batch Specification page to the following:
• Sample Type
• Sample ID
• Injection Volume
• Conversion Factor
Available Templates
All batch templates are saved in the following folder:
…\Thermo\TraceFinder\2.1\EFS\Templates\Batches
Template Layout
Displays sample information in the selected batch template.
Available Methods
Lists all master methods created with the same assay type as the selected batch template.
Help
Opens the “Creating a Batch Using the Batch Wizard” topic (this topic) in the application
Help tool.
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Table 68. Batch Template Selection parameters (Sheet 2 of 2)
Parameter
Description
Next
Returns you to the Batch Specification page where you can enter a sample ID, a sample
name, or a comment. You can also add or remove samples from the sample list or edit the
column values for the samples. See “Specifying a Batch” on page 335.
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 338.
 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 add samples to the batch
• To remove samples from the batch
• To insert samples into the batch
• To copy a sample
• To move a sample up or down in the sample list
• To browse in a raw data file
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 To add samples to the batch
1. Right-click and choose Add Sample from the shortcut menu, or click the add sample
icon,
.
The application adds a new, Unknown sample to the end of the sample list.
2. In the Filename column for each sample, type a file name.
Note Or, you can right-click and choose Browse in Raw File from the shortcut
menu. Follow the instructions “To browse in a raw data file.”
3. Select a sample type from the Sample Type list for each sample.
Available sample types
Matrix Blank
Solvent
Unknown/TIC
Cal Std
Chk Std
Unknown
LCS
MDL
MS
LCSD
Method Val
MSD
Tune
Tune/Breakdown
Breakdown
4. For detailed descriptions of sample types, see “Sample Types” on page 292.
5. For each Cal Std or Chk Std sample, select a level from the Level list.
The sample levels are defined in the master method. If there are no levels to select from
the Level list, do the following:
a. Cancel the Batch Wizard.
b. Return to the Method Development mode.
c. Open the method.
d. Click the Compounds tab.
e. Click the Calibration Levels tab.
f.
Add the levels.
g. Save the method.
h. Return to the Analysis mode, open the Batch Wizard, and begin your batch again.
For detailed instructions about defining sample levels, see Chapter 4, “Using the Method
Development Mode.”
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.
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 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, Unknown 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.
 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 84. Batch Specification page
Table 69. 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, Unknown sample to the end of the sample list.
This function is not available in Quick Mode.
Removes the selected sample.
This function is not available in Quick Mode.
Quick Mode
Limits the columns of information in the Batch Specification page to the following:
• Sample Type
• Sample ID
• Injection Volume
• Conversion Factor
In Quick Mode, the shortcut menu and add/remove sample icons are unavailable.
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Table 69. 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, Unknown sample above the selected row.
Insert Copy Sample
Copies the currently selected row and inserts a copy above the row.
Remove Selected
Samples
Removes selected samples from the sample list.
Move Sample Up
Moves the selected sample up one row in the sample list.
Move Sample Down
Moves the selected sample down one row in the sample list.
Browse In Raw File
Opens a dialog box where you can select a raw data file to use for the sample row. You can
also browse in multiple raw data files to create multiple samples.
Fill Down
Enters sequential values in the column, starting with the value in the selected row and
ending with the last row in the column. For detailed instructions about using the Fill
Down command, see Appendix B, “Using Copy Down and Fill Down.”
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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 325.
 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 342.
 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 342.
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Figure 85. Finish page
Table 70. Finish parameters (Sheet 1 of 2)
Parameter
Description
Modify Calibrations or
Active Compounds by
Group
Enables the Next button that lets you access the Calibration and Compound Selection
page.
If 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 335.
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Table 70. Finish parameters (Sheet 2 of 2)
Parameter
Description
Finish
Saves the batch and displays it in Batch View. From Batch View, you can submit the batch
for acquisition, processing, or report generation. See “Submitting a Batch” on page 325.
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
Immediately exits the Batch Wizard and does not save the batch. There is no confirming
message.
Selecting Calibration Files and Compounds
From the Calibration and Compound Selection page, you can edit the calibration file or edit
the list of compounds 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.
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3. To save calibration data from both files into a single file for this batch, click Create New.
4. When you are finished with the Calibration and Compound Selection page, click Next.
The Finish page opens. See “Submitting the Batch” on page 340.
 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 340.
Figure 86. Calibration and Compound Selection Page
Table 71. Calibration and Compound Selection parameters (Sheet 1 of 2)
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
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Table 71. Calibration and Compound Selection parameters (Sheet 2 of 2)
Parameter
Description
Compound Groups
Displays all available groups defined in the Groups page of the Master Method View. See
“Editing the Groups Page” on page 126.
Included Compounds
Displays all available compounds that you can identify in the samples. Compounds
marked as Active are identified in the batch samples.
Help
Opens the “Creating a Batch Using the Batch Wizard” topic (this topic) in the application
Help tool.
Back
Returns you to the Batch Specification page where you can enter a sample ID, sample
name, or comment. You can also add or remove samples from the sample list or edit the
column values for the samples. See “Specifying a Batch” on page 335.
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 340.
Cancel
Immediately exits the Batch Wizard and does not save the batch. There is no confirming
message.
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Working in Data Review View
Working in Data Review View
In the Data Review view, you can view the data generated by the master method. Use the Data
Review view to verify the data for a sample-specific compound before you generate reports.
You can use the functions in the Data Review view to investigate and edit the quantification
or qualification values in a batch.
 To open the Data Review view
1. Do one of the following:
From the dashboard, click Analysis.
–or–
Click Analysis in the navigation pane of the current mode.
2. In the Analysis navigation pane, click Data Review.
The Data Review view for the currently selected batch opens.
The Data Review view uses a sample list and one of two modes: Quan Mode or Qual Mode.
The Qual Mode is available only for Unknown/TIC sample types. When you view the data
for an Unknown/TIC sample type, you can switch between Qual Mode and Quan Mode.
Note In the Qual Mode, the application displays peak information for compounds with
mass spectral data only. The Qual Mode is not available for batches that have analog data
only (no mass spectra compounds).
This section includes the following topics:
• Data Review Sample List
• Quan Mode
• Qual Mode
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Data Review Sample List
Use the sample list to select a particular sample. To see the columns in a sample list and view
their descriptions, see “Data Review sample list.”
Status indicators for each sample indicate if the sample is currently acquiring, not acquired,
acquired, or processed.
The sample list includes the following features:
• Column Display
• Status Indicators
• Caution Flags
• Compound Flags
• Inactive and Excluded Compounds
The sample list is the same in both Quan Mode and Qual Mode and displays all the
quantitative data for the samples of a batch.
• In Quan Mode, the sample list works with the Compounds pane to select a unique
sample and compound combination, which then has its textual and graphical values
displayed in the Quan Mode pane. The list of compounds that are available for a specific
method is displayed in the Compounds pane.
From the sample list, you can make a compound active or inactive.
• Switching a compound to inactive status does not remove its data and calculated
values from the result set. Instead, the TraceFinder application masks the appearance
of that compound for that particular sample and grays the compound in the
compounds list.
• For a calibration standard, the application stops using the data file’s calibration point
for the calibration and removes it from the graphical view of the calibration curve
displayed in the Qualification pane. It is no longer part of the result set.
• In Qual Mode, the sample list works with the peak list to select a unique sample and peak
combination, which then has its textual and graphical values displayed in the Qual Mode
pane.
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Figure 87. Data Review sample list
Cells in the sample list that should not have a value, such as the theoretical concentration for
an unknown, are shaded and empty. Cells that should have a value, but none exists, report
N/A (not available). Results for compounds that are not detected display N/F (not found).
Table 72. Data Review sample list columns (Sheet 1 of 3)
Column
Status
Description
Sample is not acquired.
Sample is acquired but not processed.
Sample is acquired and processed.
Sample is currently acquiring.
Flags
Caution flag displayed when a compound within the sample has an error.
Filename
Name of the raw data file that contains the sample data.
Sample Type
Defines how the TraceFinder application processes the sample data. Each sample is classified
as one of the following sample types:
Matrix Blank, Solvent, Cal Std, Chk Std, Unknown, Unknown/TIC, LCS, LCSD, MDL,
MS, MSD, Method Val, Tune, Tune/Breakdown, or Breakdown
Level
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The level defined for a calibration sample or quality control sample.
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Table 72. Data Review sample list columns (Sheet 2 of 3)
Column
Description
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
Integration Mode
Indicates whether the peaks have been manually integrated or integrated from the original
method.
Height
The distance from the peak maximum to the peak base, measured perpendicular to the
ordinate. When the Resp Ratio is specified as Height, this column displays an asterisk
(*Height).
Area
The area obtained by integrating peak intensities from the start to the end of the peak.
When the Resp Ratio is specified as Area, this column displays an asterisk (*Area).
Actual RT
Actual retention time for the compound. Retention time is the time after injection when a
compound elutes and the total time that the compound is retained on the chromatograph
column.
Expected RT
Expected retention time for the compound.
Calc Amt
The amount present in the sample, as determined using the calibration curve and the
response ratio.
Theo Amt
Theoretical amount of the compound expected in the sample.
Sample Amt
The injected volume multiplied by the 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.
Resp Ratio
The ratio of the Response value to the IS Response value. If the Response is specified as Area
in the processing method, the units of both Response and IS Response are counts-sec. If the
Response is specified as Height in the processing method, the units of both Response and IS
Response are counts.
IS Amt
Amount of internal standard.
IS Resp
Response of the internal standard.
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Table 72. Data Review sample list columns (Sheet 3 of 3)
Column
Description
Active
Displays or hides a compound for a particular sample. When a calibration standard is
marked inactive, the application no longer uses the data file’s calibration point for the
calibration and removes it from the graphical view of the calibration curve displayed in the
Qualification pane. It is no longer part of the result set.
Excluded
Turns a compound on or off in the calibration curve of the Qualification pane.
%Diff
The calculated amount minus the expected amount, divided by the expected amount, and
then multiplied by 100.
%RSD
Standard deviation of the multiple samples of one level, multiplied by 100, and divided by
the average of the multiple samples of that level. This calculation is based on the calculated
amounts.
%CV
Coefficient of Variance. Standard deviation of the multiple samples of one level, multiplied
by 100, and divided by the average of the multiple samples of that level. This calculation is
based on the areas of the peaks.
Channel
Specifies the channel on which the sample was run. If the sample is not acquired, the value is
Pending. The Channel column is available only when you have enabled multiplexing in the
Configuration mode. See “Multiplexing” on page 92.
Comment
A user-defined comment for the sample.
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Column Display
The sample list can contain many columns of information. You can scroll to see all the
columns of information, and you can customize which columns to display and their display
order.
Follow these procedures:
• To scroll the sample list
• To customize the column display
 To scroll the sample list
Use the horizontal scroll bar at the bottom of the sample list to view all the information.
When you use the scroll bar at the bottom of the sample list, the Status, Flags, Filename,
and Sample Type columns stay fixed while the other columns scroll right and left.
 To customize the column display
1. Right-click the Data Review sample list and choose Modify Columns from the shortcut
menu.
The Modify Columns dialog box opens. See “Modify Columns dialog box.”
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, Flags, Filename, and Sample
Type columns.
3. To arrange the order of the columns, do the following:
a. In the Displayed Columns pane, select a column name.
b. Use 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 Data Review
sample list, and the last column in the list represents the rightmost column in the
Data Review sample list.
Note You cannot move the Status, Flags, Filename, or Sample Type 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.
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5. When you have completed your changes, click OK.
The columns in the sample list immediately reflect your changes. The application uses
these settings for all sample lists in the Data Review view.
Figure 88. Modify Columns dialog box
Table 73. Modify Column 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, Flags,
Filename, and Sample Type columns.
Moves all columns except Status, Flags, Filename, and Sample Type to the Available Columns pane.
Moves the selected column name in the Displayed Columns pane one row up in the column order.
You cannot move the Status, Flags, Filename, and Sample Type columns.
Moves the selected column name in the Displayed Columns pane one row down in the column order.
You cannot move the Status, Flags, Filename, and Sample Type columns.
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Status Indicators
Status indicators show the current status of each sample during the acquisition and
processing:
Sample is not acquired.
Sample is acquired but not processed.
Sample is acquired and processed.
Sample is currently acquiring.
Status indicators
Caution Flags
The Flags column in the sample list displays a caution flag if the sample is not in compliance
with the method criteria.
Sample caution flags remain static when you switch between compounds for chromatogram
review until a change is completed, for example, when a compound is manually integrated
and no longer falls outside the accepted criteria.
Sample caution flags
To display a summary of problems found in the sample, click the caution flag. The summary
does not list compounds that are not found in Unknown sample types.
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Compound Flags
Flags are displayed in these situations:
• When a compound has violated (or is activated by) any of the values set in the method
(See “Editing the QAQC Page” on page 183.)
• For compounds that are not found
• For compounds that are not found in Cal Std or Chk Std sample types
• For compounds that are outside the specified ion ratio range
These criteria do not apply to Matrix Blank sample types when the compound is an internal
standard.
The compounds list is sorted first by flag indicators and then by compound names.
Compound flags indicate the following:
• Red flags for compounds that have ion ratio failures or method validation failures
• Orange flags for compounds that are below the LOQ, below the LOD, or between the
LOD and LOQ values specified in the method
• Green flags for compounds that are over the LOR amount specified in the method
• No flag for compounds that have no errors or where no report options are selected
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Inactive and Excluded Compounds
Use the Active and Excluded columns to control which compounds are used for calculating
the calibration curve and for reporting.
Follow these procedures:
• To make a sample active or inactive
• To exclude a calibration point
 To make a sample active or inactive
1. Select the sample in the sample list.
All compounds in the selected sample are displayed in the Compounds pane. Inactive
compounds are grayed out.
2. In the Compounds pane, select the compound whose active/inactive status you want to
change.
3. In the sample list, select or clear the Active check box.
Use the horizontal scroll bar at the bottom of the table to scroll to the Active column.
Inactive compound
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 To 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.
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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Quan Mode
Use the Quan Mode and the associated Compounds pane to view quantitative information to
complement the textual information for the selected sample. The Quan Mode displays peak
information for selected compounds that are found in the processed samples.
Sample list
Compounds pane
Peak display panes
In addition to the Data Review Sample List, the Quan Mode view uses the following panes:
• Compounds Pane
• Peak Display Panes
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Compounds Pane
The Compounds pane works with the sample list pane to display textual and graphical values
for a unique file and compound combination.
 To sort the compounds list
In the Compounds pane, right-click and choose one of the following sort styles from the
shortcut menu.
Command
Description
Sort by Flag and
Alphabetical
Sorts the compounds first by flag and then, within each flag
group, sorts the compounds alphabetically.
Sort by Flag and
Retention Time
Sorts the compounds first by flag and then, within each flag
group, sorts the compounds by retention time.
Sort by Alphabetical
Sorts the compounds alphabetically (1–n followed by a–z).
Sort by Retention Time
Sorts the compounds from shortest retention time to longest
retention time.
 To display specific problems with a compound
Hold the cursor over the flag to view a description of the problems with the compound.
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Peak Display Panes
In the peak display panes, you can display multiple panes of data for each compound.
You can display any of the following types of data:
• Quan Peak
• Confirming Ions
• Calibration Curve
• Ion Overlay
• ISTD
• Reference Peak
• Spectra
 To display peaks for a specific compound
1. In the sample list, select a sample.
The Compounds pane lists all compounds specified in the method and found in the
sample.
2. In the Compounds pane, select a compound that was found in the sample.
By default, the first display pane shows the quantitative peak for the selected compound.
3. In the second pane, select the additional type of data that you want to display.
Figure 89. Displaying a compound peak
1. Select a sample.
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2. Select a compound. 3. Select a data type.
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Follow these procedures to change the display of the peak data:
• To change the peak panes
• To zoom in on a peak
 To change the peak panes
In any of the peak panes, right-click the header bar or click the
icon.
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 364.
Figure 90. Quantitative peak pane with multiple quantitative peaks
Peak 1 of 2
Peak 2 of 2
Follow these procedures to modify the quantitative 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.
The Add Peak command is available only when the application has not detected a peak.
2. Click to indicate the left and right base points for the peak.
The application places the peak delimiter tags at these locations and automatically
updates the peak values (area, height, and so forth) in the result set.
Manually added
base points
Note The Add Quan Peak command is also available on the Confirming Ions pane.
 To remove a manually created peak
Right-click the pane, and choose Remove Quan Peak from the shortcut menu.
The application removes the manually added peak.
Note The Remove Quan Peak command is also available on the Confirming Ions pane.
 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.
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.
Note The Method Integration Settings and Manual Integration Settings commands are
also available on the Confirming Ions pane.
 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.
Note The Peak Labels command is also available on the Confirming Ions pane.
Tip The labels do not always update on all peak displays. To update all labels, select a
different compound, and then reselect the compound whose labels you changed.
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 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.
Figure 91. Peak Detection Settings dialog box
Editing all samples in the batch
Editing only the selected sample
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2. Edit any of the detection settings.
For detailed descriptions of all detection settings, see “Detection” on page 135.
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.
Table 74. Quan Peak pane shortcut menu commands (Sheet 1 of 2)
Command
Description
Method Integration Settings
Use Local Method Peak Detection Settings: Applies the
local method integration settings to the selected
compound.
To edit these peak detection settings, use the Peak
Detection Settings > Edit Local Method Peak Detection
Settings command.
Use User Peak Detection Settings: Applies the
user-customized method integration settings to the
selected compound.
To edit these user-customized settings, use the Peak
Detection Settings > Edit User Defined Peak Detection
Settings command.
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Manual Integration Settings
Displays manual integration settings.
Add Quan Peak
–or–
Remove Quan Peak
–or–
Cancel Add Peak
Adds a peak, removes a peak, or cancels an add peak
operation in progress.
Confirming Ion List
Select the confirming ions to be viewed. Not available for
analog compounds.
Send RT to Method
Sets the current retention time as the expected retention time
for the compound in the local method.
Peak Labels
Displays or hides the peak labels (Label Area, Label
Retention Time, Label Height, or Label Signal to Noise).
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Table 74. 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 92. Quantitative peak with multiple confirming ions
Figure 93. 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 75. 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
Thermo Scientific
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 75. Confirming Ions pane shortcut menu commands (Sheet 2 of 2)
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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 94. 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 76. Calibration Curve pane shortcut menu commands
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Command
Description
Standard Type
Sets the standard type to External or Internal.
Calibration Curve Type
Sets the calibration curve type to one of the following:
• Linear: Allows all settings with this exception: When Origin
is set to Include, all Weighting values are grayed out and
Weighting is set to Equal.
• Quadratic: Allows all settings with this exception: When
Origin is set to Include, all Weighting values are grayed out
and Weighting is set to Equal.
• Average RF: Allows no Weighting or Origin selections. All
Weighting and Origin values are grayed out. Weighting is set
to Equal, and Origin is set to Ignore.
Response Via
Sets the response to Area or to Height.
Weighting
Sets the weighting to equal, 1/X, 1/X^2, 1/Y, or 1/Y^2.
Origin
Sets the origin to Ignore, Force, or Include.
Units
Sets the units.
Done with Settings
Saves the calibration curve settings.
Reset Scaling
Resets the original scale in the calibration curve pane.
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Ion Overlay
The Ion Overlay pane represents an overlay of the entire ion set—quantification and
qualifying/confirming—for the selected sample and compound. Use this pane to graphically
review the peak apex alignment and co-eluting peak profiles.
Note For compounds with an analog detection type, the application displays “No Data”
in the Ion Overlay pane.
Figure 95. 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 173.
Figure 96. Quantitative peak with an internal standard
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Reference Peak
The Reference Peak pane displays the reference peak as specified in the method. See “To
specify a chromatogram reference sample” on page 124.
Figure 97. Quantitative peak with a reference peak
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Spectra
The Spectra pane displays a comparison of the spectra found in the data and the method
reference.
Note For compounds with an analog detection type, the application displays “Not
Available” in the Spectra pane.
Figure 98. Quantitative peak with data and reference spectra
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Qual Mode
Use the Qual Mode and the associated peak list to view qualitative information that
complements the textual information for the selected Unknown/TIC sample. The Qual
Mode view displays detected peaks for the selected sample. From the Qual Mode view, you
can manually add peaks. The Qual Mode view is available only for Unknown/TIC sample
types.
Sample list
Chromatogram
navigation pane
Peak list
Qualitative peak pane
Spectra pane
Ranking pane
Tip To resize the panes, drag the separators that divide the panes.
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In addition to the Sample List, the Qual Mode view displays data in the following panes:
• Peak List
• Chromatogram Navigation Pane
• Qualitative Peak Pane
• Spectra Pane (Reference and Selected)
• Ranking Pane
Peak List
The peak list works with the sample list to display graphical values for a unique sample and
peak combination. For detailed descriptions of parameters on the peak list, see “Peak list
parameters” on page 378.
 To display peaks for a specific compound
1. From the sample list, select a sample.
Note If you select a sample type other than Unknown/TIC, the TraceFinder
application returns you to Quan Mode.
The peak list displays the retention times for peaks identified in the selected sample, the
values for the best match methods for each peak, and the compound match.
The number of peaks that are listed is specified in the method. You can change the
number of identified peaks in the Method Template Editor. See “Creating a Method
Template” on page 216.
2. From the peak list, select a peak in the sample.
The TraceFinder application displays the selected peak in the qualitative peak pane.
When you select a data-dependent sample, the peak can be from either a full scan or a
QED spectrum of an SRM-filtered chromatogram.
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The TraceFinder application displays the Spectra pane with two sections:
• The Qual Data pane shows spectra data for the peak in the raw data file.
• The Qual Library pane shows actual spectra for the identified library compound.
Reference spectra
from the library
Actual spectra for the
compound
The TraceFinder application locates the selected peak in the navigation chromatogram.
 To remove a peak
1. Select a peak in the peak list.
2. Right-click and choose Remove Selected Peak from the shortcut menu.
The TraceFinder application removes the selected peak from the peak list.
Note There is no undo for this action, but you can manually add a peak to redefine a
removed peak. See “Chromatogram Navigation Pane” on page 379.
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Figure 99. Peak list
Table 77. Peak list 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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Chromatogram Navigation Pane
The chromatogram navigation pane displays all peaks in the selected sample. The peak
selected in the peak list displays a red marker. See “Chromatogram navigation pane” on
page 380.
For a description of commands on the shortcut menu, see “Chromatogram navigation pane
shortcut menu commands” on page 380.
 To zoom in on a peak
1. In the chromatogram navigation pane, drag the cursor to delineate a rectangle around the
peak.
The delineated area expands to fill the view.
2. To restore the default view, right-click the chromatogram navigation pane and choose
Reset Scaling from the shortcut menu.
 To manually add a peak
1. Zoom in to better identify which peak to add to the results set.
2. Right-click the chromatogram navigation 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 chromatogram navigation pane.
The TraceFinder application places the peak delimiter tags at the base point locations and
automatically updates the peak values in the peak list and qualitative peak pane.
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Figure 100. Qualitative peak pane with a manually added peak
Manually added
base points
Figure 101. Chromatogram navigation pane
Table 78. Chromatogram navigation 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.
Reset Scaling
Resets the original scaling after a zoom operation.
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Qualitative Peak Pane
The qualitative peak pane displays the selected peak. See “Qualitative peak pane” on
page 383.
Follow these procedures:
• To zoom in on a peak
• To manually add a peak
• To remove a peak
• To switch between method and manual integration modes
• To change the displayed information for detected peaks
For a description of commands on the shortcut menu, see “Qualitative peak pane shortcut
menu commands” on page 383.
 To zoom in on a peak
1. In the chromatogram plot, drag the cursor to delineate a rectangle around the peak.
The delineated area expands to fill the view.
2. To restore the default view, right-click the chromatogram plot and choose Reset Scaling
from the shortcut menu.
 To manually add a peak
1. Right-click anywhere in the qualitative peak pane, and choose Add Peak from the
shortcut menu.
If a peak is already detected, the Add Peak command is not enabled.
2. Click to indicate the left and right base points for the peak.
The TraceFinder application places the peak delimiter tags at these locations and
automatically updates the peak values (area, height, and so forth) in the result set.
Manually added
base points
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 To remove a peak
Right-click the chromatogram plot, and choose Remove Peak from the shortcut menu.
The TraceFinder application removes the peak displayed in the qualitative peak pane. All
data for this peak are removed from the Qual Mode panes.
 To switch between method and manual integration modes
Right-click the chromatogram view and choose Method Integration or Manual
Integration from the shortcut menu.
Initially, the method and manual integration settings that are stored for a compound and
file are identical. When you switch modes, the saved result set does not change. However,
when manual data are available, the chromatogram plots and the result set update as you
switch between method and manual modes.
As you switch between modes, each pane reflects the changes. The generated reports for
these data identify the manual modifications.
 To change the displayed information for detected peaks
1. Right-click the chromatogram plot and hold the cursor over Peak Labels.
2. Choose to display labels for the peak retention time, peak height, peak area, or signal to
noise.
The label types in the list are selected for displayed labels and cleared for labels that are
not displayed.
3. To remove a label, select the label type again and clear it.
Label settings are globally applied to qualitative peaks, confirming peaks, and internal
standard peaks.
Tip The labels do not always update on all peak displays. To update all labels, select a
different compound, and then reselect the compound whose labels you changed.
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Figure 102. Qualitative peak pane
The qualitative peak pane shortcut menu includes the following commands:
Table 79. Qualitative peak 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
Removes the qualitative peak displayed in the Qual pane.
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Spectra Pane (Reference and Selected)
The spectra pane displays the reference spectra and the spectra for the selected sample. The
top pane displays the reference spectra for the identified compound from the library; the
bottom pane displays the spectra for the selected peak.
Figure 103. Spectra pane
Reference
spectrum from
the library
Actual spectrum
for the selected
peak
 To zoom in on a peak
1. In the spectra plot, drag the cursor to delineate a rectangle around the peak.
The delineated area expands to fill the view.
2. To restore the default view, right-click the chromatogram plot and choose Reset Scaling
from the shortcut menu.
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Ranking Pane
The ranking pane displays the three best library matches for the selected peak. Use this pane
to select a different library entry for the peak. See “Ranking pane.”
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 ranking pane parameters, see “Ranking pane parameters.”
 To change the library entry for a selected peak
In the ranking pane, select the check box for the library entry that you want to use to
identify the selected peak.
• In the Spectra pane, the reference spectra change to show the spectra for the selected
library entry.
• In the peak list, the SI, RSI, MP, and Compound values update to reflect the selected
library entry.
Selected library entry
in the ranking pane
Reference spectra
for Pyrazinamide
Peak list for
Pyrazinamide
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Figure 104. Ranking pane
Table 80. Ranking 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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Working in the Report View
Use the Report View to display or generate reports for the currently selected batch in the
Analysis mode. You must process each sample in the batch before you can view or generate a
sample-level report for that sample.
 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.
This section includes the following topics:
• Viewing Reports
• Generating Reports
• Working with Reports
• Working with the Active View
Figure 105. 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.”
Preview reports for all Standard report types are always available. You must generate
Custom and Target Screening report types before they are available in this list.
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The Report View page displays one of the following report outputs:
–
Standard reports as PDF files
–
Custom reports in XLSM format
–
Target Screening reports as PDF files
• Generate Only: Creates all specified report output formats for the selected sample- or
batch-level report. See “Generating Reports” on page 392.
Viewing Reports
Use the View Only features to view all configured standard reports and any custom or target
screening reports that you have generated. After you generate a report, the application displays
the report in the View Only report list.
Follow these procedures:
• To select a report
• To select a sample
• To select a compound
• To select a sample and a compound
 To select a report
1. Select the View Only option.
2. Open the Select a Report list to display all configured report types.
These reports reflect the Displayed Reports selections in the Configuration mode. To
change the configured reports that are available in this view, see “Specifying the Reports
Configuration” on page 68.
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.
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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.
Table 81. Filter Reports options
Option
Behavior
Only Show Automated
Batch Reports
Displays only reports that have an output format specified
in the Automated Batch Reports area in the Batch View.
See “Editing Report Output Formats” on page 320.
Standard Reports
Displays Standard report types.
Custom Reports
Displays all generated Custom report types. Custom
reports are not available for viewing until you have
generated the report.
Target Screening Reports
Displays all generated Target Screening reports. Target
Screening reports are not available for viewing until you
have generated the report.
Note When you make changes to the method in the Local Method view, to the peaks
in the Data Review view, or to the samples in the Batch View, you must regenerate the
custom or target screening reports before these changes take effect.
4. Double-click the name of the report.
The report list closes.
• When the selected report is a batch-level report, the application displays the report on
the Report View page.
• When the selected report includes separate reports for each sample, you must select a
sample file.
Follow the procedure “To select a sample” on page 390.
• When the selected report includes separate reports for each compound, you must
select a compound.
Follow the procedure “To select a compound” on page 390.
• 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 391.
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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 Check Standard Report, the sample list displays only
Chk Std samples.
Note Click the column headers to sort the samples. The application maintains this
sort order each time you open the Report View for this batch.
3. Double-click the name of the sample.
The sample list closes. The Report View page displays the sample-level report.
 To select a compound
1. 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.
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 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.
For example, if you selected the Check Standard Report, the sample list displays only
Chk Std samples.
Tip Click the column headers to sort the samples. The application saves this sort
order in the Report View for this batch.
3. Double-click the name of the sample.
The sample list closes.
4. 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 or target screening reports until you generate the report. When you
make changes to the method in the Local Method view or to the peaks in the Data Review
view, you must regenerate the custom or target screening reports to see the effects of those
changes.
Follow these procedures:
• To select a report
• To select a sample
 To select a report
1. Select the Generate Only option.
2. 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 68.
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 “Editing Report
Output Formats” on page 320.
If you have only batch-level reports specified in the
Batch View, selecting this option excludes all reports
in the Report Name list.
Standard Reports
Displays sample-level Standard report types.
Custom Reports
Displays sample-level Custom report types.
Target Screening Reports
Displays sample-level Target Screening report types.
Note Click the column headers to sort the samples. The application saves this sort
order in the Report View for this batch.
4. Double-click the name of the report.
The report list closes. You must select a sample file for the selected report.
 To select a sample
1. Open the Sample File list to display all samples in the batch.
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2. To show only samples that would be included in the selected report, select the Only
Show Samples Relevant… check box.
For example, if you selected the Check Standard Report, the sample list displays only
Chk Std samples.
Note Click the column headers to sort the samples. The application saves this sort
order in the Report View for this batch.
3. Select the check box for each sample 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.
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.
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7. To view the report you generated, follow the instructions in “Viewing Reports” on
page 388.
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.
• A PDF report view is available for all Standard and Target Screening report types.
• An Excel Macro-Enabled Workbook report view is available for any Custom report types
that you have generated with the Generate XLSM option selected.
Follow these procedures:
• To print a standard or target screening report
• To export a standard report
• To search for text
• To enlarge the report text
 To print a standard or target screening report
1. Select the report to print from the Select a Report list.
2. (Optional) Select a sample from the Sample File list.
The application displays the report on the Report View page.
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3. Click the Print Report icon,
Using the Analysis Mode
Working in the Report View
.
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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, and select a zoom scale.
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Working with the Active View
Use the Active View page to view quantitative data for each sample in a report. Data in the
Active View are labeled with flag information. These flags are based on a comparison of the
batch data to criteria defined in the master method.
 To display the Active View page
Click the Active View tab.
The Active View page displays quantitative data and QAQC error flags for each sample.
See “Active View page.”
 To display a report
1. Select a report type from the Select a Report list.
Only the report types created for the current batch are displayed in the list.
2. (Optional) When the report type includes separate reports for each sample, select a
sample file.
 To filter which compounds to display
Click the Showing button to switch the display to either all compounds or only
compounds that are flagged for failing a QAQC test.
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Figure 106. Active View page
Table 82. Active View parameters (Sheet 1 of 4)
Parameter
Description
View Only
Makes the Active View pane available.
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 82. Active View parameters (Sheet 2 of 4)
Parameter
Description
Column headings
Many column headings are specific to individual reports. See “Active View Report Contents”
on page 404.
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, Internal Standard, Surrogate, MSTune, Native, or Breakdown.
QAQC Flags
Indicates that the QAQC check for the sample failed.
Manual Integration reports do not use the QAQC column.
Quan Flags
•
•
•
•
•
Limit of Detection (LOD)
Limit of Quantitation (LOQ)
Limit of Reporting (LOR)
Values between the limit of detection and the limit of quantitation, known as the J flag
Upper Limit of Linearity (ULOL)
Quan flags do not apply to these sample types: Cal Std, Chk Std, Matrix Blank, or Solvent.
Manual Integration reports do not use the Quan Flag column.
Manual Flags
Indicates manually integrated peaks.
M: Indicates a manually integrated 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
Confirming n Mass
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Mass of the confirming peak.
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Table 82. Active View parameters (Sheet 3 of 4)
Parameter
Description
Confirming n
Response
Response of the confirming peak.
Confirming n Manual Indicates a manually integrated confirming peak.
Flag
Confirming n Ion
Ratio Flag
Indicates that the ion ratio is out of range. 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 173.
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 173.
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 150.
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 82. Active View parameters (Sheet 4 of 4)
Parameter
Description
Internal Standard reports
Std Response
Average of the internal standard’s response as found in the calibration file.
Minimum Response
Minimum response time as specified on the ISTD page in Method Development mode. See
“ISTD” on page 190.
Maximum Response
Maximum response time as specified on the ISTD page in Method Development mode. See
“ISTD” on page 190.
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 190.
Max RT
Maximum retention time as specified on the ISTD page in Method Development mode. See
“ISTD” on page 190.
Sample RT
Retention time found in the sample.
Graphical data
Quan Peak 1
Calibration curve
Displays a graphical view of the calibration curve for the selected compound and key
statistical values for evaluating the quality of the calibration.
Spectra
Displays a comparison of the spectra found in the data and the method reference.
QED Spectra
Displays the averaged QED spectra from the raw data file and the datastore match. If the
sample contains no QED data, the page is blank.
Confirming Ions
Displays a graphical view of all qualifying/confirming ions for the selected sample and
compound, and displays calculated ion ratios and ion ratio acceptance windows.
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Active View Report Contents
Each standard report that uses the Active View displays values that are common to all reports.
See “Common Active View report columns” on page 405.
In addition to the common values, the following reports display additional active view
features:
• Blank Report Active View columns
• Calibration Report Active View columns
• High Density Sample Report 1 and High Density Sample Report 1 Long Active View
columns
• High Density Sample Report 2 and High Density Sample Report 2 Long Active View
columns
• High Density Sample Report 3 and High Density Sample Report 3 Long Active View
columns
• Internal Standard Summary Report Active View columns
• Ion Ratio Failure Report Active View columns
• Manual Integration Report Active View columns
• LCSLCSD Report Active View columns
• Method Detection Limit Report Active View columns
• Method Validation Report Active View columns
• MSMSD Report Active View columns
• Quantitation Report Active View columns
• Solvent Blank Report Active View columns
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Table 83. 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, Internal Standard, Surrogate, MSTune, Native, or Breakdown.
QAQC Flags
Indicates that the QAQC check for the sample failed.
The Method Validation and MDL reports do not use the QAQC column.
Quan Flags
•
•
•
•
•
Limit of Detection (LOD)
Limit of Quantitation (LOQ)
Limit of Reporting (LOR)
Values between the limit of detection and the limit of quantitation, known as the J flag
Upper Limit of Linearity (ULOL)
Quan flags do not apply to these sample types: Cal Std, Chk Std, Matrix Blank, or Solvent.
The Calibration report does not use the Quan Flags column. The Method Validation,
Method Detection Limit, and LCSLCSD reports do 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 84. 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.
Inj Conc
Calculated amount as the sample was injected, with no conversion applied.
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Table 84. Blank Report Active View columns (Sheet 2 of 2)
Column
Description
Inj Units
Injection units specified on the Calibration page in Method Development mode. See
“Calibration” on page 173.
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 173.
Table 85. Calibration Report Active View columns
Column
Description
Curve Type
The type of curve used when calibrating the compound (linear, quadratic, or average
response factor).
Average RF
The average response factor. Applicable if curve type is Average RF.
Average Response
The average response for the internal standard across all calibration points. Applies only to
Internal Standard sample types.
A0
The value with no X. Applies only to linear and quadratic curves.
A1
The X value. Applies only to linear and quadratic curves.
A2
The X^2 value. Applies only to quadratic curves.
R^2
The minimum correlation coefficient (r2) for an acceptable calibration (when in linear or
quadratic mode).
RSD
Relative standard deviation. Applies only to internal standards and targets calibrated with
an average RF curve.
Level
The column specifies the level name; the field value specifies the data point used in
calibration. This field can be Response Factor for external calibration, Response Ratio for
internal linear or quadratic, or Relative Response Factor for Internal Average RF. There is
one column for each level in the curve. If the batch uses an extended calibration, there
might be more columns than calibration standards in the current batch.
Table 86. High Density Sample Report 1 and High Density Sample Report 1 Long Active View columns
Column
Description
m/z
Mass-to-charge ratio for the 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.
T Amount
Theoretical amount of the compound. Reports N/A when not applicable.
Conc
Calculated (injected) amount.
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Table 87. High Density Sample Report 2 and High Density Sample Report 2 Long Active View columns
Column
Description
m/z
Mass-to-charge ratio for the 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 88. High Density Sample Report 3 and High Density Sample Report 3 Long Active View columns (Sheet 1 of 2)
Column
Description
m/z
Mass-to-charge ratio for the 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.
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.
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Table 88. High Density Sample Report 3 and High Density Sample Report 3 Long Active View columns (Sheet 2 of 2)
Column
Description
Confirming 2 Ion Ratio
Actual ratio of the confirming ion response to the quantitation ion response.
Confirming 2 Range
Acceptable range for the confirming ion.
Table 89. 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 190.
Maximum Response
Maximum response time as specified on the ISTD page in Method Development
mode. See “ISTD” on page 190.
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 190.
Max RT
Maximum retention time as specified on the ISTD page in Method Development
mode. See “ISTD” on page 190.
Sample RT
Retention time found in the sample.
Table 90. 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.
Table 91. Manual Integration Report Active View columns (Sheet 1 of 2)
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.
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Table 91. Manual Integration Report Active View columns (Sheet 2 of 2)
Column
Description
Manual RT
Apex retention time for the manually integrated peak.
Manual Peak Height
Height of the manually integrated peak.
Manual Peak Area
Area of the manually integrated peak.
Table 92. LCSLCSD Report Active View columns
Column
Description
Spike Amount
Lab control theoretical concentration.
LCS Concentration
Lab control spike concentration.
LCS % Received
Lab control concentration percentage.
Lower Limit %
Recovery lower limit as specified in the master method. See the Limits section in
“Editing the QAQC Page” on page 183.
Upper Limit %
Recovery upper limit as specified in the master method. See the Limits section in
“Editing the QAQC Page” on page 183.
LCSD Concentration
Lab control spike duplicate concentration.
LCSD % Received
Lab control spike duplicate concentration percentage.
RPD
Lab control relative percentage difference.
Max RPD
Lab control spike maximum relative percentage difference (set in method).
Number of Rec Failures
Number of recovery failures for lab control spike concentration and lab control spike
concentration duplicate.
Number of RPD Failures
Number of relative percentage difference failures for lab control spike concentration
and lab control spike concentration duplicate.
Note For LCSLCSD batch reports, the application displays the active view peak graphics only when you click a
field pertaining to a sample, such as the LCS or LCSD concentration fields.
Table 93. Manual Integration Report Active View columns (Sheet 1 of 2)
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.
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Table 93. Manual Integration Report Active View columns (Sheet 2 of 2)
Column
Description
Manual Peak Height
Height of the manually integrated peak.
Manual Peak Area
Area of the manually integrated peak.
Table 94. Method Detection Limit Report Active View columns
Column
Description
Avg Conc
The average of the concentration for the compound across all samples.
Std Dev
The standard deviation of the concentration.
t-stat
The t-statistic value defined as the ratio of a coefficient to its standard error.
% RSD
%RSD of concentrations
MDL
Method detection limits. The calculated limit of detection.
Note For Method Detection Limit batch reports, the application displays the active view peak graphics only when
you click a field pertaining to a sample. These numbered fields are to the right of the MDL column.
Table 95. Method Validation Report Active View columns
Column
Description
Avg Conc
The average of the concentration for the compound across all samples.
Theo Conc
Values for each compound that represent the expected theoretical concentration of
that compound in the sample as defined in the master method. See the Meth Val
section in “Editing the QAQC Page” on page 183.
% Diff
The percentage difference calculated as ([MethodValidationMeanValue minus the
Theo Conc] divided by the Theo Conc) multiplied by 100.
Min Conc
Calculated by (Min recovery percent * Theo Conc) divided by 100.
Max Conc
Calculated by (Max recovery percent * Theo Conc) divided by 100.
% RSD
%RSD of concentrations
Max % RSD
The maximum relative standard deviation (RSD) of the set of observed
concentrations for a component across the set of method validation samples (when in
average RF mode) as defined in the master method. See the Meth Val section in
“Editing the QAQC Page” on page 183.
Calculated Amount <Sample
Name>
This field is reproduced for every Method Val sample.
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Table 96. MSMSD Report Active View columns
Column
Description
Unknown Concentration
Concentration of the unknown sample.
Spike Amount
Matrix spike theoretical concentration.
MS Concentration
Matrix spike concentration.
MS % Received
Matrix spike concentration percentage.
Lower Limit %
Recovery lower limit as specified in the master method. See the Limits section in
“Editing the QAQC Page” on page 183.
Upper Limit %
Recovery upper limit as specified in the master method. See the Limits section in
“Editing the QAQC Page” on page 183.
MSD Concentration
Matrix spike duplicate concentration.
MSD % Received
Matrix spike duplicate concentration percentage.
RPD
Matrix spike relative percentage difference.
Max RPD
Maximum relative percentage difference as specified in the master method. See the
Lab Control section in “Editing the QAQC Page” on page 183.
Number of Rec Failures
Number of matrix spike and matrix spike duplicate failures.
Number of RPD Failures
Number of relative percentage difference failures.
Note For MSMSD batch reports, the active view peak graphics are shown only when you click a field pertaining to
a sample, such as Unknown, MS, or MSD concentration fields.
Table 97. Quantitation Report Active View columns (Sheet 1 of 2)
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 150.
Response
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Sum of all quantitative peak response values for the compound.
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Table 97. Quantitation Report Active View columns (Sheet 2 of 2)
Column
Description
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 173.
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 173.
Table 98. 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 150.
Response
Sum of all Quan Peak Response values for the compound.
Method
Method of evaluation defined in the method.
Upper Limit
Defined in the method.
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Working in the Local Method View
Working in the Local Method View
A local method is a copy of a master method associated with a batch. You can edit only the
local copy of the method, or you can edit the master method and overwrite the local copy
with the edited master method.
In the Local Method view, you can edit the local method parameters. See Local Method View.
A local method is a copy of a master method associated with a batch. Local methods are
named BatchName_MasterMethodName.
 To open the Local Method View
1. Do one of the following:
From the dashboard, click Analysis.
–or–
Click Analysis in the navigation pane.
2. In the Analysis navigation pane, click Local Method.
The Local Method view for the currently selected batch opens.
You can edit many of the method parameters in a local method. Editing the local method
does not affect parameters in the master method.
For detailed descriptions of method parameters, see “Working with Master Methods” on
page 100.
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 107. Local Method View
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6 Using the Analysis Mode
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 421. 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 331.
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 421.
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 421.
 To specify template method information
1. From the Project list, select a project name.
2. From the Subproject list, select a subproject name.
Tip If there are no projects or subprojects to select, go to the Project Administration
view of the Configuration mode and create a new subproject. See “Project
Administration” on page 49.
3. To change the current method, click Select Method and select a new method.
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 To add a sample to the batch
Right-click and choose Add Sample from the shortcut menu, or click the add sample
icon,
.
The application adds a new, Unknown sample to the end of the sample list.
 To insert a sample into the list
1. Select the sample above which you will insert a new, Unknown sample.
2. Right-click and choose Insert Sample from the shortcut menu.
The application inserts a new, Unknown sample above the selected sample.
Inserted
sample
 To copy a sample
1. Select the sample 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
Thermo Scientific
Matrix Blank
Solvent
Unknown/TIC
Cal Std
Chk Std
Unknown
LCS
MDL
MS
LCSD
Method Val
MSD
Tune
Tune/Breakdown
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2. For each Chk Std or Cal Std sample, click the Level cell and select a level from the list.
The calibration and QC levels were defined in the master method. If there is nothing to
select in the Level list, do the following:
a. Close the Batch Template Editor.
b. Return to the Method Development mode.
c. Open the master method.
d. Click the Compounds tab.
e. Click the Calibration Levels tab.
f.
Add the levels.
g. Save the method.
h. Return to the Analysis mode, and begin this batch template again.
You must close your original batch template without saving it and start a new template.
For detailed instructions, see “Editing a Master Method” on page 119.
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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Working in the Batch Template Editor
3. To duplicate the selected report output formats for all samples in the batch, right-click the
cell and choose Apply Selection to All Samples from the shortcut menu.
Example
The application copies selected report output formats from the first sample.
The application 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 108. Batch Template Editor
Table 99. 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 99. Batch Template Editor parameters (Sheet 2 of 2)
Parameter
Description
Column values
Sample Type
Defines how the application processes the sample data. Each sample is classified as one of
the following sample types: Matrix Blank, Solvent, Cal Std, Chk Std, Unknown,
Unknown/TIC, LCS, LCSD, MDL, MS, MSD, Method Val, Tune, Tune/Breakdown, or
Breakdown
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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Reports
This appendix contains information about standard and custom reports.
Contents
• Specifying Reports
• Report Flags
• Sample Standard Reports
The report engine can generate several different types of reports designed to meet the needs of
the laboratory, the laboratory's customers, and key regulatory agencies that might review the
results. The reports listed in this appendix meet the requirements of various methods and
worldwide regulatory agencies and are designed to help track the performance of the system
and method. The TraceFinder application can produce both standard reports and custom
reports.
Specifying Reports
As a user in the ITAdmin or LabDirector role, you can configure a list of reports that are
available for the Method Development or Acquisition mode.
For detailed information about configuring reports in the Configuration mode, see
“Specifying the Reports Configuration” on page 68.
For detailed information about specifying reports when you create a method in the Method
Development mode, see “Editing the Reports Page” on page 202.
For detailed information about viewing batch reports in the Acquisition mode, see “Selecting
and Reviewing Reports” on page 265.
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Specifying Reports
Standard Reports
For each standard report you generate, you can create a version in hardcopy print, as a PDF
(.pdf ) file, or in an XML (.xml) output format. In addition to the report type, you can specify
a report description for each of your reports. The default report description is the report
name.
The TraceFinder application can generate the following types of standard reports:
• Batch Report
• Batch Report Rev 1
• Blank Report
• Breakdown Report
• Calibration Report
• Check Standard Report
• Chromatogram Report
• Compound Calibration Report
• Compound Calibration Report - Alternate
• Confirmation Report
• Confirmation Report 2
• High Density Calibration Report
• High Density Internal Standard Report
• High Density Internal Standard Report Long
• High Density Sample Report 1
• High Density Sample Report 1 Long
• High Density Sample Report 2
• High Density Sample Report 2 Long
• High Density Sample Report 3
• High Density Sample Report 3 Long
• Internal Standard Summary Report
• Ion Ratio Failure Report
• LCSLCSD Report
• Manual Integration Report
• Method Detection Limit Report
• Method Report
• Method Validation Report
• MSMSD Report
• Quantitation Report
• Quantitation Report - 2
• Solvent Blank Report
• Surrogate Recovery Report
• TIC Report
• TIC Summary Report
• Tune Report
To view an example of each type of standard report, see “Sample Standard Reports” on
page 430.
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Specifying Reports
Custom Reports
For each custom report you generate, you can create a hardcopy printout or an Excel
Macro-Enabled Workbook (.xlsm) output file. The default report description is the report
name.
A user in the ITAdmin or LabDirector role can configure custom reports to generate a single
report for an entire batch or 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 Long Report
• Target Screening Summary Report
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Specifying Reports
Figure 109. Reports page showing standard reports
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Specifying Reports
Figure 110. Reports page showing custom reports
Figure 111. Reports page showing target screening reports
Note Target screening reports are available only when you install the ToxID software and
enable the target screening features. See “Enabling Optional Features” on page 88.
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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 100. 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 101. 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.
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Report Flags
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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Sample Standard Reports
Sample Standard Reports
This section shows samples of the following standard report types:
• Batch Report
• Batch Report Rev 1
• Blank Report
• Breakdown Report
• Calibration Report
• Check Standard Report
• Chromatogram Report
• Compound Calibration Report
• Compound Calibration Report - Alternate
• Confirmation Report
•
•
•
•
•
•
•
•
•
•
•
Confirmation Report 2
High Density Calibration Report
High Density Internal Standard Report
High Density Internal Standard Report Long
High Density Sample Report 1
High Density Sample Report 1 Long
High Density Sample Report 2
High Density Sample Report 2 Long
High Density Sample Report 3
High Density Sample Report 3 Long
Internal Standard Summary Report
• Ion Ratio Failure Report
• LCSLCSD Report
•
•
•
•
•
Manual Integration Report
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TraceFinder User Guide
457
A
Reports
Sample Standard Reports
LCSLCSD Report
IMPORTANT When the Sample ID is the same for an unknown sample and an LCS or LCSD sample, the unknown
sample is included in the LCSLCSD report. The report information for the unknown sample is displayed as zeros.
LCSLCSD Report
Lab name:
Instrument:
User:
Batch:
Thermo Fisher Laboratory
Thermo Scientific Instrument
AMER\jamie.humphries
Preview2
Pos
Tray1:16
Tray1:9
Tray1:3
Tray1:15
Tray1:8
Sample ID
SampleID002
SampleID002
SampleID002
SampleID008
SampleID008
Page 1 of 1
Preview2_EPA536-Triazines
EPA536-Triazines
Cali File: Preview2.calx
Method:
Filename
5ppb-002
500ppt-002
Cal002
5ppb-001
500ppt-001
Level
N/A
QC
c2
N/A
QC
Sample Name
D008
D002
D002
D008
D008
File Date
6/27/2007 1:25:44 AM
6/26/2007 9:47:43 PM
6/26/2007 6:09:47 PM
6/27/2007 12:54:35 AM
6/26/2007 9:16:35 PM
Comment
New Dilutions 6/26/2007 H
New Dilutions 6/26/2007 H
New Dilutions 6/26/2007 H
New Dilutions 6/26/2007 H
New Dilutions 6/26/2007 H
SampleID002
50.00
Max Rec
RPD Fails
0
50.00
DEA
0.500
50.00
150.00
5.065
0.00
50.00
50.00
0
Cyanazine
0.500
50.00
150.00
5.127
0.00
50.00
50.00
0
0
Simazine
0.500
50.00
150.00
4.862
0.00
50.00
50.00
0
0
Atrazine
0.500
50.00
150.00
5.184
0.00
50.00
50.00
0
0
Propazine
0.500
50.00
150.00
3.829
0.00
50.00
50.00
0
0
LCSD
Conc % Rec
4.712
0.00
RPD
RPD
Fails
0
Compound
DIA
Lower
Upper
Limit % Limit %
50.00
150.00
Spike Amt
0.500
LCSD
Conc % Rec
4.712
0.00
RPD
RPD
Fails
0
0
SampleID008
0.500
4.754
0.00
Max Rec
RPD Fails
0
50.00
DEA
0.500
4.960
0.00
50.00
150.00
5.065
0.00
0.00
50.00
0
0
Cyanazine
0.500
5.218
0.00
50.00
150.00
5.127
0.00
0.00
50.00
0
0
Simazine
0.500
4.839
0.00
50.00
150.00
4.862
0.00
0.00
50.00
0
0
Atrazine
0.500
5.178
0.00
50.00
150.00
5.184
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0.00
50.00
0
0
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0.500
3.829
0.00
50.00
150.00
3.829
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0.00
50.00
0
0
Compound
DIA
Spike Amt LCS Conc
Lower
Upper
% Rec Limit % Limit %
50.00
150.00
0.00
Manually integrated
458
TraceFinder User Guide
Thermo Scientific
A Reports
Sample Standard Reports
Manual Integration Report
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459
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Reports
Sample Standard Reports
Method Detection Limit Report
Method Detection Limit Report
Lab name:
Instrument:
User:
Batch:
Thermo Fisher Laboratory
Thermo Scientific Instrument
AMER\jamie.humphries
Preview2
Page 1 of 3
Preview2_EPA536-Triazines
EPA536-Triazines
Cali File: Preview2.calx
Method:
Method Detection Limit Summary
Compound
DIA D-5
DIA
DEA D-7
DEA
Cyanazine D-5
Cyanazine
Simazine D-10
Simazine
Atrazine D-5
Atrazine
Propazine
Propazine D-14
Avg Conc
290218
Std Dev
0
t-stat
% RSD
0.00
MDL
0.095
0.000
0.000
0.00
0.000
<<<
0.000
<<<
0.000
<<<
0.000
<<<
1704578
0
0.065
0.000
2204710
0
0.062
0.000
513521
0
0.168
0.000
IS
0.00
0.000
0.00
IS
0.00
0.000
0.00
IS
0.00
0.000
0.00
IS
2292164
0
0.023
0.000
0.000
0.00
0.00
0.000
<<<
-1069.216
0.000
0.000
0.00
0.000
<<<
826
0
0.00
IS
IS
Manually integrated
460
TraceFinder User Guide
Thermo Scientific
A Reports
Sample Standard Reports
Method Detection Limit Report
Lab name:
Instrument:
User:
Batch:
Thermo Fisher Laboratory
Thermo Scientific Instrument
AMER\jamie.humphries
Preview2
Method Validation Report Data
Compound
DIA D-5
DIA
Page 2 of 3
Preview2_EPA536-Triazines
EPA536-Triazines
Cali File: Preview2.calx
Method:
1
290218
0.095
DEA D-7
DEA
1704578
0.065
Cyanazine D-5
Cyanazine
Simazine D-10
Simazine
Atrazine D-5
Atrazine
Propazine
Propazine D-14
2204710
0.062
513521
0.168
2292164
0.023
-1069.216
826
Manually integrated
Thermo Scientific
TraceFinder User Guide
461
A
Reports
Sample Standard Reports
Method Detection Limit Report
Lab name:
Instrument:
User:
Batch:
Pos
Tray1:1
Thermo Fisher Laboratory
Thermo Scientific Instrument
AMER\jamie.humphries
Preview2
Sample ID
SampleID007
Filename
Cal007
Page 3 of 3
Preview2_EPA536-Triazines
EPA536-Triazines
Cali File: Preview2.calx
Method:
Level
N/A
Sample Name
D007
File Date
6/26/2007 8:45:28 PM
Comment
New Dilutions 6/26/2007 H
Manually integrated
462
TraceFinder User Guide
Thermo Scientific
A Reports
Sample Standard Reports
Method Report
Thermo Scientific
TraceFinder User Guide
463
A
Reports
Sample Standard Reports
464
TraceFinder User Guide
Thermo Scientific
A Reports
Sample Standard Reports
Thermo Scientific
TraceFinder User Guide
465
A
Reports
Sample Standard Reports
Method Validation Report
Method Validation Report
Lab name:
Instrument:
User:
Batch:
Thermo Fisher Laboratory
Thermo Scientific Instrument
AMER\jamie.humphries
Preview2
Page 1 of 3
Preview2_EPA536-Triazines
EPA536-Triazines
Cali File: Preview2.calx
Method:
Method Validation Summary
Compound
DIA D-5
DIA
DEA D-7
Theo Conc
% Diff
Min Conc
Max Conc
0.358
0.500
-28.34
0.250
0.750
1778658
0.602
DEA
Cyanazine D-5
Cyanazine
Simazine D-10
Simazine
Atrazine D-5
Atrazine
Propazine
Propazine D-14
Manually integrated
466
Avg Conc
295652
TraceFinder User Guide
0.500
20.45
0.250
0.750
20.00
0.00
IS
20.00
0.00
0.500
12.90
0.250
0.750
505462
0.607
0.00
0.00
2224244
0.565
% RSD Max % RSD
0.00
IS
0.00
IS
20.00
0.00
IS
0.500
21.49
0.250
0.750
0.00
0.512
0.500
2.46
0.250
0.750
0.00
20.00
0.757
0.500
51.41
0.250
0.750
0.00
20.00 <<<
2334865
272050
20.00
0.00
IS
0.00
IS
<<< = Failure
Thermo Scientific
A Reports
Sample Standard Reports
Method Validation Report
Lab name:
Instrument:
User:
Batch:
Thermo Fisher Laboratory
Thermo Scientific Instrument
AMER\jamie.humphries
Preview2
Method Validation Report Data
Compound
DIA D-5
DIA
Page 2 of 3
Preview2_EPA536-Triazines
EPA536-Triazines
Cali File: Preview2.calx
Method:
1
295652
0.358
DEA D-7
DEA
1778658
0.602
Cyanazine D-5
Cyanazine
Simazine D-10
Simazine
Atrazine D-5
2224244
0.565
505462
0.607
2334865
Atrazine
0.512
Propazine
0.757
Propazine D-14
Manually integrated
Thermo Scientific
272050
<<< = Failure
TraceFinder User Guide
467
A
Reports
Sample Standard Reports
Method Validation Report
Lab name:
Instrument:
User:
Batch:
Pos
Tray1:10
Thermo Fisher Laboratory
Thermo Scientific Instrument
AMER\jamie.humphries
Preview2
Sample ID
SampleID003
Manually integrated
468
TraceFinder User Guide
Filename
500ppt-003
Page 3 of 3
Preview2_EPA536-Triazines
EPA536-Triazines
Cali File: Preview2.calx
Method:
Level
N/A
Sample Name
D003
File Date
6/26/2007 10:18:49 PM
Comment
New Dilutions 6/26/2007 H
<<< = Failure
Thermo Scientific
A Reports
Sample Standard Reports
MSMSD Report
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TraceFinder User Guide
475
A
Reports
Sample Standard Reports
TIC Summary Report
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TraceFinder User Guide
, %
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.
.
Thermo Scientific
B
Using Copy Down and Fill Down
This appendix describes the Copy Down and Fill Down commands that you can use to make
entering column values easier.
• Use the Fill Down command for the Filename, Sample Name, Sample ID, and Vial
Position columns.
• Use the Copy Down command for the Sample Type, Vial Position, Injection Volume,
Conv Factor, Level, 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
477
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.
478
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
479
C
Using Filter Criteria
The filter criteria tool is available from the compound datastore in the Configuration mode
and the acquisition list in the Method Development mode.
 To filter the compound list
1. To display only a filtered list of compounds, click the funnel icon,
header.
, in the column
For each column, a list of filterable criteria is displayed. In all columns, your filter choices
are All, Blanks, and NonBlanks. Other filter criteria are specific to the individual
columns.
2. To create a custom filter based on compound values in a specific column, choose Custom
from the column list.
The Enter Filter Criteria dialog box opens. See “ Enter Filter Criteria dialog box” on
page 482.
3. From the Operator list, select an operator.
4. From the Operand list, select an operand.
5. When all conditions are defined, click OK.
The complete filter string is displayed at the bottom of the dialog box, for example,
chemical formula = Blanks.
Note The Enter Filter Criteria dialog box is specifically named for the column on which
you are filtering. In this example, the selected column is the Compound Name column.
Thermo Scientific
TraceFinder User Guide
481
C
Using Filter Criteria
Figure 112. Enter Filter Criteria dialog box
Table 102. Enter Filter Criteria dialog box parameters
482
TraceFinder User Guide
Parameter
Description
And
Conditions
Requires meeting all filter criteria.
Or
Conditions
Requires meeting any of the specified filter criteria.
Add a
Condition
Adds a new, empty condition to the filter criteria.
Delete
Condition
Deletes the selected condition. Click the box at the left of the row to select
the condition.
Operator
The mathematical function applied to the operand.
Operand
The arguments to which the operator is applied.
Thermo Scientific
I
Index
Symbols
.csv, defined 2
.meth, defined 2
.pmd, defined 2
.raw, defined 2
.xml, defined 2
# Background Scans parameter
application configuration 80
method development 159
% Test parameter 178
%CV parameter 349
%Diff parameter 349
%RSD parameter 349
A
Account Number parameter 45
Acquire a New Raw Data File parameter 109
Acquisition command 35
Acquisition List page, Master Method View 129
Active parameter
Breakdown page 187
Data Review sample list 349
Identification page 134
Active View page 399
Actual RT parameter 348
Add a Condition parameter 482
Add Compound command 63
Add Confirming Ion command 65
Add Group command 201
Add Quan Peak command 64
Add Sample command
Acquisition mode 263
Batch View sample list 307
Batch Wizard 339
Add This Mass as New Confirming Ion command 170
Add This Mass to Existing Quan Mass Ranges command 170
Add to CDS command 112
Thermo Scientific
Add User parameter 45
Adduct 1–n parameter 214
Amount parameter 174
Analysis command 36
And Conditions parameter 482
Area Noise Factor parameter
application configuration 82
Detect page 162
Area parameter 348
Area Scan Window parameter
application configuration 83
Detect page 163
Area Tail Extension parameter
application configuration 83
Detect page 163
Area Threshold, event type 86
Assay Type parameter
Batch Wizard 333
Master Method View 127
Associate a Raw Data File dialog box 113
Associate a Raw Data File parameter 113
Auto TSRM Update parameter 276
Autocalc Initial Events parameter, Avalon 165
automated background subtraction options 123
Automatically Create the Master Method parameter 109
Available Methods parameter 333
Available Templates parameter 333
Avalon detection algorithm 76
Avalon Event List dialog box 85
B
background subtraction options 123
Background Subtraction Range Option parameter 127
Barcode Actual parameter 306
Barcode Expected parameter 306
Baseline Window parameter
application configuration 82
Detect page 162
TraceFinder User Guide
483
Index: C
Batch Level parameter
method development 204
report configuration 68
Batch view 297
Batch/Template Selection view 250
batches
Acquisition mode 246
Analysis mode 297
calibration 270
development batch 235
Best Match Method parameter 223
Breakdown sample type, defined 292
Browse In Raw File command 307
Bunch Factor, event type 86
C
cal1-caln parameter 176
Calc Amt parameter 348
Calculation Based On parameter 214
Calculation Type parameter 306
Calibration Curve Type command 370
Calibration Levels page, Master Method View 174
Calibration Method parameter 223
Calibration page
Compounds page 173
QAQC page 185
Calibration parameter 276
calibration standard (Cal Std) sample type, defined 292
Cancel Changes parameter 45
Carryover Limit parameter 184
CAS No parameter, Identification page 134
Category parameter
Acquisition List 131
Compound Datastore 59
caution flags 352
Channel parameter
Batch View 306
Data Review 349
check standard (Chk Std) sample type, defined 292
Chemical Formula parameter
Acquisition List 131
Compound Datastore 60
Chk Std page, Master Method View 186
Collision Energy parameter
Acquisition List
confirming ion 132
quantitative peak 132
Compound Datastore
confirming ion 61
quantitative peak 60
color codes, Sample Definition view 264
484
TraceFinder User Guide
commands
Acquisition 35
Add Compound 63
Add Confirming Ion 65
Add Group 201
Add Quan Peak 64
Add Sample
Acquisition mode 263
Batch View sample list 307
Batch Wizard 339
Add This Mass as New Confirming Ion 170
Add This Mass to Existing Quan Mass Ranges 170
Add to CDS 112
Analysis 36
Apply to All Peaks in Compound
Avalon 165
Genesis 160
ICIS 163
Apply to All Peaks in Method
Avalon 165
Genesis 159
ICIS 163
Apply to All Peaks with Like Sensitivity Settings
Avalon 165
Genesis 160
ICIS 163
Browse In Raw File 307
Calibration Curve Type 370
Configuration 36
Confirming Ion List 364
Continue to Method 112
Copy Down 477
Copy With Headers
Acquisition mode 264
Batch View sample list 307
Create New 343
Enable Target Screening 90
Exit TraceFinder 12
Export to CSV File
Acquisition mode 264
Batch View sample list 308
Extend Calibrations 343
Fill Down 477
Import Compounds 62
Import Published Method 226
Import Samples 307
Insert Copy Sample
Acquisition mode 263
Batch View sample list 307
Batch Wizard 339
Insert Sample
Acquisition mode 263
Batch View sample list 307
Batch Wizard 339
Thermo Scientific
Index: C
Load Compound Datastore 57
Log Off 35
Manual Integration Settings 364
Map Raw Files to Samples 307
Method Integration Settings 364
Methods 36
Modify Columns
Batch View sample list 299
Data Review sample list 350
Move Sample Down 339
Move Sample Up 339
New Compound Datastore 57
Pause Queue 287
Peak Detection Settings 365
Peak Labels 364
Real Time Status 35
Reinject Selected Samples
Acquisition mode 263
Batch view sample list 307
Remove Pending Batch 289
Remove Pending Batches 288
Remove Pending Samples 289
Remove Selected Samples
Acquisition mode 263
Batch view sample list 307
Batch Wizard 339
Save As Compound Datastore 58
Save Compound Datastore 57
Send RT to Method 364
Set This Mass as a New Quan Peak 170
Set This Mass as Quan Mass 170
Show Peak Info 365
Sort by Alphabetical 357
Sort by Flag and Alphabetical 357
Sort by Flag and Retention Time 357
Sort by Retention Time 357
Stop Active Batch 287
Stop All Batches 288
Stop Batch 289
Turn Device Off 271
Turn Device On 270
Turn Device Standby 270
Update Confirming Ion Ratios with This Spectrum
170
comma-separated values, defined 2
Comment parameter
Batch View 306
Data Review 349
Company Logo parameter 213
Company Name parameter 213
Compound Datastore view 59
Compound Datastore, administration 55
Thermo Scientific
Compound Name parameter
Acquisition List 131
Compound Datastore 59
Compound parameter
Calibration page 185
Lab Control page 193
QC levels page 178
Compound Type parameter
Calibration 173
Identification page 134
compound types
internal standards
Detection page 136
Identification page 133
non quan
Detection page 136
Identification page 133
quan
Detection page 136
Identification page 133
surrogates, Detection page 136
target
Detection page 136
Identification page 133
Compounds for Group parameter 187
Compounds page, Master Method View 129
compounds, importing to compound datastore 62
Configuration command 36
Configuration navigation pane 38
Confirming Ion List command 364
Confirming n Ion Ratio Flag parameter 402
Confirming n Ion Ratio parameter 402
Confirming n Manual Flag parameter 402
Confirming n Mass parameter 401
Confirming n Range parameter 402
Confirming n Response parameter 402
Constrain Peak Width parameter
Genesis
application configuration 79
Detect page 158
ICIS
application configuration 82
Detect page 162
Continue to Method command 112
Conversion Factor parameter 306
Copy Down command 477
Copy With Headers command
Acquisition mode 264
Batch View sample list 307
Correct Surrogates parameter 209
Create Master Method dialog box 101
TraceFinder User Guide
485
Index: D
Create Method parameter 98
Create New command 343
Create PDF parameter
Batch Template Editor 422
Master Method view 203
Create Tune Report as PDF parameter 199
Create XLSM parameter
Batch Template Editor 422
Master Method View 204
Create XML parameter
Batch Template Editor 422
Master Method View 203
Curve Type parameter
Calibration page 174
Method Template Editor 223
custom reports, listed 7
CV Test (%) parameter 190
D
Data Review view 345
Decimal Places to be Reported parameter 208
Delay Calibration Calculation option 93
Delete Condition parameter 482
Detection Method parameter
Avalon
application configuration 84
Detect page 164
Genesis
application configuration 78
Detect page 158
ICIS
application configuration 81
Detect page 162
Detection page, Master Method View 135
Detection Type parameter, Times page 148
Detector parameter, Signal page 155
Development Batch view 235
Device Name parameter
Acquisition mode 274
Batch View 328
dialog boxes
Add Library 15
Associate a Raw Data File 113
Avalon Event List 85
Create Master Method 101
Edit Compound Dependent Parameters 111
Import an Xcalibur Method 110
Invalid Compound Datastore Not Saved 58
Open Chromatograph Reference Sample 124
Open Compound Datastore 57
Save Compound Datastore 58
Select Compounds to Add 117
486
TraceFinder User Guide
Thermo Library Manager 15
Thermo Xcalibur Instrument Setup 122
Thermo Xcalibur Roadmap 14
Dilution Factor parameter 306
Disable Cluster Off, event type 87
Disable Cluster On, event type 87
Display Compounds Above Set Limit parameter 208
Display Quan Flags and Legend parameter 208
Displayed Reports parameter 72
E
Edit Compound Dependent Parameters dialog box 111
Edit User parameter 45
Email Address parameter 45
Enable parameter, Ratios page 172
Enable Peak Threshold parameter 223
Enable Target Screening command 90
Enable Tune Time Tracking parameter 209
Enable Valley Detection parameter
application configuration 79
method development 158
Enabled parameter 45
End RT parameter, Times page 149
End Threshold, event type 86
Energy Ramp parameter
application configuration 61
method development 132
Event parameter 85
Event types 86
Exact Mass Window parameter 214
Example parameter, Reports page 203
Exclude Matching Quan Peaks parameter 225
Excluded parameter 349
Exclusion Window parameter 225
Exit TraceFinder command 12
Expected RT parameter 348
Expected RT parameter, Times page 148
Expected Width parameter
application configuration 79
method development 158
Experiment Type parameter
Acquisition List 131
Compound Datastore 59
experiment types 66
Export SRM Data parameter 99
Export to CSV File command
Acquisition mode 264
Batch View sample list 308
Extend Calibrations command 343
Extracted Ion Chromatogram 66
Thermo Scientific
Index: F
F
I
feature summary 4
file types, supported 2
Filename parameter
Batch View 305
Data Review 347
Fill Down command 477
Filter parameter, Detection 155
Filter parameter, Signal page 154
Final Units parameter 306
Finish view 269
Flag Values Above Carryover parameter 209
Flag Values Above LOR parameter 209
Flag Values Above ULOL parameter 209
Flag Values Below LOD parameter 209
Flag Values Below LOQ parameter 209
Flag Values Between LOD and LOQ parameter 209
Flags parameter 347
Force Cluster Off, event type 87
Force Cluster On, event type 87
Full Name parameter 45
ICIS detection algorithm 76
Identification page, Master Method View 133
Import an Xcalibur Method dialog box 110
Import Compounds command 62
Import parameter 72
Import Published Method command 226
Import Published Method parameter 99
Import Samples command 307
Import Xcalibur Processing Method parameter 110
Include Compound Peak Spectrum as Reference Spectrum
parameter 223
Include Confirming Ions parameter 223
Injection Amount parameter 109
Injection Concentration parameter 402
Injection Units parameter 402
Injection Volume parameter
Batch View 306
method development 127
sample list 348
Insert Copy Sample command
Acquisition mode 263
Batch View sample list 307
Batch Wizard 339
Insert Sample command
Acquisition mode 263
Batch View sample list 307
Batch Wizard 339
Installed Reports parameter 72
installing NIST and QED libraries 14
installing TraceFinder 10
Instrument Method parameter
Batch View 306
General page 127
Method Forge 109
instrument status indicators 271
Instrument view 228
instruments, supported ix
Integration Mode parameter 348
Invalid Compound Datastore Not Saved dialog box 58
Ion Coelution parameter
application configuration 77
Ratios page 172
Ion Range Calc Method parameter 127
Ion Ratio Window parameter 214
Ionization parameter
Acquisition List 131
Compound Datastore 60
IS Amt parameter 348
IS Resp parameter 348
ISTD Matching parameter 224
G
General page
Background Subtraction Range Option 127
editing 121
Injection Volume parameter
Batch View 306
method development 127
Instrument Method parameter 127
Ion Range Calc Method parameter 127
Mass Precision parameter 127
Mass Tolerance parameter 128
Number of Scans to Subtract parameter 128
Qualitative Peak Processing Template parameter 127
Set Chromatogram Reference Sample parameter 128
Set Reference sample parameter 128
Stepoff Value parameter 128
Tune/Breakdown parameter 127
General page, Master Method View 121
Generate Only parameter 400
Genesis detection algorithm 76
Groups page, Master Method View 200
Groups parameter, Breakdown page 187
H
Height parameter 348
Thermo Scientific
TraceFinder User Guide
487
Index: L
ISTD page, Master Method View 190
ISTD parameter 174
IT Administrator role 46
L
Lab Control page, Master Method View 193
lab control sample (LCS) sample type, defined 292
lab control sample duplicate (LCSD) sample type, defined
292
Lab Name parameter 127
Laboratory Name parameter 213
Lens parameter
application configuration 60
method development 132
Level parameter
Batch View 305
Data Review 347
QC Levels page 178
licenses, types of x
Limit Library Hits parameter 223
Limit the Retention Time Range parameter 223
Limits page, Master Method View 184
Load Compound Datastore command 57
Local Method view 413
LOD (Detection Limit) parameter 184
Log Off command 35
Login parameter 12
login screen 12
LOQ (Quantitation Limit) parameter 184
LOR (Reporting limit) parameter 184
M
m/z Window parameter 213
Manual Flags parameter 401
Manual Injection parameter 109
Manual Integration Settings command 364
Map Raw Files to Samples command 307
Mass parameter
confirming ion
Acquisition List 132
Compound Datastore 61
quantitative peak
Acquisition List 131
Compound Datastore 60
Mass Precision parameter 127
Mass Tolerance parameter 128
488
TraceFinder User Guide
Master Method View
Acquisition List page 129
Calibration Levels page 174
Calibration page
Compounds page 173
QAQC page 185
Chk Std page 186
Compounds page 129
Detection page 135
General page 121
Groups page 200
Identification page 133
ISTD page 190
Lab Control page 193
Limits page 184
Matrix Blank page 188
Matrix Spike page 195
Method Val page 194
QC Check page 186
QC Levels page 176
Ratios page 171
Real Time Viewer page 179
Reports page 202
Solvent Blank page 191
Spectrum page 166
Surrogate page 192
Master Method View, QAQC page 183
Matrix Blank page, Master Method View 188
Matrix Blank sample type, defined 292
matrix spike (MS) sample type, defined 292
matrix spike duplicate (MSD) sample type, defined 292
Matrix Spike page, Master Method View 195
Max % Breakdown parameter 187
Max Amt Diff (%) parameter 185
Max Conc parameter 189
Max Recovery (%) parameter
Lab Control page 193
Matrix Spike page 195
Method Val page 194
Surrogate page 192
Max Recovery (%) parameter, ISTD page 190
Max RF Diff (%) parameter 186
Max RPD parameter
Lab Control page 193
Matrix Spike page 195
Max RSD (%) parameter
Method Val page 194
Max RSD (%) parameter, Calibration page 185
Max RT (+min) parameter, ISTD page 190
Max Stepoff parameter 199
Measurement Unit parameter 214
method detection limits (MDL) sample type, defined 292
Thermo Scientific
Index: N
Method Integration Settings command 364
Method parameter
Matrix Blank page 188
Solvent Blank page 191
Method Template Editor 222
Method Val page, Master Method View 194
method validation (Meth Val) sample type, defined 292
Method view 101
methods
importing Xcalibur 110
instrument 228
local 413
master 100
Method Template Editor 222
update TSQ method 269
Methods command 36
Min Peak Height (S/N) parameter
Genesis
application configuration 79
Detect page 159
ICIS
application configuration 82
Detect page 162
Min Peak Width parameter
application configuration 83
Detect page 163
Min recovery (%) parameter
ISTD page 190
Lab Control page 193
Matrix Spike page 195
Method Val page 194
Surrogate page 192
Min RF parameter 186
Min RT (–min) parameter 190
modes
choosing 32
defined 35
Modify Calibrations or Active Compounds by Group
parameter 341
Modify Columns command
Batch View sample list 299
Data Review sample list 350
Move Sample Down command 339
Move Sample Up command 339
MS2 Search Library parameter 214
MS3 Search Library parameter 214
Multiplet Resolution parameter
application configuration 83
Detect page 163
Multiplexing Channels parameter 263
Thermo Scientific
N
Name the Master Method parameter 109
Negative Peaks, event type 86
New Compound Datastore command 57
New Instrument Method parameter 99
New Sample List parameter 99
NIST library, installing 14
No Specified Retention Time parameter 214
Noise Method parameter
application configuration 82
Detect page 163
Number of Confirming Ions parameter 223
Number of Scans to Subtract parameter 128
O
Only Select Top Peaks parameter 223
Open Chromatograph Reference Sample dialog box 124
Open Compound Datastore dialog box 57
Open Instrument Method parameter 99
Open Method parameter 98
Open Qual Browser parameter 99
Operand parameter 482
Operator parameter 482
Or Conditions parameter 482
Origin parameter
Calibration 174
Method Template Editor 224
P
parameters
# Background Scans 159
application configuration 80
% Test 178
%CV 349
%Diff 349
%RSD 349
Account Number 45
Acquire a New Raw Data File 109
Active
Breakdown page 187
Data Review sample list 349
Identification page 134
Actual RT 348
Add a Condition 482
Add User 45
Adduct 1–n 214
Amount 174
And Conditions 482
Area 348
TraceFinder User Guide
489
Index: P
Area Noise Factor
application configuration 82
Detect page 162
Area Scan Window
application configuration 83
Detect page 163
Area Tail Extension
application configuration 83
Detect page 163
Assay Type
Batch Wizard 333
Master Method View 127
Associate a Raw Data File 113
Auto TSRM Update 276
Autocalc Initial Events, Avalon 165
Automatically Create the Master Method 109
Available Methods 333
Available Templates 333
Background Subtraction Range Option 127
Barcode Actual 306
Barcode Expected 306
Baseline Window
application configuration 82
Detect page 162
Batch Level
method development 204
report configuration 68
Best Match Method 223
cal1-caln 176
Calc Amt 348
Calculation Based On 214
Calculation Type 306
Calibration 276
Calibration Method 223
Cancel Changes 45
Carryover Limit 184
CAS No, Identification page 134
Category
Acquisition List 131
Compound Datastore 59
Channel
Batch View 306
Data Review 349
Chemical Formula
Acquisition List 131
Compound Datastore 60
Collision Energy
Acquisition List
confirming ion 132
quantitative peak 132
Compound Datastore
confirming ion 61
quantitative peak 60
490
TraceFinder User Guide
Comment
Batch View 306
Data Review 349
Company Logo 213
Company Name 213
Compound
Calibration page 185
Lab Control page 193
QC levels page 178
Compound Name
Acquisition List 131
Compound Datastore 59
Compound Type
Calibration 173
Identification page 134
Compounds for Group 187
Confirming n Ion Ratio 402
Confirming n Ion Ratio Flag 402
Confirming n Manual Flag 402
Confirming n Mass 401
Confirming n Range 402
Confirming n Response 402
Constrain Peak Width
Genesis
application configuration 79
Detect page 158
ICIS
application configuration 82
Detect page 162
Conversion Factor 306
Correct Surrogates 209
Create Method 98
Create PDF
Batch Template Editor 422
Master Method view 203
Create Tune Report as PDF 199
Create XLSM
Batch Template Editor 422
Master Method View 204
Create XML
Batch Template Editor 422
Master Method View 203
Curve Type
Calibration page 174
Method Template Editor 223
CV Test (%) 190
Decimal Places to be Reported 208
Delete Condition 482
Thermo Scientific
Index: P
Detection Method
Avalon
application configuration 84
Detect page 164
Genesis
application configuration 78
Detect page 158
ICIS
application configuration 81
Detect page 162
Detection Type, Times page 148
Detector 155
Device Name
Acquisition mode 274
Batch View 328
Dilution Factor 306
Display Compounds Above Set Limit 208
Display Quan Flags and Legend 208
Displayed Reports 72
Edit User 45
Email Address 45
Enable Peak Threshold 223
Enable Tune Time Tracking 209
Enable Valley Detection
application configuration 79
method development 158
Enable, Ratios page 172
Enabled 45
End RT, Times page 149
Energy Ramp
application configuration 61
method development 132
Event 85
Exact Mass Window 214
Example, Reports page 203
Exclude Matching Quan Peaks 225
Excluded 349
Exclusion Window 225
Expected RT 348
Expected RT, Times page 148
Expected Width
application configuration 79
method development 158
Experiment Type
Acquisition List 131
Compound Datastore 59
Export SRM Data 99
Filename
Batch View 305
Data Review 347
Filter 154
Filter, Detection 155
Final Units 306
Flag Values Above Carryover 209
Thermo Scientific
Flag Values Above LOR 209
Flag Values Above ULOL 209
Flag Values Below LOD 209
Flag Values Below LOQ 209
Flag Values Between LOD and LOQ 209
Flags 347
Full Name 45
Generate Only 400
Groups, Breakdown page 187
Height 348
Import 72
Import Published Method 99
Import Xcalibur Processing Method 110
Include Compound Peak Spectrum as Reference
Spectrum 223
Include Confirming Ions 223
Injection Amount 109
Injection Concentration 402
Injection Units 402
Injection Volume
Batch View 306
method development 127
sample list 348
Installed Reports 72
Instrument Method
Batch View 306
General page 127
Method Forge 109
Integration Mode 348
Ion Coelution
application configuration 77
Ratios page 172
Ion Range Calc Method 127
Ion Ratio Window 214
Ionization
Acquisition List 131
Compound Datastore 60
IS Amt 348
IS Resp 348
ISTD 174
ISTD Matching 224
Lab Name 127
Laboratory Name 213
Lens
application configuration 60
method development 132
Level
Batch View 305
Data Review 347
QC levels page 178
Limit Library Hits 223
Limit the Retention Time Range 223
LOD (Detection Limit) 184
Login 12
TraceFinder User Guide
491
Index: P
LOQ (Quantitation Limit) 184
LOR (Reporting limit) 184
m/z Window 213
Manual Flags 401
Manual Injection 109
Mass
confirming ion
Acquisition List 132
Compound Datastore 61
quantitative peak
Acquisition List 131
Compound Datastore 60
Mass Precision 127
Mass Tolerance 128
Max % Breakdown 187
Max Amt Diff (%) 185
Max Conc 189
Max Recovery (%)
Lab Control page 193
Matrix Spike page 195
Method Val page 194
Surrogate page 192
Max Recovery (%), ISTD page 190
Max RF Diff (%) 186
Max RPD
Lab Control page 193
Matrix Spike page 195
Max RSD (%)
Method Val page 194
Max RSD (%), Calibration page 185
Max RT (+min), ISTD page 190
Max Stepoff 199
Measurement Unit 214
Method
Matrix Blank page 188
Solvent Blank page 191
Min Peak Height (S/N)
Genesis
application configuration 79
Detect page 159
ICIS
application configuration 82
Detect page 162
Min Peak Width
application configuration 83
Detect page 163
Min recovery (%)
ISTD page 190
Lab Control page 193
Matrix Spike page 195
Method Val page 194
Surrogate page 192
492
TraceFinder User Guide
Min RF 186
Min RT (–min) 190
Modify Calibrations or Active Compounds by Group
341
MS2 Search Library 214
MS3 Search Library 214
Multiplet Resolution
application configuration 83
Detect page 163
Multiplexing Channels 263
Name the Master Method 109
New Instrument Method 99
New Sample List 99
No Specified Retention Time 214
Noise Method
application configuration 82
Detect page 163
Number of Confirming Ions 223
Number of Scans to Subtract 128
Only Select Top Peaks 223
Open Instrument Method 99
Open Method 98
Open Qual Browser 99
Operand 482
Operator 482
Or Conditions 482
Origin
Calibration 174
Method Template Editor 224
Password
login screen 12
user administration 45
Path 109
Peak Height (%)
Genesis
application configuration 79
Detect page 158
ICIS
application configuration 82
method development 162
Peak Noise Factor
application configuration 82
method development 162
Peak S/N Cutoff
application configuration 80
Detect page 159
Percentage 189
Perform Background Subtraction 199
Phone Number 45
Polarity
Acquisition List 132
Compound Datastore 60
Thermo Scientific
Index: P
Post-run System State 274, 328
Precursor Mass
Acquisition List
confirming ion 132
quantitative peak 131
Compound Datastore
confirming ion 61
quantitative peak 60
Priority Sequence 274, 328
Processing Configuration File 213
Product Mass
Acquisition List
confirming ion 132
quantitative peak 131
Compound Datastore
confirming ion 61
quantitative peak 60
QAQC Flags 401
QC1-QCn 178
QIon 402
Qualitative Peak Processing Template 127
Quan Flags 401
Quan Mass 402
Quan Peak m/z 401
Quan Peak Response 401
Quan Peak RT 401
Quick Mode 333
R^2 Threshold 185
Ranges, compound detection 155
Raw Filename 109
Recent Files, Method view 99
Reference Compound, Identification page 134
Remove User 45
Report All Compounds Listed in Configuration File
214
Report Concentration 208
Report Description 203
Report Name 203
Report Noise As
application configuration 80
Detect page 159
Report Semi-Quantitative Result 214
Report Type 203
Reset Password 45
user administration 45
Resp Ratio 348
Response 402
Response Via
Calibration 174
Method Template Editor 224
Retention Time 402
RMS
application configuration 83
Detect page 163
Role 45
Thermo Scientific
RT
Acquisition List 132
Calibration 173
Calibration levels 176
Calibration page 185
Chk Std page 186
Compound Datastore 60
Identification page 134
ISTD page 190
Lab Control page 193
Limits page 184
Matrix Blank page 188
Matrix Spike page 195
Method Val page 194
QC levels page 178
Solvent Blank page 191
Surrogate page 192
RT Window 214
S/N Threshold
application configuration 79
method development 158
Sample Amt 348
Sample Comment 109
Sample Concentration 402
Sample File 400
Sample ID
Batch View 305
Data Review 348
Sample Name
Batch View 306
Data Review 348
Sample Type
Batch View 305
Data Review 347
Sample Units 402
Sample Volume 306
Sample Weight 306
Save Changes 45
Screening Method 213
Select a Custom Template 108
Select a Report 400
Select Batch Location 99
Select Compounds from CDS 117
Select File and Mass Spectrum 199
Sensitivity
Avalon
application configuration 84
Detect page 164
Genesis
application configuration 78
Detect page 158
ICIS
application configuration 81
Detect page 162
Method Template Editor 223
TraceFinder User Guide
493
Index: P
Separate Ion Overlay Display 208
Set Chromatogram Reference Sample 128
Set Ion Ratio to All Confirming Peaks in Compound
172
Set Ion Ratio to All Confirming Peaks in Method 172
Set Peak Windows Settings to All Peaks in Compound
149
Set Peak Windows Settings to All Peaks in Method
149
Set Reference sample 128
Shade Row when Sample is Outside of Evaluation
Criteria 208
Show Chromatogram on Quantitation Report 208
Show Quan Peaks Only 179
Showing, Active View 400
Smoothing
Avalon
application configuration 84
Detect page 165
Genesis
application configuration 79
Detect page 158
ICIS
application configuration 81
Detect page 162
Specify Default Ion Ratio Ranges 223
Standard type 174
Start Device 274, 328
Start RT
Times page 149
Start When Ready 274, 328
Starting vial number 333
Status
Active View 401
Batch View 305
Data Review 347
Stepoff Value 128
System Shutdown Method 276
System Startup Method 276
System Status 276
Tailing Factor
Genesis
application configuration 79
method development 158
ICIS
application configuration 82
method development 162
Target Ratio 172
Template Layout 333
Theo Amt 348
Theo Conc
Lab Control page 193
Matrix Spike page 195
Method Val page 194
Surrogate page 192
494
TraceFinder User Guide
Theoretical Amount 401
Time 85
Time/Event/Value 84
Total Batch Rows 333
Total Response 401
Total Rows 400
Trace, Detection 155
Tune Compound 199
Tune File Lifetime 209
Tune/Breakdown, General page 127
ULOL (Linearity Limit) 184
Units 174
Upper Limit
Solvent Blank page 191
Use Alternate Calibration Report Format 208
Use an Existing Raw Data File 109
Use as RT Reference, Identification page 134
Use Autosampler 109
Use Average Scan 214
Use Data Dependent Scans 225
Use Full MS Scan to Confirm 214
Use Genesis Algorithm for Qual Processing 224
Use Method Forge 102, 106
Use Only Selected Method 199
Use Scan at Peak Apex 214
Use the Default Template 108
Use These Libraries 223
User Security 90
Username 12, 45
Valley Rise (%)
application configuration 80
Detect page 159
Valley S/N
application configuration 80
method development 159
Value 85
Vial Position
Batch View 306
Data Review 348
Method Forge 109
View Only 400
View Width
application configuration 77
Times page 149
Weighting
Calibration 174
Method Template Editor 224
Window
Acquisition List 132
application configuration
ion ratio 77
retention time 77
Compound Datastore 60
Ratios page 172
Times page 148
Thermo Scientific
Index: P
Window Type
application configuration 77
Ratios page 172
XIC 154
Password parameter
login screen 12
user administration 45
password, administrator 11
Path parameter 109
Pause Queue command 287
Peak Detection Settings command 365
Peak Height (%) parameter
Genesis
application configuration 79
Detect page 158
ICIS
application configuration 82
method development 162
Peak Labels command 364
Peak Noise Factor parameter
application configuration 82
method development 162
Peak S/N Cutoff parameter
application configuration 80
Detect page 159
Percentage parameter 189
Perform Background Subtraction parameter 199
Phone Number parameter 45
Polarity parameter
Acquisition List 132
Compound Datastore 60
Post-run System State parameter 274, 328
P-P Threshold, event type 86
Precursor Mass parameter
Acquisition List
confirming ion 132
quantitative peak 131
Compound Datastore
confirming ion 61
quantitative peak 60
Priority Sequence parameter 274, 328
procedures
acquisition mode
access real-time display 279
add samples to the sample list 256
assign a specific channel to a sample 262
create a batch template 254
export reports to a folder 266
import samples into the sample list 259
insert samples into the sample list 257
pause all batches in a queue 286
preview a standard report 265
Thermo Scientific
re-inject a sample from 261
remove a batch from a queue 288
remove a pending batch from a queue 288
remove a pending sample from a queued batch 289
remove a single batch from a queue 287
remove all batches in a queue 287
remove all pending batches in a queue 287
remove pending samples from a queued batch 289
remove samples from the sample list 261
save a to-be-run batch 271
select a previously acquired batch 253
select a ready-to-acquire batch 252
specify a calibration batch 270
specify device states 270
specify startup or shutdown methods 269
start a new batch 250
start an acquisition 271
update TSRM data 269
view output files 275
analysis mode
access the Analysis mode 294
add samples to the samples list 310
change the displayed information for detected peaks
qualitative peak 382
quantitative peak
Data Review 362
method development 136
change the library entry for a selected peak 385
change the peak panes display 359
copy a sample in the samples list 312
create a new batch 309
customize the column display
Batch View 315
Data Review view 350
display peaks for a specific compound 376
quantitative peak 358
display specific problems with a compound 357
edit samples in a batch 318
edit the batch-level output formats 321
edit the sample-level output formats 320
enlarge the report text 398
exclude a calibration point 355
export a report 397
insert samples in the samples list 311
make a compound active or inactive 354
manually add a peak
chromatogram pane 379
qual peak pane 381
quantitation peak 361
manually exclude a calibration point 369
manually integrate a confirming ion peak 367
manually integrate a quantitative peak 361
modify the peak detection settings 363
open a recent batch 318
TraceFinder User Guide
495
Index: P
open a saved batch 317
open the Batch View 297
open the Data Review view 345
open the Local Method View 413
open the Report View 387
print a report 396
reinject a sample 313
reinject a sample from a previously acquired batch
318
remove a manually created peak 361
remove a peak from the peak list 377
remove a peak from the qual peak pane 382
remove samples from the samples list 312
scroll the samples list 299, 350
search for text 398
select a compound 390
select a report
generating reports 392
viewing reports 388
select a sample
generating reports 393
viewing reports 390
sort the compounds list 357
submit all samples in the batch 325
submit selected samples 326
switch between method and manual integration
qual mode 382
quan mode 362
zoom in on a peak
chromatogram navigation 379
qual peak 381
quantitation peak 359
spectra pane 384
configuration mode
access the Configuration mode 37
add a compound to the datastore 63
add a confirming ion to a quan peak 65
add a quantitation peak to a compound 64
add a user 41
change the default drive 51
choose a drive 50
copy the folder hierarchy from another drive 54
create a new compound datastore 57
create projects or subprojects 52
delete projects or subprojects 53
edit user information 42
enable user security 90
hide a drive from display 51
import compounds 62
import new report types 69
open a compound datastore 57
open the Application Configuration view 67
open the Compound Datastore editor 56
open the Defaults page 73
496
TraceFinder User Guide
open the Project Administration view 49
open the User Administration view 40
refresh the drives display 51
remove a compound 63
remove a confirming ion 65
remove a user 44
remove all empty folders 53
save a datastore 57
save a datastore to a new name 58
specify common detection parameters 76
specify default laboratory and instrument names 74
specify default mass precision and intensity scale 74
getting started
choose a node 32
display a log of instrument errors 33
install the NIST library 14
install the QED library 14
log in to the TraceFinder application 11
monitor the instrument status 33
start the TraceFinder application 11
watch the real-time display from the dashboard 34
method development mode 174
access the Method Development mode 97
acquire selected samples 240
acquire the batch 240
add a compound to the list 130
add a mass as a new compound 141
add a mass as a new confirming ion peak 145
add a mass to the existing quan mass ranges 140
add a quan peak 141
add a quan peak to an existing compound 168
add compounds to the method 115, 137
add confirming ions to an existing compound 169
add ions to get an accumulated signal 168
add sample to the development batch 236
associate a raw data file with the method 113
automatically select compounds to create a new
method 102
calculate and report semi-quantitative results 211
calibrate the compounds 219
change the compound reference spectrum 140
change the quantitation mass used for a quan peak
166
copy a sample 237
correct surrogates 207
create a group 200
create a new instrument method 229
create a new multiplexing instrument method 231
delete a compound from the list 130
edit the instrument method parameters 122
enter a note for the method 221
enter column values 238
export SRM data to an XML file 227
filter the displayed compounds 133, 136
Thermo Scientific
Index: Q
identify the peaks 218
import a master method 226
import an instrument method 234
import an Xcalibur method 110
insert samples into the development batch 237
manually select compounds to create a new method
106
open a saved master method 119
open an instrument method 233
open the Development Batch view 235
open the Instrument View 228
open the Qual Browser 241
remove all samples from the samples list 239
remove selected samples from the samples list 239
replace a confirming ion peak 145
replace a quantitation mass 140
replace a quantitative peak with a confirming ion
peak 143
resize or reorganize the columns 239
save the method template 221
save the new method 145
select compounds from the datastore 117
set a confirming ion peak as an additional
quantitative peak 143
set automated background subtraction options 123
specify a chromatogram reference sample 124
specify a location for development batch data 236
specify an internal standard for a compound 173
specify general information for a master method 121
specify ion ratio criteria 171
specify mass tolerance 125
specify peak criteria 217
specify QC levels and concentrations 176
specify qualitative peak processing 220
specify quantitation flag options 206
specify quantitation limits 205
specify ranges of ions for detection and integration
150
specify standard report types and output formats 202
specify the default parameters 210
specify the exact mass window 212
specify the Exactive parameters 212
specify the ion ratio calculation method 212
specify the maximum concentration as a percentage
188
specify user interface options 206
track the use of the tune file 207
update confirming ion ratios 166
zoom in the chromatogram or spectrum displays 169
Processing Configuration File parameter 213
Product Mass parameter
Acquisition List
confirming ion 132
quantitative peak 131
Thermo Scientific
Compound Datastore
confirming ion 61
quantitative peak 60
Project Administration view 49
projects and subprojects, creating 49
Q
QAQC Flags parameter 401
QAQC page, Master Method View 183
QAQC role 48
QC Check page, Master Method View 186
QC Levels page, Master Method View 176
QC1-QCn parameter 178
QED library, installing 14
QIon parameter 402
Qual Mode 345
Qualitative Peak Processing Template parameter 127
Quan Flags parameter 401
Quan Mass parameter 402
Quan Mode 345
Quan Peak m/z parameter 401
Quan Peak Response parameter 401
Quan Peak RT parameter 401
quan report settings, specifying 205, 210
Quick Mode parameter 333
R
R^2 Threshold parameter 185
Ranges parameter, compound detection 155
Ratios page, Master Method View 171
Raw Filename parameter 109
Real Time Status command 35
Real Time Viewer page, Master Method View 179
real-time display 279
Recent Files parameter, Method View 99
Reference Compound parameter, Identification page 134
reference spectra 384
Reinject Selected Samples command
Acquisition mode 263
Batch view sample list 307
Remove Pending Batch command 289
Remove Pending Batches command 288
Remove Pending Samples command 289
Remove Selected Samples command
Acquisition mode 263
Batch view sample list 307
Batch Wizard 339
Remove User parameter 45
TraceFinder User Guide
497
Index: S
Report All Compounds Listed in Configuration File
parameter 214
Report Concentration parameter 208
Report Description parameter 203
report formats, specifying 202
Report Name parameter 203
Report Noise As parameter
application configuration 80
Detect page 159
Report selection view 265
Report Semi-Quantitative Result parameter 214
Report Type parameter 203
Report View 387
reports
Acquisition mode 265
Analysis mode 387
configuring 68
flags defined 428
listed 6
sample PDFs 430
viewing landscape in PDF 430
Reports page, Master Method View 202
Reset Password parameter 45
user administration 45
Resp Ratio parameter 348
Response parameter 402
Response Via parameter
Calibration 174
Method Template Editor 224
Retention Time parameter 402
RMS parameter
application configuration 83
Detect page 163
Role parameter 45
RT parameter
Acquisition List 132
Calibration 173
Calibration levels 176
Calibration page 185
Chk Std page 186
Compound Datastore 60
Identification page 134
ISTD page 190
Lab Control page 193
Limits page 184
Matrix Blank page 188
Matrix Spike page 195
Method Val page 194
QC levels page 178
Solvent Blank page 191
Surrogate page 192
RT Window parameter 214
498
TraceFinder User Guide
S
S/N Threshold parameter
application configuration 79
method development 158
Sample Amt parameter 348
Sample Comment parameter 109
Sample Concentration parameter 402
Sample definition view 255
Sample File parameter 400
Sample ID parameter
Batch View 305
Data Review 348
Sample Name parameter
Batch View 306
Data Review 348
Sample Type parameter
Batch View 305
Data Review 347
sample types, defined 292
Sample Units parameter 402
Sample Volume parameter 306
Sample Weight parameter 306
Save As Compound Datastore command 58
Save Changes parameter 45
Save Compound Datastore command 57
Save Compound Datastore dialog box 58
Screening Method parameter 213
Select a Custom Template parameter 108
Select a Report parameter 400
Select Batch Location parameter 99
Select Compounds from CDS parameter 117
Select Compounds to Add dialog box 117
Select File and Mass Spectrum parameter 199
Selected Reaction Monitoring 66
Send RT to Method command 364
Sensitivity parameter
Avalon
application configuration 84
Detect page 164
Genesis
application configuration 78
Detect page 158
ICIS
application configuration 81
Detect page 162
Method Template Editor 223
Separate Ion Overlay Display parameter 208
Set Chromatogram Reference Sample parameter 128
Set Ion Ratio to All Confirming Peaks in Compound
parameter 172
Thermo Scientific
Index: T
Set Ion Ratio to All Confirming Peaks in Method parameter
172
Set Peak Windows Settings to All Peaks in Compound
parameter 149
Set Peak Windows Settings to All Peaks in Method parameter
149
Set Reference sample parameter 128
Set This Mass as a New Quan Peak command 170
Set This Mass as Quan Mass command 170
Shade Row when Sample is Outside of Evaluation Criteria
parameter 208
Shoulders On, event type 87
Show Chromatogram on Quantitation Report parameter
208
Show Peak Info command 365
Show Quan Peaks Only parameter 179
Showing parameter, Active View 400
SIM experiment type 66
Single Ion Monitoring 66
Smoothing parameter
Avalon
application configuration 84
Detect page 165
Genesis
application configuration 79
Detect page 158
ICIS
application configuration 81
Detect page 162
Solvent Blank page, Master Method View 191
Solvent sample type, defined 292
Sort by Alphabetical command 357
Sort by Flag and Alphabetical command 357
Sort by Flag and Retention Time command 357
Sort by Retention Time command 357
Specify Default Ion Ratio Ranges parameter 223
Spectrum page, Master Method View 166
SRM data, exporting 227
SRM experiment type 66
standard reports, listed 6
Standard type parameter 174
Start Device parameter 274, 328
Start RT parameter
Times page 149
Start Threshold, event type 86–87
Start When Ready parameter 274, 328
Starting vial number parameter 333
status color codes, Sample Definition view 264
Status parameter
Active View 401
Batch View 305
Data Review 347
Thermo Scientific
Stepoff Value parameter 128
Stop Active Batch command 287
Stop All Batches command 288
Stop Batch command 289
Supervisor role 47
supported file types, defined 2
supported software and hardware ix
Surrogate page, Master Method View 192
system requirements ix
System Shutdown Method parameter 276
System Startup Method parameter 276
System Status parameter 276
T
Tailing Factor parameter
Genesis
application configuration 79
method development 158
ICIS
application configuration 82
method development 162
Tangent Skim, event type 87
Target Ratio parameter 172
target screening reports, listed 7
Technician role 47
Template Layout parameter 333
templates
batch 254
method 216
Tension, event type 87
Theo Amt parameter 348
Theo Conc parameter
Lab Control page 193
Matrix Spike page 195
Method Val page 194
Surrogate page 192
Theoretical Amount parameter 401
Thermo Xcalibur Instrument Setup dialog box 122
Time parameter 85
Time/Event/Value parameter 84
Total Batch Rows parameter 333
Total Response parameter 401
Total Rows parameter 400
Trace parameter, Detection 155
Tune Compound parameter 199
Tune File Lifetime parameter 209
Tune sample type, defined 292
Tune/Breakdown parameter, General page 127
Tune/Breakdown sample type, defined 292
Turn Device Off command 271
Turn Device On command 270
Turn Device Standby command 270
TraceFinder User Guide
499
Index: U
U
ULOL (Linearity Limit) parameter 184
Units parameter 174
Unknown sample type, defined 292
Unknown/TIC sample type, defined 292
Update Confirming Ion Ratios with This Spectrum
command 170
Upper Limit parameter
Solvent Blank page 191
Use Alternate Calibration Report Format parameter 208
Use an Existing Raw Data File parameter 109
Use as RT Reference parameter, Identification page 134
Use Autosampler parameter 109
Use Average Scan parameter 214
Use Data Dependent Scans parameter 225
Use Full MS Scan to Confirm parameter 214
Use Genesis Algorithm for Qual Processing parameter 224
Use Method Forge parameter 102, 106
Use Only Selected Method parameter 199
Use Scan at Peak Apex parameter 214
Use the Default Template parameter 108
Use These Libraries parameter 223
user accounts, creating 40
User Administration view 40
user roles and permissions 46
user roles, defined 46
User Security parameter 90
user security, enabling 90
Username parameter 12, 45
V
Valley Rise (%) parameter
application configuration 80
Detect page 159
Valley S/N parameter
application configuration 80
method development 159
Value parameter 85
Vial Position parameter
Batch View 306
Data Review 348
Method Forge 109
View Only parameter 400
View Width parameter
application configuration 77
Times page 149
views
Batch 297
Batch/Template Selection 250
Compound Datastore 59
Data Review 345
500
TraceFinder User Guide
Development Batch 235
Finish 269
Instrument 228
Local Method 413
Method 101
Project Administration 49
Report selection 265
Report View 387
Sample definition 255
User Administration 40
W
Weighting parameter
Calibration 174
Method Template Editor 224
Window parameter
Acquisition List 132
application configuration
ion ratio 77
retention time 77
Compound Datastore 60
Ratios page 172
Times page 148
Window Type parameter
application configuration 77
Ratios page 172
workflow
acquisition mode 248
general 5
X
XIC experiment type 66
XIC parameter, Signal page 154
Thermo Scientific
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