Thermo Fisher Scientific TraceFinder 3.0 User guide

Thermo

TraceFinder

Version 3.0

User Guide

Optimized for Clinical Research

XCALI-97499 Revision A October 2012

Aria, Exactive, FOCUS, LCquan, ToxID, and TriPlus are trademarks, and Accela, Dionex, Thermo Scientific,

Trace GC Ultra, TSQ Quantum, and Xcalibur are registered trademarks of Thermo Fisher Scientific Inc. in the

United States.

NIST is a registered trademark of the National Institute of Standards and Technology in the United States.

Windows, Excel, and Microsoft are registered trademarks of Microsoft Corporation in the United States and

other countries. Adobe, Acrobat, and Reader are registered trademarks of Adobe Systems Inc. in the United

States and other countries.

Agilent is a registered trademark of Agilent Technologies Inc.

All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries.

Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the

product operation. This document is copyright protected and any reproduction of the whole or any part of this

document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.

The contents of this document are subject to change without notice. All technical information in this

document is for reference purposes only. System configurations and specifications in this document supersede

all previous information received by the purchaser.

Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or 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, October 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.

Thermo Scientific TraceFinder User Guide iii

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Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii

Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii

Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .viii

System Activation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix

Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi

Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1

About the TraceFinder Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

TraceFinder Summary of Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

TraceFinder Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Reporting Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Standard Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Custom Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Target Screening Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

ToxID Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Chapter 2 Getting Started. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9

Installing the TraceFinder Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Installing the Power Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Installing the NIST and QED Libraries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Launching the NIST Library Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Launching the Qual Browser. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Converting Legacy Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Converting Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Converting Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Converting Method Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Converting Batch Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Choosing a Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Chapter 3 Using the Application Configuration Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .39

Specifying the Reports Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

Specifying Application Defaults. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Specifying Default Peak Detection Parameters . . . . . . . . . . . . . . . . . . . . . . . . . 48

Specifying Adducts Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62

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iv TraceFinder User Guide Thermo Scientific

Activating Optional Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

User Security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

ToxID . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

Delay Calibration Calculation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

Batch Wizard Style . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

Multiplexing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

Intelligent Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

Acquisition Submission Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

Screening Library. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

Managing User Administration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Editing User Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72

Choosing User Roles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

Chapter 4 Using the Method Development Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .81

Working with Master Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85

Creating a New Master Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86

Editing a Quantitation Master Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108

Editing a Target Screening Master Method . . . . . . . . . . . . . . . . . . . . . . . . . 204

Creating a Method Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 226

Importing Published Master Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237

Exporting SRM Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 238

Working with the Compound Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241

Opening and Saving a Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 242

Compound Database Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245

Editing Compounds in the Database. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253

Choosing Experiment Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260

Exporting and Importing Compounds . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263

Working with Instrument Methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271

Working with Development Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277

Creating a Development Batch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277

Editing Samples in a Development Batch . . . . . . . . . . . . . . . . . . . . . . . . . . 279

Acquiring Samples in a Development Batch . . . . . . . . . . . . . . . . . . . . . . . . 282

Viewing Raw Data Files in the Qual Browser . . . . . . . . . . . . . . . . . . . . . . . 283

Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 285

Chapter 5 Using the Acquisition Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .287

Working with Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 288

Opening and Navigating the Acquisition Mode . . . . . . . . . . . . . . . . . . . . . 288

Creating and Submitting Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 290

Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323

Contents

Thermo Scientific TraceFinder User Guide v

Real Time Status Pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 325

Acquisition Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 326

Instrument Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 327

Devices Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 328

Queues Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 332

Real-Time Trace Display. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337

Sample Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 339

Chapter 6 Using the Analysis Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .341

Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 343

Working in the Batch View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 345

Samples Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 346

Auto Samples Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 379

Reference Samples Page. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381

Creating a Batch Using the Batch Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . 382

Working in Data Review for Quantitation Methods . . . . . . . . . . . . . . . . . . . . 396

Sample View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 397

Compound View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 409

Qualitative View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 419

Features Common to All Data Review Pages . . . . . . . . . . . . . . . . . . . . . . . . 435

Working in Data Review for Target Screening Methods . . . . . . . . . . . . . . . . . 457

Samples Pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 460

Compounds Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 461

Chromatogram Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 464

Spectrum Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 465

Working in the Report View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 471

Viewing Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 472

Generating Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 476

Working with Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 480

Working with the Active View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 483

Working in the Project Administration View . . . . . . . . . . . . . . . . . . . . . . . . . 495

Working with Drives. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 496

Working with Projects. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 498

Working in the Local Method View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 501

Working in the Batch Template Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 503

Appendix A Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .511

Specifying Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 511

Standard Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 512

Custom Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 513

Target Screening Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 513

ToxID Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 513

Report Flags . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 514

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vi TraceFinder User Guide Thermo Scientific

Sample Standard Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 515

Batch Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 516

Batch Report Rev 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 517

Calibration Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 518

Calibration Density Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 521

Chromatogram Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 522

Compound Calibration Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 523

Compound Calibration Report - Alternate . . . . . . . . . . . . . . . . . . . . . . . . . 525

Confirmation Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 527

Confirmation Report 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 528

High Density Calibration Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 529

High Density Internal Standard Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . 530

High Density Internal Standard Report Long . . . . . . . . . . . . . . . . . . . . . . . 531

High Density Sample Report 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 532

High Density Sample Report 1 Long. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 533

High Density Sample Report 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 534

High Density Sample Report 2 Long. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 535

High Density Sample Report 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 536

High Density Sample Report 3 Long. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 537

Internal Standard Summary Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 538

Ion Ratio Failure Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 539

Manual Integration Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 540

Method Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 541

Method Validation Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 544

MSMSD Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 547

Quality Control Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 548

Quantitation Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 549

Quantitation Report - 2. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 550

Solvent Blank Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 552

Appendix B Using Copy Down and Fill Down . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .555

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .559

Thermo Scientific TraceFinder User Guide vii

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Preface

Thermo TraceFinder™ 3.0 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 Quick Reference Guide

• TraceFinder Acquisition Quick Reference Guide

• TraceFinder Analysis Quick Reference Guide

• TraceFinder Shortcut Menus Quick Reference Guide

• TraceFinder Custom Reports Tutorial

Contents

•Related Documentation

•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 the user guide or one of the quick reference guides, choose Help > Manuals >

TraceFinder User Guide or TraceFinder * Quick Reference Guide.

The PDF of the selected guide opens in a new window.

Special Notices

This guide includes the following types of special notices:

IMPORTANT Highlights information necessary to prevent damage to software, loss of

data, or invalid test results; or might contain information that is critical for optimal

performance of the system.

Note Highlights information of general interest.

Tip Highlights helpful information that can make a task easier.

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 60-day free trial. If your free trial has expired, the License Activation

window opens.

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:ThermoMSLicensing@thermofisher.com

• Fax: 408-965-6120

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.

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.

Note The barcode might already be filled in for you.

Preface

Thermo Scientific TraceFinder User Guide xi

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.

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.

Note You must run the TraceFinder application with ITAdmin or LabDirector rights

when entering the activation key.

Note The License Activation window for power modules automatically opens when

you try to enable the power module features in the Application Configuration mode.

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 clinical research market. It supports a focused

quantification workflow for specific nonbioanalytical laboratory use, instrument control, and

method development functionality. TraceFinder is the primary application for the TSQ

Quantum™ XLS triple quadrupole mass spectrometers.

The TraceFinder application can export SRM data in .xml format so that other applications,

including TSQ and Q Exactive™, can import the files into their databases.

The TraceFinder application can import the following file types:

• Sample lists in .csv or .xml format

See “Defining the Sample List” on page 298.

• Processing (.pmd) and instrument (.meth) method files from the Xcalibur data system

For detailed information about creating processing methods, see “Working with Master

Methods” on page 83.

For detailed information about creating instrument methods, see “Working with

Instrument Methods” on page 269.

• Compounds from files that use the database (.xml or .cdb) format

See “Editing Compounds in the Database” on page 251.

Contents

•About the TraceFinder Application

•TraceFinder Summary of Features

•Tr a c e Finde 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, or 2.1

– QuanLab Forms or ToxLab Forms 2.5 or 3.0

See “Converting Legacy Data” on page 21.

The TraceFinder application checks the accuracy and precision of data against systems that

have previously been certified against a standard processing program, such as the Statistical

Analysis System (SAS).

Supported File Types

The TraceFinder application supports the following file types:

• Comma-separated values (.csv): A set of file formats used to store tabular data in which

numbers and text are stored in plain textual form that can be read in a text editor. Lines in

the text file represent rows of a table, and commas in a line separate fields in the tables

row.

• Extensible Markup Language (.xml): A generic framework for storing any amount of text

or any data whose structure can be represented as a tree. The only indispensable

syntactical requirement is that the document has exactly one root element (also called the

document element). This means that the text must be enclosed between a root start-tag

and a corresponding end-tag.

• Instrument method (.meth): A proprietary file format for the Xcalibur software suite with

specific instructions that enable scientific instruments to perform data acquisition.

• Processing method (.pmd): A proprietary file format for the Xcalibur software suite with

specific instructions on processing data that was acquired through the instruments

attached to the system.

• Raw data (.raw): The file type for acquired samples on the system.

• Compound database (.cdb): The file type for TraceFinder or ExactFinder compound

database data.

1 Introduction

TraceFinder Summary of Features

Thermo Scientific TraceFinder User Guide 3

TraceFinder Directory Structure

The TraceFinder application creates folders for projects/subprojects/batches and templates in

the C:\Thermo\TraceFinder\3.0\Clinical directory. Within each batch folder, the application

creates folders for data, methods, and reports.

Figure 1. Example batch directory structure

TraceFinder Summary of Features

The TraceFinder system provides a workflow-oriented approach to high-throughput

quantitation. The system uses a batch-centric approach and tools to automate and speed up

the processes of method creation, loading samples, automatically generating data, manually

reviewing and editing results, and finalizing the data review and reporting process.

The TraceFinder software package includes data acquisition, processing, reviewing, and

reporting capabilities designed to assist analysts in clinical research applications. The

application has a fully automated acquisition mode and a manual data analysis mode. You can

use the data acquisition system to create and submit batches and monitor real-time review of

results.

The TraceFinder application uses a comprehensive processing method to provide improved

handling of ion ratio calculations, reviewing, and reporting. In addition, it can compare the

mass spectra and integrate the processes of data review and reporting.

Key features include the following:

• Role-based authorization for LabDirector, ITAdmin, Supervisor, Technician, and QAQC

(quality assurance) roles

• Configuration mode for report configuration, detection defaults, and application

administration

• Method Development mode for editing instrument methods, setting processing and error

flag parameters, and setting report options

IMPORTANT You cannot rename or move the folders created by the TraceFinder

application.

1 Introduction

TraceFinder Workflow

4TraceFinder User Guide Thermo Scientific

• Choice of acquisition wizards:

– Acquisition batch mode that guides you in creating batches and running samples

– Batch template wizard similar to the interface used in the ToxLab Forms application

• Analysis mode with project administration, batch views, data review, local method views,

and report views

• Database-capable method development

• Quantification workflows, supporting capabilities present in the LCquan™ and ToxLab

Forms applications

• Target screening workflows

• Standard and customized report formats

Features of the common workflow core include the following:

• Acquisition and processing

•Peak detection

• Quantification to include calibration

• Error analysis and flag setting

•Reporting

• Data persistence

• Raw data file handling

TraceFinder Workflow

The TraceFinder application is structured with a typical laboratory workflow in mind. You

create a batch, and the system injects samples into the instrument, runs the samples, analyzes

the data, and generates a report. You can set up a master method for specific compound

groups or assays that you expect to run in your laboratory. When you are ready to run a

particular type of sample, select the appropriate method and begin.

When using the TraceFinder application, follow these basic steps:

1. Create and save a master method in the Method Development mode.

A master method combines the instrument method and processing method that define

the following:

• How the raw data is acquired and processed

• How the error checking information evaluates the results

• How the results appear in reports

1 Introduction

Reporting Features

Thermo Scientific TraceFinder User Guide 5

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.

Reporting Features

The report engine can generate several different types of reports designed to meet the needs of

the laboratory, the laboratory's customers, and key regulatory agencies that might review the

results. The following types of reports meet the requirements of various methods and

worldwide regulatory agencies, helping to track the performance of LC and GC systems and

methods. The reports divide into four groups: Standard, Custom, Target Screening, and

ToxID.

For additional information about standard, custom, target screening, or ToxID reports and

examples of each standard report type, see “Reports” on page 509.

Examples of standard reports (as PDF files) are also located in the following folder:

C:\Thermo\TraceFinder\3.0\Clinical\ExampleReports

Standard Report Types

•Batch Report

• Batch Summary Report

• Batch Report Rev 1

•Calibration Report

•Calibration Curve Report

• Chromatogram Report

• Compound Calibration Report

• Compound Calibration Report - Alternate

•Confirmation Report

• High Density Calibration Report

• High Density Internal Standard Report

• High Density Internal Standard Report Long

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

6TraceFinder User Guide Thermo Scientific

•High Density Sample Report 1

• High Density Sample Report 1 Long

•High Density Sample Report 2

• High Density Sample Report 2 Long

•High Density Sample Report 3

• High Density Sample Report 3 Long

• Intelligent Sequencing Report

• Internal Standard Summary Report

• Ion Ratio Failure Report

• Manual Integration Report

•Method Report

•Negative Report

•Qualitative Peak Report

• Qualitative Summary Report

• Quality Control Report

• Quantitation Report

• Quantitation Report - 2

• Sample Report

• Sample Report Long

•Solvent Blank Report

Custom Report Types

• 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

1 Introduction

Reporting Features

Thermo Scientific TraceFinder User Guide 7

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 3.0 User guide

Thermo Fisher Scientific TraceFinder 3.0 User guide

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