Thermo Fisher Scientific TraceFinder 3.1 User guide

Category
Software
Type
User guide
Thermo
TraceFinder
User Guide
Software Version 3.1
Optimized for Environmental and Food Safety
XCALI-97525 Revision A June 2013
© 2013 Thermo Fisher Scientific Inc. All rights reserved.
Aria, Q Exactive, FOCUS, LCquan, ToxID, TSQ 8000, and TriPlus are trademarks, and Accela, Dionex,
Exactive, Thermo Scientific, Trace GC Ultra, TSQ Quantum, TSQ Endura, TSQ Quantiva, TurboFlow and
Xcalibur are registered trademarks of Thermo Fisher Scientific Inc. in the United States.
NIST is a registered trademark of the National Institute of Standards and Technology in the United States.
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. in the United States and other countries.
Waters and ACQUITY are trademarks of Waters Corporation.
All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries.
Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
product operation. This document is copyright protected and any reproduction of the whole or any part of this
document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.
The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.
Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-
free 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, June 2013
Software version: Microsoft Windows 7 Professional; (Thermo) Foundation 2.0 SP1; Xcalibur 2.2 SP1;
LC Devices 2.5 SP2; GC Devices 2.2
For Research Use Only. Not for use in diagnostic procedures.
Thermo Scientific TraceFinder User Guide iii
C
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix
Safety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
System Activation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiv
Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
About the TraceFinder Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
TraceFinder Summary of Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
TraceFinder Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Reporting Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Standard Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Custom Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Target Screening Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
ToxID Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Chapter 2 Getting Started. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Installing the TraceFinder Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Installing the Power Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Installing the NIST and QED Libraries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Launching the NIST Library Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Launching the Qual Browser. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Converting Legacy Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Version Compatibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Converting Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Converting Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Converting Method Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Converting Batch Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Choosing a Mode or Console . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Contents
Contents
iv TraceFinder User Guide Thermo Scientific
Chapter 3 Using the Configuration Console . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37
Specifying the Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Specifying Application Defaults. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Specifying Default Peak Detection Parameters . . . . . . . . . . . . . . . . . . . . . . . . . 47
Specifying Adducts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Activating Optional Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
ToxID . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
EPA Tune Criteria. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Delay Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
User Peak Detection Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Auto Sampler Tray Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Batch Wizard Style . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Acquisition Submission Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Screening Libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Multiplexing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Intelligent Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Creating Custom Columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Creating Custom Flags . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Chapter 4 Using the Method Development Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .83
Working with Master Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Creating a New Master Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Editing a Quantitation Master Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Editing a Target Screening Master Method . . . . . . . . . . . . . . . . . . . . . . . . . 233
Saving a Master Method to a New Name . . . . . . . . . . . . . . . . . . . . . . . . . . 264
Creating a Method Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265
Importing Published Master Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . 276
Exporting Mass Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
Working with the Compound Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 280
Opening and Saving a Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281
Exporting and Importing Compounds . . . . . . . . . . . . . . . . . . . . . . . . . . . . 285
Compound Detail Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 290
Grid Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 304
Compound Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 308
Experiment Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 313
Compound Database Names Mapped to CSV Column Names. . . . . . . . . . 316
Working with Instrument Methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 320
Working with Development Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 326
Creating a Development Batch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 326
Editing Samples in a Development Batch . . . . . . . . . . . . . . . . . . . . . . . . . . 329
Acquiring Samples in a Development Batch . . . . . . . . . . . . . . . . . . . . . . . . 332
Viewing Raw Data Files in the Qual Browser . . . . . . . . . . . . . . . . . . . . . . . 333
Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335
Contents
Thermo Scientific TraceFinder User Guide v
Chapter 5 Using the Acquisition Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .337
Working with Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 338
Opening and Navigating the Acquisition Mode . . . . . . . . . . . . . . . . . . . . . 338
Creating and Submitting Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 340
Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 376
Real Time Status Pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 378
Acquisition Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 379
Instrument Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 380
Devices Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381
Queues Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 386
Real-Time Trace Display. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 392
Sample Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 394
Chapter 6 Using the Analysis Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .397
Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 399
Working in the Batch View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 401
Samples Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 402
Auto Samples Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 443
Reference Samples Page. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 445
Threshold Samples Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 446
Creating a Batch Using the Batch Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . 447
Working in Data Review for Quantitation Methods . . . . . . . . . . . . . . . . . . . . 463
Sample View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 464
Compound View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 476
Comparative View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 487
Qualitative View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 496
Features Common to All Data Review Pages . . . . . . . . . . . . . . . . . . . . . . . . 513
Working in Data Review for Target Screening Methods . . . . . . . . . . . . . . . . . 537
Samples Pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 539
Compounds Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 540
Chromatogram Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 554
Spectrum Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 555
Working in the Report View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 568
Viewing Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 569
Generating Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 573
Working with Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 577
Working with the Active View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 580
Working in the Local Method View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 594
Working in the Batch Template Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 596
Contents
vi TraceFinder User Guide Thermo Scientific
Appendix A Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .605
Specifying Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 605
Standard Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 606
Custom Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 607
Target Screening Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 607
ToxID Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 607
Report Flags . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 608
Sample Standard Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 609
Batch Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 610
Batch Report Rev 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 611
Blank Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 612
Breakdown Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 613
Calibration Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 614
Calibration Density Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 617
Check Standard Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 618
Chromatogram Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 619
Compound Calibration Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 620
Compound Calibration Report - Alternate . . . . . . . . . . . . . . . . . . . . . . . . . 622
Confirmation Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 624
Confirmation Report 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 625
High Density Calibration Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 626
High Density Internal Standard Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . 627
High Density Internal Standard Report Long . . . . . . . . . . . . . . . . . . . . . . . 628
High Density Sample Report 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 629
High Density Sample Report 1 Long. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 630
High Density Sample Report 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 631
High Density Sample Report 2 Long. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 632
High Density Sample Report 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 633
High Density Sample Report 3 Long. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 634
Internal Standard Summary Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 635
Ion Ratio Failure Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 636
LCSLCSD Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 637
Manual Integration Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 638
Method Detection Limit Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 639
Method Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 642
Method Validation Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 645
MSMSD Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 648
Quantitation Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 649
Quantitation Report - 2. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 650
Solvent Blank Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 652
Surrogate Recovery Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 653
TIC Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 654
TIC Summary Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 655
Contents
Thermo Scientific TraceFinder User Guide vii
Appendix B Isotopic Pattern Details . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .657
Isotopic Distribution in Exact Mass Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . 657
Isotopic Pattern Score Calculations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 661
Data Set Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 661
Calculating Mass and Intensity Deviations . . . . . . . . . . . . . . . . . . . . . . . . . 664
Calculating Isotopic Pattern Score. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 666
Finding the Noise Value . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 671
Appendix C Using Copy Down and Fill Down . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .673
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .677
Thermo Scientific TraceFinder User Guide ix
P
Preface
Thermo TraceFinder™ 3.1 is the newest application in the Thermo Scientific™ series of
GC/MS and LC/MS analytical software.
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 Console User Guide
TraceFinder Acquisition Quick Reference Guide
TraceFinder Analysis Quick Reference Guide
TraceFinder Shortcut Menus Quick Reference Guide
TraceFinder Custom Reports Tutorial
Contents
Related Documentation
Safety and Special Notices
System Activation
Contacting Us
Preface
xTraceFinder User Guide Thermo Scientific
To view TraceFinder documents using the Start menu
Choose Start > All Programs > Thermo TraceFinder > Manuals.
To open TraceFinder Help and access related documents from the application
1. Open the TraceFinder application and choose Help > TraceFinder Help.
To find a particular topic, use the Contents, Index, or Search panes.
To create your own bookmarks, use the Favorites pane.
2. To view one of the user guides or one of the quick reference guides, choose Help >
Manuals > * User Guide or * Quick Reference Guide.
The PDF file of the selected guide opens in a new window.
Safety and Special Notices
Make sure you follow the precautionary statements presented in this guide. The safety and
other special notices appear in boxes.
Safety and special notices include the following:
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.
Preface
Thermo Scientific TraceFinder User Guide xi
System Activation
When you first start the TraceFinder application, a dialog box displays the number of days
remaining in your 120-day free trial. If your free trial has expired, the License Activation
window opens.
Two types of licenses are available:
120-Day Evaluation Version (free of charge)
Full Version Single License
The evaluation version is full-featured and automatically expires 120 days after activation.
Any attempt to set back the system date automatically terminates this version. You can
purchase and then activate the full version of the TraceFinder application at any time, during
or after the free evaluation, without reinstalling the software.
Each activation key is valid only for a single license. Any additional installation generates a
different license and requires a different activation key.
For questions regarding activation, contact Thermo Fisher Scientific Technical Support in
San Jose, CA:
•E-mail:ThermoMSLicensing@thermofisher.com
Fax: 408-965-6120
Tip Highlights helpful information that can make a task easier.
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.
Preface
xii TraceFinder User Guide Thermo Scientific
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 the information, click Copy.
The application copies this XML text to the Clipboard.
If you have not completed all the information, a pop-up box identifies the missing
information.
Note The barcode might already be filled in for you.
Preface
Thermo Scientific TraceFinder User Guide xiii
4. Paste this XML text in the body of an e-mail and send the e-mail to
ThermoMSLicensing@thermofisher.com.
You will receive an e-mail response containing the activation key.
To use your 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.
Note The License Activation window for power modules automatically opens when
you try to enable the power module features in the Configuration console.
Preface
xiv TraceFinder User Guide Thermo Scientific
Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need.
To contact Technical Support
Find software updates and utilities to download at mssupport.thermo.com.
To contact Customer Service for ordering information
To get local contact information for sales or service
Go to www.thermoscientific.com/wps/portal/ts/contactus.
Phone 800-532-4752
Fax 561-688-8736
E-mail us.techsupport.analyze@thermofisher.com
Knowledge base www.thermokb.com
Phone 800-532-4752
Fax 561-688-8731
E-mail us.customer-support.analyze@thermofisher.com
Web site www.thermo.com/ms
Thermo Scientific TraceFinder User Guide 1
1
Introduction
This chapter describes general features of the TraceFinder software.
About the TraceFinder Application
The TraceFinder application targets the environmental and food safety market. It supports a
focused quantification workflow for specific nonbioanalytical laboratory use, instrument
control, and method development functionality. TraceFinder is the primary application for
the TSQ Quantum™ XLS triple quadrupole mass spectrometers.
The TraceFinder application can export mass data in the Acquisition List to XML format so
that other applications, including TSQ 8000, TSQ Quantum™, ISQ, and Q Exactive™, can
import the files into their databases.
The TraceFinder application can import the following file types:
Sample lists in .csv or .xml format
See “Defining the Sample List” on page 350.
Processing (.pmd) and instrument (.meth) method files from the Xcalibur data system
For detailed information about creating processing methods, see “Working with Master
Methods” on page 87.
For detailed information about creating instrument methods, see “Working with
Instrument Methods” on page 320.
Compounds from files that use the database (.xml or .cdb) format
See “Editing Compounds in the Database” on page 296.
Contents
About the TraceFinder Application
TraceFinder Summary of Features
Tr a c e Find e r Wo r k f l ow
Reporting Features
1 Introduction
About the TraceFinder Application
2TraceFinder User Guide Thermo Scientific
Batches, methods, or templates from the following applications:
TraceFinder 1.0, 1.1, 2.0, 2.1, or 3.0
QuanLab Forms or EnviroLab Forms 2.5 or 3.0
See “Converting Legacy Dataon page 20.
The TraceFinder application checks the accuracy and precision of data against systems that
have previously been certified against a standard processing program, such as the Statistical
Analysis System (SAS).
Supported File Types
The TraceFinder application supports the following file types:
Comma-separated values (.csv): A set of file formats used to store tabular data in which
numbers and text are stored in plain textual form that can be read in a text editor. Lines in
the text file represent rows of a table, and commas in a line separate fields in the tables
row.
Extensible Markup Language (.xml): A generic framework for storing any amount of text
or any data whose structure can be represented as a tree. The only indispensable
syntactical requirement is that the document has exactly one root element (also called the
document element). This means that the text must be enclosed between a root start-tag
and a corresponding end-tag.
Instrument method (.meth): A proprietary file format for the Xcalibur software suite with
specific instructions that enable scientific instruments to perform data acquisition.
Processing method (.pmd): A proprietary file format for the Xcalibur software suite with
specific instructions on processing data that was acquired through the instruments
attached to the system.
Raw data (.raw): The file type for acquired samples on the system.
Compound database (.cdb): The file type for TraceFinder or ExactFinder compound
database data.
Library (.db): A library used for target screening.
1 Introduction
About the TraceFinder Application
Thermo Scientific TraceFinder User Guide 3
TraceFinder Directory Structure
The TraceFinder application creates folders for batches, methods, and templates in the
…\TraceFinderData directory. Within each batch folder, the application creates folders for
data, methods, and reports.
You can create batches in the TraceFinderData\Projects folder, or you can create subfolders
within the Projects folder for your batches. You can create as many subfolders as you want for
your batches, but you cannot create a batch within another batch folder.
Figure 1. Example batch directory structure
IMPORTANT You cannot rename or move the folders created by the TraceFinder
application.
1 Introduction
TraceFinder Summary of Features
4TraceFinder User Guide Thermo Scientific
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
Administrator Console for user security, role-based permissions, and data repositories
Configuration console for report configuration, detection and acquisition defaults,
screening library selection, and customized columns and flags
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
Target screening workflows
Standard and customized report formats
1 Introduction
TraceFinder Summary of Features
Thermo Scientific TraceFinder User Guide 5
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
1 Introduction
TraceFinder Workflow
6TraceFinder User Guide Thermo Scientific
TraceFinder Workflow
The TraceFinder application is structured with a typical laboratory workflow in mind. You
create a batch, and the system injects samples into the instrument, runs the samples, analyzes
the data, and generates a report. You can set up a master method for specific compound
groups or assays that you expect to run in your laboratory. When you are ready to run a
particular type of sample, select the appropriate method and begin.
When using the TraceFinder application, follow these basic steps:
1. Create and save a master method in the Method Development mode.
A master method combines the instrument method and processing method that define
the following:
How the raw data is acquired and processed
How the error checking information evaluates the results
How the results appear in reports
2. Create and submit a batch using one of the batch wizards.
A batch lists samples for processing and reporting using a specified method. Each row of a
batch represents a unique sample.
3. Monitor the status of the batch in the Real Time Status view.
The real-time display is visible from all the TraceFinder modes. You can begin another
batch while you watch the real-time display of the currently acquiring batch.
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.
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).
  • Page 1 1
  • Page 2 2
  • Page 3 3
  • Page 4 4
  • Page 5 5
  • Page 6 6
  • Page 7 7
  • Page 8 8
  • Page 9 9
  • Page 10 10
  • Page 11 11
  • Page 12 12
  • Page 13 13
  • Page 14 14
  • Page 15 15
  • Page 16 16
  • Page 17 17
  • Page 18 18
  • Page 19 19
  • Page 20 20
  • Page 21 21
  • Page 22 22
  • Page 23 23
  • Page 24 24
  • Page 25 25
  • Page 26 26
  • Page 27 27
  • Page 28 28
  • Page 29 29
  • Page 30 30
  • Page 31 31
  • Page 32 32
  • Page 33 33
  • Page 34 34
  • Page 35 35
  • Page 36 36
  • Page 37 37
  • Page 38 38
  • Page 39 39
  • Page 40 40
  • Page 41 41
  • Page 42 42
  • Page 43 43
  • Page 44 44
  • Page 45 45
  • Page 46 46
  • Page 47 47
  • Page 48 48
  • Page 49 49
  • Page 50 50
  • Page 51 51
  • Page 52 52
  • Page 53 53
  • Page 54 54
  • Page 55 55
  • Page 56 56
  • Page 57 57
  • Page 58 58
  • Page 59 59
  • Page 60 60
  • Page 61 61
  • Page 62 62
  • Page 63 63
  • Page 64 64
  • Page 65 65
  • Page 66 66
  • Page 67 67
  • Page 68 68
  • Page 69 69
  • Page 70 70
  • Page 71 71
  • Page 72 72
  • Page 73 73
  • Page 74 74
  • Page 75 75
  • Page 76 76
  • Page 77 77
  • Page 78 78
  • Page 79 79
  • Page 80 80
  • Page 81 81
  • Page 82 82
  • Page 83 83
  • Page 84 84
  • Page 85 85
  • Page 86 86
  • Page 87 87
  • Page 88 88
  • Page 89 89
  • Page 90 90
  • Page 91 91
  • Page 92 92
  • Page 93 93
  • Page 94 94
  • Page 95 95
  • Page 96 96
  • Page 97 97
  • Page 98 98
  • Page 99 99
  • Page 100 100
  • Page 101 101
  • Page 102 102
  • Page 103 103
  • Page 104 104
  • Page 105 105
  • Page 106 106
  • Page 107 107
  • Page 108 108
  • Page 109 109
  • Page 110 110
  • Page 111 111
  • Page 112 112
  • Page 113 113
  • Page 114 114
  • Page 115 115
  • Page 116 116
  • Page 117 117
  • Page 118 118
  • Page 119 119
  • Page 120 120
  • Page 121 121
  • Page 122 122
  • Page 123 123
  • Page 124 124
  • Page 125 125
  • Page 126 126
  • Page 127 127
  • Page 128 128
  • Page 129 129
  • Page 130 130
  • Page 131 131
  • Page 132 132
  • Page 133 133
  • Page 134 134
  • Page 135 135
  • Page 136 136
  • Page 137 137
  • Page 138 138
  • Page 139 139
  • Page 140 140
  • Page 141 141
  • Page 142 142
  • Page 143 143
  • Page 144 144
  • Page 145 145
  • Page 146 146
  • Page 147 147
  • Page 148 148
  • Page 149 149
  • Page 150 150
  • Page 151 151
  • Page 152 152
  • Page 153 153
  • Page 154 154
  • Page 155 155
  • Page 156 156
  • Page 157 157
  • Page 158 158
  • Page 159 159
  • Page 160 160
  • Page 161 161
  • Page 162 162
  • Page 163 163
  • Page 164 164
  • Page 165 165
  • Page 166 166
  • Page 167 167
  • Page 168 168
  • Page 169 169
  • Page 170 170
  • Page 171 171
  • Page 172 172
  • Page 173 173
  • Page 174 174
  • Page 175 175
  • Page 176 176
  • Page 177 177
  • Page 178 178
  • Page 179 179
  • Page 180 180
  • Page 181 181
  • Page 182 182
  • Page 183 183
  • Page 184 184
  • Page 185 185
  • Page 186 186
  • Page 187 187
  • Page 188 188
  • Page 189 189
  • Page 190 190
  • Page 191 191
  • Page 192 192
  • Page 193 193
  • Page 194 194
  • Page 195 195
  • Page 196 196
  • Page 197 197
  • Page 198 198
  • Page 199 199
  • Page 200 200
  • Page 201 201
  • Page 202 202
  • Page 203 203
  • Page 204 204
  • Page 205 205
  • Page 206 206
  • Page 207 207
  • Page 208 208
  • Page 209 209
  • Page 210 210
  • Page 211 211
  • Page 212 212
  • Page 213 213
  • Page 214 214
  • Page 215 215
  • Page 216 216
  • Page 217 217
  • Page 218 218
  • Page 219 219
  • Page 220 220
  • Page 221 221
  • Page 222 222
  • Page 223 223
  • Page 224 224
  • Page 225 225
  • Page 226 226
  • Page 227 227
  • Page 228 228
  • Page 229 229
  • Page 230 230
  • Page 231 231
  • Page 232 232
  • Page 233 233
  • Page 234 234
  • Page 235 235
  • Page 236 236
  • Page 237 237
  • Page 238 238
  • Page 239 239
  • Page 240 240
  • Page 241 241
  • Page 242 242
  • Page 243 243
  • Page 244 244
  • Page 245 245
  • Page 246 246
  • Page 247 247
  • Page 248 248
  • Page 249 249
  • Page 250 250
  • Page 251 251
  • Page 252 252
  • Page 253 253
  • Page 254 254
  • Page 255 255
  • Page 256 256
  • Page 257 257
  • Page 258 258
  • Page 259 259
  • Page 260 260
  • Page 261 261
  • Page 262 262
  • Page 263 263
  • Page 264 264
  • Page 265 265
  • Page 266 266
  • Page 267 267
  • Page 268 268
  • Page 269 269
  • Page 270 270
  • Page 271 271
  • Page 272 272
  • Page 273 273
  • Page 274 274
  • Page 275 275
  • Page 276 276
  • Page 277 277
  • Page 278 278
  • Page 279 279
  • Page 280 280
  • Page 281 281
  • Page 282 282
  • Page 283 283
  • Page 284 284
  • Page 285 285
  • Page 286 286
  • Page 287 287
  • Page 288 288
  • Page 289 289
  • Page 290 290
  • Page 291 291
  • Page 292 292
  • Page 293 293
  • Page 294 294
  • Page 295 295
  • Page 296 296
  • Page 297 297
  • Page 298 298
  • Page 299 299
  • Page 300 300
  • Page 301 301
  • Page 302 302
  • Page 303 303
  • Page 304 304
  • Page 305 305
  • Page 306 306
  • Page 307 307
  • Page 308 308
  • Page 309 309
  • Page 310 310
  • Page 311 311
  • Page 312 312
  • Page 313 313
  • Page 314 314
  • Page 315 315
  • Page 316 316
  • Page 317 317
  • Page 318 318
  • Page 319 319
  • Page 320 320
  • Page 321 321
  • Page 322 322
  • Page 323 323
  • Page 324 324
  • Page 325 325
  • Page 326 326
  • Page 327 327
  • Page 328 328
  • Page 329 329
  • Page 330 330
  • Page 331 331
  • Page 332 332
  • Page 333 333
  • Page 334 334
  • Page 335 335
  • Page 336 336
  • Page 337 337
  • Page 338 338
  • Page 339 339
  • Page 340 340
  • Page 341 341
  • Page 342 342
  • Page 343 343
  • Page 344 344
  • Page 345 345
  • Page 346 346
  • Page 347 347
  • Page 348 348
  • Page 349 349
  • Page 350 350
  • Page 351 351
  • Page 352 352
  • Page 353 353
  • Page 354 354
  • Page 355 355
  • Page 356 356
  • Page 357 357
  • Page 358 358
  • Page 359 359
  • Page 360 360
  • Page 361 361
  • Page 362 362
  • Page 363 363
  • Page 364 364
  • Page 365 365
  • Page 366 366
  • Page 367 367
  • Page 368 368
  • Page 369 369
  • Page 370 370
  • Page 371 371
  • Page 372 372
  • Page 373 373
  • Page 374 374
  • Page 375 375
  • Page 376 376
  • Page 377 377
  • Page 378 378
  • Page 379 379
  • Page 380 380
  • Page 381 381
  • Page 382 382
  • Page 383 383
  • Page 384 384
  • Page 385 385
  • Page 386 386
  • Page 387 387
  • Page 388 388
  • Page 389 389
  • Page 390 390
  • Page 391 391
  • Page 392 392
  • Page 393 393
  • Page 394 394
  • Page 395 395
  • Page 396 396
  • Page 397 397
  • Page 398 398
  • Page 399 399
  • Page 400 400
  • Page 401 401
  • Page 402 402
  • Page 403 403
  • Page 404 404
  • Page 405 405
  • Page 406 406
  • Page 407 407
  • Page 408 408
  • Page 409 409
  • Page 410 410
  • Page 411 411
  • Page 412 412
  • Page 413 413
  • Page 414 414
  • Page 415 415
  • Page 416 416
  • Page 417 417
  • Page 418 418
  • Page 419 419
  • Page 420 420
  • Page 421 421
  • Page 422 422
  • Page 423 423
  • Page 424 424
  • Page 425 425
  • Page 426 426
  • Page 427 427
  • Page 428 428
  • Page 429 429
  • Page 430 430
  • Page 431 431
  • Page 432 432
  • Page 433 433
  • Page 434 434
  • Page 435 435
  • Page 436 436
  • Page 437 437
  • Page 438 438
  • Page 439 439
  • Page 440 440
  • Page 441 441
  • Page 442 442
  • Page 443 443
  • Page 444 444
  • Page 445 445
  • Page 446 446
  • Page 447 447
  • Page 448 448
  • Page 449 449
  • Page 450 450
  • Page 451 451
  • Page 452 452
  • Page 453 453
  • Page 454 454
  • Page 455 455
  • Page 456 456
  • Page 457 457
  • Page 458 458
  • Page 459 459
  • Page 460 460
  • Page 461 461
  • Page 462 462
  • Page 463 463
  • Page 464 464
  • Page 465 465
  • Page 466 466
  • Page 467 467
  • Page 468 468
  • Page 469 469
  • Page 470 470
  • Page 471 471
  • Page 472 472
  • Page 473 473
  • Page 474 474
  • Page 475 475
  • Page 476 476
  • Page 477 477
  • Page 478 478
  • Page 479 479
  • Page 480 480
  • Page 481 481
  • Page 482 482
  • Page 483 483
  • Page 484 484
  • Page 485 485
  • Page 486 486
  • Page 487 487
  • Page 488 488
  • Page 489 489
  • Page 490 490
  • Page 491 491
  • Page 492 492
  • Page 493 493
  • Page 494 494
  • Page 495 495
  • Page 496 496
  • Page 497 497
  • Page 498 498
  • Page 499 499
  • Page 500 500
  • Page 501 501
  • Page 502 502
  • Page 503 503
  • Page 504 504
  • Page 505 505
  • Page 506 506
  • Page 507 507
  • Page 508 508
  • Page 509 509
  • Page 510 510
  • Page 511 511
  • Page 512 512
  • Page 513 513
  • Page 514 514
  • Page 515 515
  • Page 516 516
  • Page 517 517
  • Page 518 518
  • Page 519 519
  • Page 520 520
  • Page 521 521
  • Page 522 522
  • Page 523 523
  • Page 524 524
  • Page 525 525
  • Page 526 526
  • Page 527 527
  • Page 528 528
  • Page 529 529
  • Page 530 530
  • Page 531 531
  • Page 532 532
  • Page 533 533
  • Page 534 534
  • Page 535 535
  • Page 536 536
  • Page 537 537
  • Page 538 538
  • Page 539 539
  • Page 540 540
  • Page 541 541
  • Page 542 542
  • Page 543 543
  • Page 544 544
  • Page 545 545
  • Page 546 546
  • Page 547 547
  • Page 548 548
  • Page 549 549
  • Page 550 550
  • Page 551 551
  • Page 552 552
  • Page 553 553
  • Page 554 554
  • Page 555 555
  • Page 556 556
  • Page 557 557
  • Page 558 558
  • Page 559 559
  • Page 560 560
  • Page 561 561
  • Page 562 562
  • Page 563 563
  • Page 564 564
  • Page 565 565
  • Page 566 566
  • Page 567 567
  • Page 568 568
  • Page 569 569
  • Page 570 570
  • Page 571 571
  • Page 572 572
  • Page 573 573
  • Page 574 574
  • Page 575 575
  • Page 576 576
  • Page 577 577
  • Page 578 578
  • Page 579 579
  • Page 580 580
  • Page 581 581
  • Page 582 582
  • Page 583 583
  • Page 584 584
  • Page 585 585
  • Page 586 586
  • Page 587 587
  • Page 588 588
  • Page 589 589
  • Page 590 590
  • Page 591 591
  • Page 592 592
  • Page 593 593
  • Page 594 594
  • Page 595 595
  • Page 596 596
  • Page 597 597
  • Page 598 598
  • Page 599 599
  • Page 600 600
  • Page 601 601
  • Page 602 602
  • Page 603 603
  • Page 604 604
  • Page 605 605
  • Page 606 606
  • Page 607 607
  • Page 608 608
  • Page 609 609
  • Page 610 610
  • Page 611 611
  • Page 612 612
  • Page 613 613
  • Page 614 614
  • Page 615 615
  • Page 616 616
  • Page 617 617
  • Page 618 618
  • Page 619 619
  • Page 620 620
  • Page 621 621
  • Page 622 622
  • Page 623 623
  • Page 624 624
  • Page 625 625
  • Page 626 626
  • Page 627 627
  • Page 628 628
  • Page 629 629
  • Page 630 630
  • Page 631 631
  • Page 632 632
  • Page 633 633
  • Page 634 634
  • Page 635 635
  • Page 636 636
  • Page 637 637
  • Page 638 638
  • Page 639 639
  • Page 640 640
  • Page 641 641
  • Page 642 642
  • Page 643 643
  • Page 644 644
  • Page 645 645
  • Page 646 646
  • Page 647 647
  • Page 648 648
  • Page 649 649
  • Page 650 650
  • Page 651 651
  • Page 652 652
  • Page 653 653
  • Page 654 654
  • Page 655 655
  • Page 656 656
  • Page 657 657
  • Page 658 658
  • Page 659 659
  • Page 660 660
  • Page 661 661
  • Page 662 662
  • Page 663 663
  • Page 664 664
  • Page 665 665
  • Page 666 666
  • Page 667 667
  • Page 668 668
  • Page 669 669
  • Page 670 670
  • Page 671 671
  • Page 672 672
  • Page 673 673
  • Page 674 674
  • Page 675 675
  • Page 676 676
  • Page 677 677
  • Page 678 678
  • Page 679 679
  • Page 680 680
  • Page 681 681
  • Page 682 682
  • Page 683 683
  • Page 684 684
  • Page 685 685
  • Page 686 686
  • Page 687 687
  • Page 688 688
  • Page 689 689
  • Page 690 690
  • Page 691 691
  • Page 692 692
  • Page 693 693
  • Page 694 694
  • Page 695 695
  • Page 696 696
  • Page 697 697
  • Page 698 698
  • Page 699 699
  • Page 700 700
  • Page 701 701
  • Page 702 702
  • Page 703 703
  • Page 704 704
  • Page 705 705
  • Page 706 706
  • Page 707 707
  • Page 708 708

Thermo Fisher Scientific TraceFinder 3.1 User guide

Category
Software
Type
User guide

Ask a question and I''ll find the answer in the document

Finding information in a document is now easier with AI