Thermo Fisher Scientific TraceFinder 3.1 User guide

Category
Software
Type
User guide
Thermo
TraceFinder
User Guide
Software Version 3.1
Optimized for General Quantitation
XCALI-97530 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.
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other countries. Adobe, Acrobat, and Reader are registered trademarks of Adobe Systems Inc. in the United
States and other countries.
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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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Safety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .viii
System Activation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii
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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
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
Chapter 3 Using the Configuration Console . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37
Specifying the Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Specifying Application Defaults. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Specifying Default Peak Detection Parameters . . . . . . . . . . . . . . . . . . . . . . . . . 47
Specifying Adducts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Contents
Contents
iv TraceFinder User Guide Thermo Scientific
Activating Optional Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
ToxID . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Delay Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
User Peak Detection Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Auto Sampler Tray Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Batch Wizard Style . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Acquisition Submission Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Screening Libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Multiplexing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Intelligent Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Creating Custom Columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Creating Custom Flags . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Chapter 4 Using the Method Development Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .81
Working with Master Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Creating a New Master Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Editing a Quantitation Master Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
Editing a Target Screening Master Method . . . . . . . . . . . . . . . . . . . . . . . . . 220
Saving a Master Method to a New Name . . . . . . . . . . . . . . . . . . . . . . . . . . 251
Creating a Method Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252
Importing Published Master Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263
Exporting Mass Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 264
Working with the Compound Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267
Opening and Saving a Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 268
Exporting and Importing Compounds . . . . . . . . . . . . . . . . . . . . . . . . . . . . 272
Compound Detail Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
Grid Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291
Compound Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295
Experiment Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 300
Compound Database Names Mapped to CSV Column Names. . . . . . . . . . 303
Working with Instrument Methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 307
Working with Development Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 313
Creating a Development Batch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 313
Editing Samples in a Development Batch . . . . . . . . . . . . . . . . . . . . . . . . . . 316
Acquiring Samples in a Development Batch . . . . . . . . . . . . . . . . . . . . . . . . 319
Viewing Raw Data Files in the Qual Browser . . . . . . . . . . . . . . . . . . . . . . . 320
Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 322
Chapter 5 Using the Acquisition Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .325
Working with Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 326
Opening and Navigating the Acquisition Mode . . . . . . . . . . . . . . . . . . . . . 326
Creating and Submitting Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 328
Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 364
Contents
Thermo Scientific TraceFinder User Guide v
Real Time Status Pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 366
Acquisition Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 367
Instrument Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 368
Devices Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 369
Queues Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 374
Real-Time Trace Display. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 380
Sample Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 382
Chapter 6 Using the Analysis Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .383
Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 385
Working in the Batch View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 387
Samples Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 388
Auto Samples Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 429
Reference Samples Page. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 431
Threshold Samples Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 432
Creating a Batch Using the Batch Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . 433
Working in Data Review for Quantitation Methods . . . . . . . . . . . . . . . . . . . . 449
Sample View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 450
Compound View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 462
Comparative View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 472
Qualitative View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 481
Features Common to All Data Review Pages . . . . . . . . . . . . . . . . . . . . . . . . 498
Working in Data Review for Target Screening Methods . . . . . . . . . . . . . . . . . 523
Samples Pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 525
Compounds Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 526
Chromatogram Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 540
Spectrum Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 541
Working in the Report View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 554
Viewing Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 555
Generating Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 559
Working with Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 563
Working with the Active View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 566
Working in the Local Method View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 578
Working in the Batch Template Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 580
Appendix A Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .591
Specifying Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 591
Standard Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 592
Custom Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 593
Target Screening Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 593
ToxID Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 593
Report Flags . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 594
Contents
vi TraceFinder User Guide Thermo Scientific
Sample Standard Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 595
Batch Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 596
Batch Report Rev 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 597
Calibration Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 598
Calibration Density Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 601
Chromatogram Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 602
Compound Calibration Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 603
Compound Calibration Report - Alternate . . . . . . . . . . . . . . . . . . . . . . . . . 605
Confirmation Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 607
Confirmation Report 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 608
High Density Calibration Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 609
High Density Internal Standard Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . 610
High Density Internal Standard Report Long . . . . . . . . . . . . . . . . . . . . . . . 611
High Density Sample Report 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 612
High Density Sample Report 1 Long. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 613
Internal Standard Summary Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 614
Ion Ratio Failure Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 615
Manual Integration Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 616
Method Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 617
Method Validation Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 620
QC Standard Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 624
Quantitation Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 625
Quantitation Report - 2. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 626
Solvent Blank Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 628
Appendix B Isotopic Pattern Details . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .629
Isotopic Distribution in Exact Mass Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . 629
Isotopic Pattern Score Calculations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 633
Data Set Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 633
Calculating Mass and Intensity Deviations . . . . . . . . . . . . . . . . . . . . . . . . . 636
Calculating Isotopic Pattern Score. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 638
Finding the Noise Value . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 643
Appendix C Using Copy Down and Fill Down . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .645
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .649
Thermo Scientific TraceFinder User Guide vii
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
viii TraceFinder 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 ix
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
xTraceFinder 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 xi
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
xii 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 general quantitation market. It supports a focused
quantification workflow for specific nonbioanalytical laboratory use, instrument control, and
method development functionality. TraceFinder is the primary application for the TSQ
Quantum™ XLS triple quadrupole mass spectrometers.
The TraceFinder application can export mass data in the Acquisition List to XML format so
that other applications, including TSQ 8000, TSQ Quantum™, ISQ, and Q Exactive™, can
import the files into their databases.
The TraceFinder application can import the following file types:
Sample lists in .csv or .xml format
See “Defining the Sample List” on page 338.
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 85.
For detailed information about creating instrument methods, see “Working with
Instrument Methods” on page 307.
Compounds from files that use the database (.xml or .cdb) format
See “Editing Compounds in the Database” on page 283.
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 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 general quantitation applications. The
application has a fully automated acquisition mode and a manual data analysis mode. You can
use the data acquisition system to create and submit batches and monitor real-time review of
results.
The TraceFinder application uses a comprehensive processing method to provide improved
handling of ion ratio calculations, reviewing, and reporting. In addition, it can compare the
mass spectra and integrate the processes of data review and reporting.
Key features include the following:
Role-based authorization for 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 QuanLab 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 QuanLab
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).
1 Introduction
Reporting Features
Thermo Scientific TraceFinder User Guide 7
Reporting Features
The report engine can generate several different types of reports designed to meet the needs of
the laboratory, the laboratory's customers, and key regulatory agencies that might review the
results. The following types of reports meet the requirements of various methods and
worldwide regulatory agencies, helping to track the performance of LC and GC systems and
methods. The reports divide into four groups: Standard, Custom, Target Screening, and
ToxID.
For additional information about standard, custom, target screening, or ToxID™ reports and
examples of each standard report type, see “Reports on page 591.
Examples of standard reports (as PDF files) are also located in the following folder:
C:\Thermo\TraceFinder\3.1\General\ExampleReports
Standard Report Types
•Batch Report
Batch Report Rev 1
•Blank Report
•Calibration Report
Chromatogram Report
Compound Calibration Report
Compound Calibration Report - Alternate
•Confirmation Report
High Density Calibration Report
High Density Internal Standard Report Long
High Density Sample Report 1 Long
Intelligent Sequencing Report
Internal Standard Summary Report
Ion Ratio Failure Report
Manual Integration Report
•Method Report
•QC Standard Report
•Qualitative Peak Report
Qualitative Summary Report
Quantitation Report
Quantitation Report - 2
•Solvent Blank Report
Custom Report Types
• AltCalibrationReport
Alternate BatchReport
Alternate CalibrationReport
Alternate ConfirmationReport
Alternate MatrixSpikeReport
Alternate SampleReport
Alternate SummaryReport
1 Introduction
Reporting Features
8TraceFinder User Guide Thermo Scientific
•BatchReport
•BlankReport
CalibrationDensityReport
•CalibrationReport
•CheckStandardReport
CompoundCalibrationReport
ConfirmationReport
• ConfirmationReport2
•HighDensitySampleReport1Long
•HighDensitySampleReport2Long
•HighDensitySampleReport3Long
•HighDensitySampleReport4
•HighDensitySampleReport5
• QuantitationReport
•SteroidAnalysisReport
Target Screening Report Types
Target Screening High Density Sample Report
Target Screening Summary Report
ToxID Report Types
•Target Screening Long Report
Target Screening Summary Report
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Thermo Fisher Scientific TraceFinder 3.1 User guide

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