Thermo TraceFinder Version 3.0 User Guide Optimized for Forensic Toxicology XCALI-97504 Revision A October 2012 © 2012 Thermo Fisher Scientific Inc. All rights reserved. Aria, Exactive, FOCUS, LCquan, ToxID, and TriPlus are trademarks, and Accela, Dionex, Thermo Scientific, Trace GC Ultra, TSQ Quantum, and Xcalibur are registered trademarks of Thermo Fisher Scientific Inc. in the United States. NIST is a registered trademark of the National Institute of Standards and Technology in the United States. Windows, Excel, and Microsoft are registered trademarks of Microsoft Corporation in the United States and other countries. Adobe, Acrobat, and Reader are registered trademarks of Adobe Systems Inc. in the United States and other countries. Agilent is a registered trademark of Agilent Technologies Inc. All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries. Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the product operation. This document is copyright protected and any reproduction of the whole or any part of this document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc. The contents of this document are subject to change without notice. All technical information in this document is for reference purposes only. System configurations and specifications in this document supersede all previous information received by the purchaser. Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or errorfree and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might result from any use of this document, even if the information in the document is followed properly. This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of Sale shall govern all conflicting information between the two documents. Release history: Revision A, March 2012 Software version: Thermo Foundation 2.0 SP1; Thermo Xcalibur 2.2 SP1; Microsoft Windows XP Professional SP3 or Windows 7 Professional; Thermo LC Devices 2.5 SP2; Thermo GC Devices 2.2 For Research Use Only. Not for use in diagnostic procedures. C Contents Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .viii System Activation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi Thermo Scientific Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1 About the TraceFinder Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 TraceFinder Summary of Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 TraceFinder Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 Reporting Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 Standard Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 Custom Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Target Screening Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 ToxID Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 Chapter 2 Getting Started. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9 Installing the TraceFinder Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 Installing the Power Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 Installing the NIST and QED Libraries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 Launching the NIST Library Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 Launching the Qual Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 Converting Legacy Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 Converting Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 Converting Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 Converting Method Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28 Converting Batch Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 Choosing a Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 Chapter 3 Using the Application Configuration Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37 Specifying the Reports Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39 Specifying Application Defaults. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44 Specifying Default Peak Detection Parameters . . . . . . . . . . . . . . . . . . . . . . . . . 46 Specifying Adducts Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 TraceFinder User Guide iii Contents Activating Optional Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63 User Security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64 ToxID . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64 Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64 Delay Calibration Calculation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65 Batch Wizard Style . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65 Multiplexing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66 Intelligent Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66 Acquisition Submission Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67 Screening Library. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68 Managing User Administration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69 Editing User Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70 Choosing User Roles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75 iv Chapter 4 Using the Method Development Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .79 Working with Master Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83 Creating a New Master Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84 Editing a Quantitation Master Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106 Editing a Target Screening Master Method . . . . . . . . . . . . . . . . . . . . . . . . . 202 Creating a Method Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224 Importing Published Master Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235 Exporting SRM Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 236 Working with the Compound Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239 Opening and Saving a Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240 Compound Database Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243 Editing Compounds in the Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251 Choosing Experiment Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 258 Exporting and Importing Compounds . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261 Working with Instrument Methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 269 Working with Development Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275 Creating a Development Batch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275 Editing Samples in a Development Batch . . . . . . . . . . . . . . . . . . . . . . . . . . 277 Acquiring Samples in a Development Batch . . . . . . . . . . . . . . . . . . . . . . . . 280 Viewing Raw Data Files in the Qual Browser . . . . . . . . . . . . . . . . . . . . . . . 281 Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283 Chapter 5 Using the Acquisition Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .285 Working with Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 286 Opening and Navigating the Acquisition Mode . . . . . . . . . . . . . . . . . . . . . 286 Creating and Submitting Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 288 Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321 TraceFinder User Guide Thermo Scientific Contents Real Time Status Pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323 Acquisition Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 324 Instrument Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 325 Devices Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 326 Queues Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 330 Real-Time Trace Display. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335 Sample Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337 Chapter 6 Using the Analysis Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .339 Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 341 Working in the Batch View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 343 Samples Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 344 Auto Samples Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 376 Reference Samples Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 378 Creating a Batch Using the Batch Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . 379 Working in Data Review for Quantitation Methods . . . . . . . . . . . . . . . . . . . . 393 Sample View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 394 Compound View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 406 Qualitative View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 416 Features Common to All Data Review Pages . . . . . . . . . . . . . . . . . . . . . . . . 432 Working in Data Review for Target Screening Methods . . . . . . . . . . . . . . . . . 454 Samples Pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 457 Compounds Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 458 Chromatogram Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 461 Spectrum Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 462 Working in the Report View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 468 Viewing Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 469 Generating Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 473 Working with Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 477 Working with the Active View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 480 Working in the Project Administration View . . . . . . . . . . . . . . . . . . . . . . . . . 492 Working with Drives. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 493 Working with Projects. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 495 Working in the Local Method View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 498 Working in the Batch Template Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 500 Appendix A Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .509 Specifying Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 509 Standard Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 510 Custom Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 511 Target Screening Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 511 ToxID Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 511 Report Flags . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 512 Thermo Scientific TraceFinder User Guide v Contents Sample Standard Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 513 Batch Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 514 Batch Report Rev 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 515 Calibration Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 516 Calibration Density Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 519 Chromatogram Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 520 Compound Calibration Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 521 Compound Calibration Report - Alternate . . . . . . . . . . . . . . . . . . . . . . . . . 523 Confirmation Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 525 Confirmation Report 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 526 High Density Calibration Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 527 High Density Internal Standard Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . 528 High Density Internal Standard Report Long . . . . . . . . . . . . . . . . . . . . . . . 529 High Density Sample Report 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 530 High Density Sample Report 1 Long. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 531 High Density Sample Report 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 532 High Density Sample Report 2 Long. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 533 High Density Sample Report 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 534 High Density Sample Report 3 Long. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 535 Internal Standard Summary Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 536 Ion Ratio Failure Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 537 Manual Integration Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 538 Method Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 539 Method Validation Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 542 MSMSD Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 545 Quality Control Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 546 Quantitation Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 547 Quantitation Report - 2. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 548 Solvent Blank Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 550 Appendix B Using Copy Down and Fill Down . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .551 Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .555 vi TraceFinder User Guide Thermo Scientific P Preface Thermo TraceFinder™ 3.0 is the newest application in the Thermo Scientific™ series of GC/MS and LC/MS analytical software. Contents • Related Documentation • Special Notices • System Activation • Contacting Us To suggest changes to documentation or to Help Complete a brief survey about this document by clicking the button below. Thank you in advance for your help. Related Documentation TraceFinder includes Help and these manuals as PDF files: • TraceFinder User Guide • TraceFinder Administrator Quick Reference Guide • TraceFinder Acquisition Quick Reference Guide • TraceFinder Analysis Quick Reference Guide • TraceFinder Shortcut Menus Quick Reference Guide • TraceFinder Custom Reports Tutorial Thermo Scientific TraceFinder User Guide vii Preface To view TraceFinder documents using the Start menu Choose Start > All Programs > Thermo TraceFinder > Manuals. To open TraceFinder Help and access related documents from the application 1. Open the TraceFinder application and choose Help > TraceFinder Help. • To find a particular topic, use the 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. viii TraceFinder User Guide Thermo Scientific Preface System Activation When you first start the TraceFinder application, a dialog box displays the number of days remaining in your 60-day free trial. If your free trial has expired, the License Activation window opens. Note You can open the License Activation window at any time during your trial period by choosing Help > License Activation from the TraceFinder menu. If you already have a permanent license, a message tells you that your product is fully licensed. Two types of licenses are available: • 60-Day Evaluation Version (free of charge) • Full Version Single License The evaluation version is full-featured and automatically expires 60 days after activation. Any attempt to set back the system date automatically terminates this version. You can purchase and then activate the full version of the TraceFinder application at any time, during or after the free evaluation, without reinstalling the software. Each activation key is valid only for a single license. Any additional installation generates a different license and requires a different activation key. For questions regarding activation, contact Thermo Fisher Scientific Technical Support in San Jose, CA: • E-mail: Th[email protected] • Fax: 408-965-6120 Thermo Scientific TraceFinder User Guide ix Preface To request an activation key 1. In the License Activation window, enter your information in the User Info area. As you type, the License Text box creates an XML text string with your information. 2. In the Barcode box, type the barcode printed on the TraceFinder CD. The form of the barcode number is either xxxx-xxxx-xxxx or xxxx-xxxx-xxxx-xxxx. Note The barcode might already be filled in for you. 3. When you finish entering all the information, click Copy. The application copies this XML text to the Clipboard. If you have not completed all the information, a pop-up box identifies the missing information. 4. Paste this XML text in the body of an e-mail and send the e-mail to [email protected] You will receive an e-mail response containing the activation key. x TraceFinder User Guide Thermo Scientific Preface To use your activation key Note You must run the TraceFinder application with ITAdmin or LabDirector rights when entering the activation key. 1. When you receive your activation key, copy it from the e-mail. 2. Choose Help > License Activation from the TraceFinder menu. The License Activation window opens. Note The License Activation window for power modules automatically opens when you try to enable the power module features in the Application Configuration mode. 3. Click Paste. The application pastes the contents of the Clipboard to the License Text box. 4. Click Set. The application is activated according to the type of authorization your license gives you. Contacting Us There are several ways to contact Thermo Fisher Scientific for the information you need. To contact Technical Support Phone 800-532-4752 Fax 561-688-8736 E-mail [email protected] Knowledge base www.thermokb.com Find software updates and utilities to download at mssupport.thermo.com. To contact Customer Service for ordering information Phone 800-532-4752 Fax 561-688-8731 E-mail [email protected] Web site www.thermo.com/ms To get local contact information for sales or service Go to www.thermoscientific.com/wps/portal/ts/contactus. Thermo Scientific TraceFinder User Guide xi 1 Introduction This chapter describes general features of the TraceFinder software. Contents • About the TraceFinder Application • TraceFinder Summary of Features • TraceFinder Workflow • Reporting Features About the TraceFinder Application The TraceFinder application targets the forensic toxicology market. It supports a focused quantification workflow for specific nonbioanalytical laboratory use, instrument control, and method development functionality. TraceFinder is the primary application for the TSQ Quantum™ XLS triple quadrupole mass spectrometers. The TraceFinder application can export SRM data in .xml format so that other applications, including TSQ and Q Exactive™, can import the files into their databases. The TraceFinder application can import the following file types: • Sample lists in .csv or .xml format See “Defining the Sample List” on page 298. • Processing (.pmd) and instrument (.meth) method files from the Xcalibur data system For detailed information about creating processing methods, see “Working with Master Methods” on page 83. For detailed information about creating instrument methods, see “Working with Instrument Methods” on page 269. • Compounds from files that use the database (.xml or .cdb) format See “Editing Compounds in the Database” on page 251. Thermo Scientific TraceFinder User Guide 1 1 Introduction About the TraceFinder Application • Batches, methods, or templates from the following applications: – TraceFinder 1.0, 1.1, 2.0, or 2.1 – QuanLab Forms or ToxLab Forms 2.5 or 3.0 See “Converting Legacy Data” on page 21. The TraceFinder application checks the accuracy and precision of data against systems that have previously been certified against a standard processing program, such as the Statistical Analysis System (SAS). Supported File Types The TraceFinder application supports the following file types: • Comma-separated values (.csv): A set of file formats used to store tabular data in which numbers and text are stored in plain textual form that can be read in a text editor. Lines in the text file represent rows of a table, and commas in a line separate fields in the tables row. • Extensible Markup Language (.xml): A generic framework for storing any amount of text or any data whose structure can be represented as a tree. The only indispensable syntactical requirement is that the document has exactly one root element (also called the document element). This means that the text must be enclosed between a root start-tag and a corresponding end-tag. • Instrument method (.meth): A proprietary file format for the Xcalibur software suite with specific instructions that enable scientific instruments to perform data acquisition. • Processing method (.pmd): A proprietary file format for the Xcalibur software suite with specific instructions on processing data that was acquired through the instruments attached to the system. • Raw data (.raw): The file type for acquired samples on the system. • Compound database (.cdb): The file type for TraceFinder or ExactFinder compound database data. 2 TraceFinder User Guide Thermo Scientific 1 Introduction TraceFinder Summary of Features TraceFinder Directory Structure The TraceFinder application creates folders for projects/subprojects/batches and templates in the C:\Thermo\TraceFinder\3.0\Forensic directory. Within each batch folder, the application creates folders for data, methods, and reports. IMPORTANT You cannot rename or move the folders created by the TraceFinder application. Figure 1. Example batch directory structure TraceFinder Summary of Features The TraceFinder system provides a workflow-oriented approach to high-throughput quantitation. The system uses a batch-centric approach and tools to automate and speed up the processes of method creation, loading samples, automatically generating data, manually reviewing and editing results, and finalizing the data review and reporting process. The TraceFinder software package includes data acquisition, processing, reviewing, and reporting capabilities designed to assist analysts in forensic toxicology applications. The application has a fully automated acquisition mode and a manual data analysis mode. You can use the data acquisition system to create and submit batches and monitor real-time review of results. The TraceFinder application uses a comprehensive processing method to provide improved handling of ion ratio calculations, reviewing, and reporting. In addition, it can compare the mass spectra and integrate the processes of data review and reporting. Key features include the following: • Role-based authorization for LabDirector, ITAdmin, Supervisor, Technician, and QAQC (quality assurance) roles • Configuration mode for report configuration, detection defaults, and application administration • Method Development mode for editing instrument methods, setting processing and error flag parameters, and setting report options Thermo Scientific TraceFinder User Guide 3 1 Introduction TraceFinder Workflow • Choice of acquisition wizards: – Acquisition batch mode that guides you in creating batches and running samples – Batch template wizard similar to the interface used in the ToxLab Forms application • Analysis mode with project administration, batch views, data review, local method views, and report views • Database-capable method development • Quantification workflows, supporting capabilities present in the LCquan™ and ToxLab Forms applications • Target screening workflows • Standard and customized report formats Features of the common workflow core include the following: • Acquisition and processing • Peak detection • Quantification to include calibration • Error analysis and flag setting • Reporting • Data persistence • Raw data file handling TraceFinder Workflow The TraceFinder application is structured with a typical laboratory workflow in mind. You create a batch, and the system injects samples into the instrument, runs the samples, analyzes the data, and generates a report. You can set up a master method for specific compound groups or assays that you expect to run in your laboratory. When you are ready to run a particular type of sample, select the appropriate method and begin. When using the TraceFinder application, follow these basic steps: 1. Create and save a master method in the Method Development mode. A master method combines the instrument method and processing method that define the following: • How the raw data is acquired and processed • How the error checking information evaluates the results • How the results appear in reports 4 TraceFinder User Guide Thermo Scientific 1 Introduction Reporting Features 2. Create and submit a batch using one of the batch wizards. A batch lists samples for processing and reporting using a specified method. Each row of a batch represents a unique sample. 3. Monitor the status of the batch in the Real Time Status view. The real-time display is visible from all the TraceFinder modes. You can begin another batch while you watch the real-time display of the currently acquiring batch. Note At any time, you can quickly view the system status by looking in the lower right corner of the TraceFinder window. This area displays a green, yellow, or red status light and a description of the number of samples in the queue (if any). 4. Evaluate the data in the Analysis mode. The Analysis mode includes views where you can review batches, batch data, reports, and local methods. 5. View and print reports in the Report View of the Analysis mode. Use the Report View to view or print the reports for the currently selected batch. Reporting Features The report engine can generate several different types of reports designed to meet the needs of the laboratory, the laboratory's customers, and key regulatory agencies that might review the results. The following types of reports meet the requirements of various methods and worldwide regulatory agencies, helping to track the performance of LC and GC systems and methods. The reports divide into four groups: Standard, Custom, Target Screening, and ToxID. For additional information about standard, custom, target screening, or ToxID reports and examples of each standard report type, see “Reports” on page 509. Examples of standard reports (as PDF files) are also located in the following folder: C:\Thermo\TraceFinder\3.0\Forensic\ExampleReports Standard Report Types • • • • • • • • • • • • Thermo Scientific Batch Report Batch Summary Report Batch Report Rev 1 Calibration Report Calibration Curve Report Chromatogram Report Compound Calibration Report Compound Calibration Report - Alternate Confirmation Report High Density Calibration Report High Density Internal Standard Report High Density Internal Standard Report Long TraceFinder User Guide 5 1 Introduction Reporting Features • • • • • • • • • • • • • • • • • • • • High Density Sample Report 1 High Density Sample Report 1 Long High Density Sample Report 2 High Density Sample Report 2 Long High Density Sample Report 3 High Density Sample Report 3 Long Intelligent Sequencing Report Internal Standard Summary Report Ion Ratio Failure Report Manual Integration Report Method Report Negative Report Qualitative Peak Report Qualitative Summary Report Quality Control Report Quantitation Report Quantitation Report - 2 Sample Report Sample Report Long Solvent Blank Report Custom Report Types • • • • • • • • • • • • • • • • • • • • • • 6 TraceFinder User Guide 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 Thermo Scientific 1 Introduction Reporting Features Target Screening Report Types • Target Screening High Density Sample Report • Target Screening Summary Report ToxID Report Types • Target Screening Long Report • Target Screening Summary Report Thermo Scientific TraceFinder User Guide 7 2 Getting Started This chapter includes the procedures for getting started with the TraceFinder application. Contents • Installing the TraceFinder Application • Installing the Power Modules • Installing the NIST and QED Libraries • Launching the NIST Library Browser • Launching the Qual Browser • Converting Legacy Data • Choosing a Mode Thermo Scientific TraceFinder User Guide 9 2 Getting Started Installing the TraceFinder Application Installing the TraceFinder Application To initially install the TraceFinder 3.0 application, follow the instructions in the TraceFinder Installation Guide. Later, you might need to reinstall the TraceFinder application or other features on the InstallShield Wizard, such as the power modules. Follow these instructions to reinstall, start, and log in to the TraceFinder application. To reinstall the TraceFinder application 1. From the Thermo Foundation Instrument Configuration window, remove all instruments. 2. From the Windows™ Control Panel, uninstall the TraceFinder application and then uninstall all Thermo instrument drivers. 3. Insert the TraceFinder CD, and install both the TraceFinder 3.0 application and the NIST library as follows: a. Open the TraceFinder launcher and click Next. The InstallShield Wizard opens. b. Click TraceFinder 3.0, and follow the instructions in the InstallShield Wizard. c. At the prompt, click Yes to completely remove any previously installed TraceFinder applications. 10 TraceFinder User Guide Thermo Scientific 2 Getting Started Installing the TraceFinder Application d. Open the TraceFinder launcher again and click Next. e. Click TraceFinder 3.0, and follow the instructions in the InstallShield Wizard. IMPORTANT For the TraceFinder application to properly install, you might be prompted to uninstall Thermo Foundation™. Do the following: 1. Click Yes, and then when prompted to restart your computer, click OK. The wizard continues the TraceFinder installation. 2. When prompted to install Thermo Foundation, click Yes, and then when prompted to restart your computer, click OK. The wizard continues the installation. f. When prompted, choose to install either the GC or LC version of the software. g. When the installation completes, open the TraceFinder launcher again and click Next. h. (Required for ToxID) If you have not previously installed the NIST library, click NIST Library and follow the instructions to install the library. 3. (Optional) Click Example Data, and follow the instructions to install an example project that contains example batch data. 4. Install the appropriate device drivers, and configure the instruments in the Thermo Foundation Instrument Configuration window. Follow these instructions to start the TraceFinder application. To start the TraceFinder application 1. Configure your instruments. You must close the TraceFinder application before you can configure your instruments. 2. Double-click the TraceFinder icon on your desktop, or choose Start > All Programs > Thermo TraceFinder > TraceFinder Forensic Toxicology. By default, user security is not activated and the application does not require a password. To activate user security, see “User Security” on page 64. Thermo Scientific TraceFinder User Guide 11 2 Getting Started Installing the TraceFinder Application To log in to the TraceFinder application (when user security is activated) Note Before you can log in to the TraceFinder application when user security is activated, a system administrator must set up a user account for you. The administrator assigns you a user name and password and gives you permission to access specific modes. 1. Enter your assigned user name in the TraceFinder login window. IMPORTANT If you are the administrator logging in for the first time with user security activated, use Administrator/Password as the username/password. 2. Enter your password. If your user name or password does not match, the system reports this error: Correct the user name or password, or contact your system administrator. 3. Click Login. The TraceFinder login window opens. 12 TraceFinder User Guide Thermo Scientific 2 Getting Started Installing the TraceFinder Application Figure 2. Main window with user security activated User name and Log Off button available only when user security is activated Figure 3. Thermo Scientific TraceFinder login window TraceFinder User Guide 13 2 Getting Started Installing the TraceFinder Application Table 1. Login window parameters 14 TraceFinder User Guide Parameter Description Login text box The user’s assigned user name. Password The assigned password for the user name. Login button Verifies the user name and password, and opens the TraceFinder application. Cancel Closes the TraceFinder login window. Thermo Scientific 2 Getting Started Installing the Power Modules Installing the Power Modules Follow these instructions to install and activate the TraceFinder power modules for multiplexing and intelligent sequencing. To install the power modules 1. Follow the instructions to install the TraceFinder application. See “Installing the TraceFinder Application” on page 10. 2. Open the TraceFinder launcher again and click Next. 3. Click TraceFinder Power Modules, and follow the instructions to install the multiplexing and intelligent sequencing modules. 4. License the power modules. To license the power modules, follow the same procedures for licensing the TraceFinder application. See “System Activation” on page ix. The features associated with these power modules are mutually exclusive and are not automatically activated. 5. To activate these power modules, see “Activating Optional Features” on page 63. Thermo Scientific TraceFinder User Guide 15 2 Getting Started Installing the NIST and QED Libraries Installing the NIST and QED Libraries When you are using triple quadrupole instruments, such as the TSQ Quantum XLS, follow these instructions to install the NIST and QED libraries. To install the NIST library 1. Open the TraceFinder launcher, and click Next. 2. Click NIST Library. The NIST 08 MS Search and AMDIS Setup wizard opens. 3. Follow the instructions in the setup wizard. 4. When the wizard prompts you to select a destination folder, select C:\Program Files\NISTMS. To install the QED library 1. On your desktop, double-click the Xcalibur icon, . The Thermo Xcalibur Roadmap opens. 16 TraceFinder User Guide Thermo Scientific 2 Getting Started Installing the NIST and QED Libraries 2. Choose Tools > Library Manager from the main menu. The Thermo Library Manager dialog box opens, showing the NIST Libraries list. 3. Click Add. The Add Library dialog box opens. 4. Click Browse, and locate your QED library in the C:\Thermo folder. 5. Click OK. The Xcalibur application reports that it has added the library to the NIST application. 6. Click Dismiss to close the message box. The Xcalibur application adds the QED library to the NIST Libraries list in the Library Manager dialog box. Thermo Scientific TraceFinder User Guide 17 2 Getting Started Installing the NIST and QED Libraries 7. Click Exit in the Thermo Library Manager dialog box. 8. To confirm the library installation, do the following: a. Start the TraceFinder application. b. Click Method Development in the navigation pane. c. Click Method View in the Method Development navigation pane. d. Choose File > New > Method Template from the main menu. The Method Template Editor displays the QED NIST Library in the Use These Libraries list. 18 TraceFinder User Guide Thermo Scientific 2 Getting Started Launching the NIST Library Browser Launching the NIST Library Browser Use the NIST MS Search tool to search the NIST library. To open the NIST library browser Choose Go > Launch Library Browser from the TraceFinder main menu. The NIST MS Search window opens. For detailed instructions about using the library browser, refer to the Help in the NIST MS Search window. Thermo Scientific TraceFinder User Guide 19 2 Getting Started Launching the Qual Browser Launching the Qual Browser Use the Xcalibur application’s Qual Browser to view chromatograms and spectra from raw data files or qualitative processing results. To open the Qual Browser Choose Go > Launch Qual Browser from the TraceFinder main menu. The Thermo Xcalibur Qual Browser opens. For detailed instructions about using the Qual Browser, refer to the Help in the Qual Browser window. 20 TraceFinder User Guide Thermo Scientific 2 Getting Started Converting Legacy Data Converting Legacy Data Use the TraceFinder Legacy Data Converter to convert methods, batches, method templates, or batch templates from the source versions to compatible TraceFinder 3.0 target configurations. See Version compatibility. • You can convert legacy data from TraceFinder versions 1.0.1, 1.1, 2.0, or 2.1. • You can convert data from EnviroLab Forms, QuanLab Forms, or ToxLab Forms. • You can convert data from TraceFinder 3.0 for general quantitation to another installed configuration of TraceFinder 3.0. To open the TraceFinder Legacy Data Converter Choose Go > Launch Legacy Data Converter from the TraceFinder main menu. The TraceFinder Legacy Data Converter window opens. This section includes the following topics: • Converting Methods • Converting Batches • Converting Method Templates • Converting Batch Templates Table 2. Version compatibility (Sheet 1 of 2) Source TraceFinder 3.0 target EFS Clinical Research TraceFinder 2.1 Clinical Research TraceFinder 2.1 Forensic Toxicology General TraceFinder 3.0 General TraceFinder 2.1 General TraceFinder 2.1 EFS TraceFinder 2.0 General TraceFinder 2.0 EFS Thermo Scientific Forensic Toxicology TraceFinder User Guide 21 2 Getting Started Converting Legacy Data Table 2. Version compatibility (Sheet 2 of 2) Source TraceFinder 3.0 target General EFS TraceFinder 2.0 Clinical Research TraceFinder 1.1 General TraceFinder 1.1 EFS TraceFinder 1.0.1 EnviroLab Forms 3.1 QuanLab Forms 3.1 ToxLab Forms 3.1 ToxLab Forms 2.5.2 22 TraceFinder User Guide Forensic Toxicology EnviroLab Forms 2.5.2 QuanLab Forms 2.5.2 Clinical Research Thermo Scientific 2 Getting Started Converting Legacy Data Converting Methods Use the data converter to convert legacy methods to TraceFinder 3.0 methods. To convert a method 1. In the Data Type list, select Method. The TraceFinder Legacy Data Converter displays the interface for converting methods. 2. In the Source Version list, select the version of the method that you will convert. The Methods to be Converted table displays the methods in the Methods folder for the selected source version. The application verifies that the method file is in the .mmx file format. 3. To convert a method that is not in the default list, do the following: a. Click the Change Default Source Folder icon, . The application adds a Source Folder box to the window. b. Click Browse and locate a method folder. You can select a specific method folder or a folder that contains multiple methods. c. Click OK in the Browse for Folder dialog box. The application displays the selected folder in the Methods to be Converted table. When you select a folder that contains multiple method folders, the application displays all the methods. 4. In the Target Version list, select the version that you are converting to. The list displays only TraceFinder configurations with compatible data. See “Version compatibility” on page 21. Thermo Scientific TraceFinder User Guide 23 2 Getting Started Converting Legacy Data 5. In the Target Drive list, select a fixed drive. You cannot write the converted files to a mapped drive. 6. (Optional) In the New Name column, change the default new name for each method that you want converted. When you populate the Methods to be Converted table, the application checks each method to see if a method with this name exists in the target folder. • If the method name already exists in the target folder, the default new name is the original name with “_1” appended. • If the method name does not exist in the target folder, the application keeps the original method name. IMPORTANT The conversion cannot overwrite an existing file name. If the new name is identical to an existing method file, the conversion will not work. When you manually enter a new name, you must verify that the name does not already exist. 7. Select the check box for each method that you will convert, and click . The application confirms that all methods to be converted use the .mmx file format. When the conversion process begins, the application displays a status bar and a Cancel button. You can cancel pending conversions, but not the method that is currently converting. When the Status column reports that a method is successfully converted, the application writes the converted file to the C:\Thermo\TargetVersion\Methods folder. Note If a method conversion is unsuccessful, the Status column displays an error icon. Hold your cursor over the icon to display the error message. 8. To view a log of the conversion, click View Log. The application opens a cumulative log file for the session in a Microsoft Notepad text editor window. Figure 4. 24 Sample log file for converting a method TraceFinder User Guide Thermo Scientific 2 Getting Started Converting Legacy Data Converting Batches Use the data converter to convert legacy batches to TraceFinder 3.0 batches. To convert a batch 1. In the Data Type list, select Batch. The TraceFinder Legacy Data Converter displays the interface for converting batches. 2. In the Source Version list, select the version of the batch that you will convert. The Batches to be Converted table displays all batches in the Projects folder for the selected source version. IMPORTANT A valid batch file (.btx) must be inside a folder with the same name. For example: 3. To convert a batch that is not in the default list, do the following: a. Click the Source Folder icon, . The application adds a Source Folder box to the window. b. Click Browse and locate a batch folder. You can select a specific batch folder or a project or subproject folder that contains multiple batches. Thermo Scientific TraceFinder User Guide 25 2 Getting Started Converting Legacy Data c. Click OK in the Browse for Folder dialog box. The application displays the selected folder and all batches in that folder in the Batches to be Converted table. When you select a project or subproject folder that contains multiple batch folders, the application displays all the batches. 4. In the Target Version list, select the version that you are converting to. The list displays only TraceFinder configurations with compatible data. See “Version compatibility” on page 21. 5. In the Target Drive list, select a fixed drive. You cannot write the converted files to a mapped drive. 6. Do one of the following to create a project and subproject for the converted batch: In the Target Default Project and Subproject boxes, type the name of a project and subproject. –or– Select the Replicate Original Project/Subproject check box. 7. (Optional) In the New Name column, change the default new name for each batch that you want converted. When you populate the Batches to be Converted table, the application checks each batch to see if a batch with this name exists in the target folder. • If the batch name already exists in the target folder, the default new name is the original name with “_1” appended. • If the batch name does not exist in the target folder, the application keeps the original batch name. IMPORTANT The conversion cannot overwrite an existing file name. If the new name is identical to an existing batch folder, the conversion will not work. When you manually enter a new name, you must verify that the name does not already exist. 8. Select the check box for each batch that you will convert, and click . The application confirms that all batches to be converted use the .btx file format. When the conversion process begins, the application displays a status bar and a Cancel button. You can cancel pending conversions, but not the batch that is currently converting. 26 TraceFinder User Guide Thermo Scientific 2 Getting Started Converting Legacy Data When the Status column reports that a batch is successfully converted, the application writes the converted batch to the C:\Thermo\TargetVersion\Projects folder and uses either the original project and subproject names or the new names that you entered. Note If a batch conversion is unsuccessful, the Status column displays an error icon. Hold your cursor over the icon to display the error message. 9. To view a log of the conversion, click View Log. The application opens a cumulative log file for the session in a Notepad text editor window. Figure 5. Sample log file for converting a batch Thermo Scientific TraceFinder User Guide 27 2 Getting Started Converting Legacy Data Converting Method Templates Use the data converter to convert legacy method templates to TraceFinder 3.0 method templates. To convert a method template 1. In the Data Type list, select Method Template. The TraceFinder Legacy Data Converter displays the interface for converting method templates. 2. In the Source Version list, select the version of the method template that you will convert. The Method Templates to be Converted table displays the method templates in the Templates folder for the selected source version. The application verifies that the method template file is in the .pmtx file format. 3. To convert a method template that is not in the default list, do the following: a. Click the Source Folder icon, . The application adds a Source Folder box to the window. b. Click Browse and locate a template folder. You can select a specific template folder or a folder that contains multiple templates. c. Click OK in the Browse for Folder dialog box. The application displays the selected folder in the Method Templates to be Converted table. When you select a folder that contains multiple method template folders, the application displays all the method templates. 4. In the Target Version list, select the version that you are converting to. The list displays only TraceFinder configurations with compatible data. See “Version compatibility” on page 21. 28 TraceFinder User Guide Thermo Scientific 2 Getting Started Converting Legacy Data 5. In the Target Drive list, select a fixed drive. You cannot write the converted files to a mapped drive. 6. (Optional) In the New Name column, change the default new name for each method template that you want converted. When you populate the Method Templates to be Converted table, the application checks each method template to see if a method template with this name exists in the target folder. • If the method template name already exists in the target folder, the default new name is the original name with “_1” appended. • If the method template name does not exist in the target folder, the application keeps the original method template name. IMPORTANT The conversion cannot overwrite an existing file name. If the new name is identical to an existing method template file, the conversion will fail. When you manually enter a new name, you must verify that the name does not already exist. 7. Select the check box for each method template that you will convert, and click . The application confirms that all method templates to be converted use the .pmtx file format. When the conversion process begins, the application displays a status bar and a Cancel button. You can cancel pending conversions, but not the template that is currently converting. When the Status column reports that the template is successfully converted, the application writes the converted template to the following folder: C:\Thermo\TargetVersion\Templates\Methods folder Note If a template conversion fails, the Status column displays an error icon. Hold your cursor over the icon to display the error message. 8. To view a log of the conversion, click View Log. The application opens a cumulative log file for the session in a Notepad text editor window. Figure 6. Sample log file for converting a method template Thermo Scientific TraceFinder User Guide 29 2 Getting Started Converting Legacy Data Converting Batch Templates Use the data converter to convert legacy batch templates to TraceFinder 3.0 batch templates. To convert a batch template 1. In the Data Type list, select Batch Template. You can choose either LabForms batch templates or TraceFinder batch templates. The TraceFinder Legacy Data Converter displays the interface for converting batch templates. 2. In the Source Version list, select the version of the batch template that you will convert. The Batch Templates to be Converted table displays the batch templates in the Templates folder for the selected source version. IMPORTANT A valid batch template file (.btx) must be inside a folder with the same name. For example: 3. To convert a batch template that is not in the default list, do the following: a. Click the Source Folder icon, . The application adds a Source Folder box to the window. b. Click Browse and locate a template folder. You can select a specific batch template folder or a folder that contains multiple batch templates. c. Click OK in the Browse for Folder dialog box. The application displays the selected folder in the Batch Templates to be Converted table. When you select a folder that contains multiple batch template folders, the application displays all the batch templates. 4. In the Target Version list, select the version that you are converting to. The list displays only TraceFinder configurations with compatible data. See “Version compatibility” on page 21. 30 TraceFinder User Guide Thermo Scientific 2 Getting Started Converting Legacy Data 5. In the Target Drive list, select a fixed drive. You cannot write the converted files to a mapped drive. 6. (Optional) In the New Name column, change the default new name for each batch template that you want converted. When you populate the Batch Templates to be Converted table, the application checks each batch template to see if a batch template with this name exists in the target folder. • If the batch template name already exists in the target folder, the default new name is the original name with “_1” appended. • If the batch template name does not exist in the target folder, the application keeps the original batch template name. IMPORTANT The conversion cannot overwrite an existing file name. If the new name is identical to an existing batch template file, the conversion will fail. When you manually enter a new name, you must verify that the name does not already exist. 7. Select the check box for each batch template that you will convert, and click . The application confirms that all batch templates to be converted use the .btx file format. When the conversion process begins, the application displays a status bar and a Cancel button. You can cancel pending conversions, but not the template that is currently converting. When the Status column reports that the template is successfully converted, the application writes the converted template folder to the C:\Thermo\TargetVersion\Templates\Batches folder. Note If a template conversion fails, the Status column displays an error icon. Hold your cursor over the icon to display the error message. 8. To view a log of the conversion, click View Log. The application opens a cumulative log file for the session in a Notepad text editor window. Figure 7. Sample log file for converting a batch template Thermo Scientific TraceFinder User Guide 31 2 Getting Started Choosing a Mode Choosing a Mode When user security is activated, the navigation pane displays the modes available to the current user’s assigned role. The following table shows the available modes for each user role. Table 3. User roles and mode access User role Method Development Acquisition Analysis Application Configuration LabDirector ITAdmin Supervisor Technician QAQC Note When user security is not activated, all modes are available to all users. Follow these procedures: • To choose a mode • To display a log of instrument errors • To monitor instrument status • To watch acquisition and processing in real time 32 TraceFinder User Guide Thermo Scientific 2 Getting Started Choosing a Mode To choose a mode Do one of the following: • To access a mode from the navigation pane, click the mode where you want to work. The navigation pane shows only the modes that you have permission to use. Mode Description Acquisition Opens the Acquisition mode where you can create and review batches, batch data, reports, and local methods. See Chapter 5, “Using the Acquisition Mode.” This mode is available only when you select the Acquisition Batch Wizard style in the Configuration mode. See “Batch Wizard Style” on page 65. Analysis Opens the Analysis mode where you can review batches, batch data, reports, and local methods. See Chapter 6, “Using the Analysis Mode.” Method Development Opens the Method Development mode where you can create a master method, an instrument method, or a development batch. See Chapter 4, “Using the Method Development Mode.” –or– • Click the Application Configuration icon, TraceFinder window. , in the upper right corner of the When user security is activated, only users in the LabDirector or ITAdmin role have permission to use the Application Configuration mode. Thermo Scientific TraceFinder User Guide 33 2 Getting Started Choosing a Mode To display a log of instrument errors 1. Click the status light in the upper right corner of the TraceFinder window. Status light The Instrument Log dialog box opens. The Instrument Log displays all instrument errors that have occurred since the TraceFinder application started or since the last time that you cleared the message log. 2. Do any of the following: • Click Refresh to display errors that occur after you open the Instrument Log dialog box. • Click Clear Messages to remove messages from the Instrument Log display. The application clears messages only from the Instrument Log display. These messages remain in the following log file: C:\Thermo\TraceFinder\3.0\Forensic\Logs\TraceFinder.log • Click OK to dismiss the Instrument Log dialog box. To monitor instrument status Look at the status light in the upper right corner of the TraceFinder window. Green indicates that the instrument is ready. Yellow indicates that the instrument is in standby mode. Red indicates that the instrument is turned off or no device is configured. 34 TraceFinder User Guide Thermo Scientific 2 Getting Started Choosing a Mode To watch acquisition and processing in real time Click Real Time Status in the upper right corner of the TraceFinder window. The application displays the Real Time Status pane at the bottom of the window. For descriptions of all the features of the Real Time Status pane, see “Real Time Status Pane” on page 323. Thermo Scientific TraceFinder User Guide 35 2 Getting Started Choosing a Mode TraceFinder Window Features A TraceFinder window with user security for a user in the LabDirector role has these functions. Table 4. TraceFinder window parameters 36 TraceFinder User Guide Parameter Description Real Time Status Opens the Real Time Status pane for the current acquisition. The acquisition progress is displayed within the current mode window. CurrentUserName Displays the name of the current user. This is displayed only when user security is activated. See “User Security” on page 64. Log Off Logs off the current user and displays the login screen. This function is available only when user security is activated. See “User Security” on page 64. Help Opens the TraceFinder Help. Application Configuration Opens the Application Configuration mode where you can configure several options for using the TraceFinder application. See Chapter 3, “Using the Application Configuration Mode.” Thermo Scientific 3 Using the Application Configuration Mode This chapter discusses the configuration tasks assigned to the ITAdmin and LabDirector roles when user security is activated. When user security is not activated, all users have access to all features in the Application Configuration mode except the User Administration tasks. When user security is activated, in either the LabDirector or ITAdmin role, you can activate features such as available reports, user security, reporting defaults, multiplexing, detection algorithms, and target screening. You can also choose the reports that are available to users, the application defaults, and the defaults used for peak detection. Contents • Specifying the Reports Configuration • Specifying Application Defaults • Specifying Default Peak Detection Parameters • Specifying Adducts Configuration • Activating Optional Features • Managing User Administration To access the Application Configuration mode Click the Application Configuration icon, window. , in the upper right corner of any The navigation pane for this mode opens with the following functions (see Navigation pane functions in the Application Configuration mode). Available only to users in the LabDirector or ITAdmin role Thermo Scientific TraceFinder User Guide 37 3 Using the Application Configuration Mode Table 5. 38 TraceFinder User Guide Navigation pane functions in the Application Configuration mode Function Description Reports From the Reports view, you can configure standard, custom, ToxID, or target screening reports. See “Specifying the Reports Configuration” on page 39. Defaults From the Defaults view, you can specify the default laboratory and instrument names, the displayed mass precision, and the intensity scale to use for reporting. See “Specifying Application Defaults” on page 44. Peak Detection Defaults Use the Peak Detection Defaults view to specify a peak detection algorithm and its options and to determine the area under a curve. See “Specifying Default Peak Detection Parameters” on page 46. Adducts Use the Adducts Configuration view to specify the adducts that will be available for you to use in method development. See “Specifying Adducts Configuration” on page 60. Optional Features See “Activating Optional Features” on page 63. User Administration With user security activated, in either the LabDirector or ITAdmin role, you can add, remove, or edit user accounts and permissions. See “Managing User Administration” on page 69. Thermo Scientific 3 Using the Application Configuration Mode Specifying the Reports Configuration Specifying the Reports Configuration When user security is activated, as a user in either the LabDirector or ITAdmin role, you can configure a list of reports that are available to all users when they generate reports from the Method Development, Analysis, or Acquisition modes. From the Reports view, you can configure standard, custom, ToxID, or target screening reports. When you first open the report configuration, all reports are included in the Displayed Reports pane and are available for use in any method you create. By default, the Intelligent Sequencing Report is not included in the Displayed Reports pane. Note The Intelligent Sequencing Report is available only when you install the Intelligent Sequencing power module and enable the Intelligent Sequencing features. See “Installing the Power Modules” on page 15 and “Intelligent Sequencing” on page 66. Note ToxID reports are available only when you activate the ToxID features. See “ToxID” on page 64. Example PDF files of report formats are located in the following folder: C:\Thermo\TraceFinder\3.0\Forensic\ExampleReports Follow these procedures: • To open the Reports Configuration • To specify which reports are available • To import new reports To open the Reports Configuration In the Application Configuration mode, click Reports. The Reports view of the Application Configuration mode opens. For a list of all reports for the forensic toxicology market, see “Reports” on page 41. To specify which reports are available 1. Use the directional arrows to move reports between the Installed Reports pane and the Displayed Reports pane. Tip Use the CTRL or SHIFT keys to select multiple reports. In the Method Development, Analysis, and Acquisition modes, users can access all reports in the Displayed Reports pane. 2. To create a single composite report for an entire batch (rather than a separate report for each sample), select the Batch Level check box for the report. Rather than creating separate reports for each sample, the application uses a composite of the data from all the samples to create a single report for the entire batch. The application adds a B to the beginning of all batch-level report names to differentiate them. Thermo Scientific TraceFinder User Guide 39 3 Using the Application Configuration Mode Specifying the Reports Configuration Note Only reports that can aggregate data at the batch level have the Batch Level check box activated. By default, the application selects the Batch Level feature for all these reports. 3. Apply the current selections as follows: a. Click Apply. A message prompts you to restart the TraceFinder application so that a user can access the reports you selected for the Method Development, Analysis, and Acquisition modes. b. To restart the TraceFinder application now, click Yes, or to remain in the Reports view, click No. If you want to return the report selections to their original state (when you first opened this view), click Undo Changes. To import new reports 1. Click Import. The Open dialog box opens. 2. In the Open dialog box, locate a Crystal Reports .dll file or a Custom Reports .xltm file and open it. The application writes the imported report to the TraceFinder installation directory and displays the new report in the Installed Reports pane. 40 TraceFinder User Guide Thermo Scientific 3 Using the Application Configuration Mode Specifying the Reports Configuration Reports The application uses the following standard, custom, target screening, and ToxID reports. For descriptions of the parameters in the Reports view, see “Reports view parameters” on page 43. Figure 8. Reports view showing standard reports Thermo Scientific TraceFinder User Guide 41 3 Using the Application Configuration Mode Specifying the Reports Configuration Figure 9. Reports view showing custom reports Figure 10. Reports view showing target screening reports 42 TraceFinder User Guide Thermo Scientific 3 Using the Application Configuration Mode Specifying the Reports Configuration Figure 11. Reports view showing ToxID reports Note ToxID reports are available only when you install the ToxID™ software and activate the ToxID features. For a detailed procedure for activating ToxID features, see “ToxID” on page 64. Table 6. Thermo Scientific Reports view parameters Parameter Description Installed Reports All reports listed in this pane are potentially available but are not selected for use in the application. Displayed Reports All reports listed in this pane are selected for use in the application. >> Moves all reports from the Installed Reports list to the Displayed Reports list. > Moves the selected reports from the Installed Reports list to the Displayed Reports list. < Moves the selected reports from the Displayed Reports list to the Installed Reports list. << Moves all reports from the Displayed Reports list to the Installed Reports list. Import Opens a browser where you can select a report file to add to the Installed Reports list. Cancel Returns the report selections to their original state (when you first opened this view). Apply Applies the current selections, and prompts you to restart the TraceFinder application so that a user can access the reports you selected for the Method Development, Analysis, and Acquisition modes. TraceFinder User Guide 43 3 Using the Application Configuration Mode Specifying Application Defaults Specifying Application Defaults Use the Application Defaults view of the Application Configuration mode to specify the default laboratory and instrument names, the displayed mass precision, and the chromatogram intensity scale to use for reporting. When user security is activated, you can access these features only in the LabDirector or ITAdmin role. Follow these procedures: • To open the Application Defaults view • To specify a default laboratory name and instrument name • To specify default mass precision and the intensity scale To open the Application Defaults view In the navigation pane for the Application Configuration mode, click Defaults. The Application Defaults view of the Application Configuration mode opens. To specify a default laboratory name and instrument name 1. Type the name of your laboratory in the Lab Name box. When you create a method, the application uses this default laboratory name for the Laboratory Name value on the General page of the Method View. The application uses this laboratory name in the report headings. The application does not apply this default laboratory name to previously created methods. By default, the laboratory name is Default Laboratory. 2. Type the name of your instrument in the Instrument Name box. When you create a batch, the application uses this default instrument name for the Instrument Name value. The application uses this instrument name in the report headings. 44 TraceFinder User Guide Thermo Scientific 3 Using the Application Configuration Mode Specifying Application Defaults 3. In the Application Configuration mode, click Apply. The application does not apply this default instrument name to previously created batches. By default, the instrument name is Thermo Scientific Instrument. 4. When asked if you want to restart the application, click Restart Now. To specify default mass precision and the intensity scale 1. In the Display Mass Precision box, set the decimal value for the mass precision to an integer from 2 to 6, inclusive. The default number of digits to display is 2. The TraceFinder application uses this mass precision value to display mass values in the following locations: • Reports: – Blank Report – Confirmation Report (data spectra, library spectra, quantitation ion display, and qualitative ion display) – All High Density reports (m/z values) – Ion Ratio Failure Report (quantitation ion and qualitative ion) – Manual Integration Report (m/z value) – Qualitative Summary Report (all m/z values) – Quantitation Report (QIon) • All peaks on the Detection pages in the Method Development mode • The spectrum display in the Analysis mode • The spectrum display in the Method Forge dialog box IMPORTANT When you create a method using a raw data file, the application reads the filter precision value from the raw data file to create scan filters; however, the Tracefinder application uses the Display Mass Precision value when showing masses that are not embedded within filter strings and masses that are displayed on spectral plots. 2. Select Relative or Absolute from the Chromatogram Intensity Scale list. This sets the default display type for both quantitation and qualitative chromatograms displayed in data review and reports. 3. In the Application Configuration mode, click Apply. 4. When asked if you want to restart the application, click Restart Now. Thermo Scientific TraceFinder User Guide 45 3 Using the Application Configuration Mode Specifying Default Peak Detection Parameters Specifying Default Peak Detection Parameters When user security is activated, as a user in either the LabDirector or ITAdmin role, you can specify default peak detection parameters for the Genesis, ICIS, or Avalon detection algorithms. Use the Peak Detection Defaults view to specify a peak detection algorithm and its options and to determine the area under a curve. These parameters are available for quantitation methods only. This section includes procedures for specifying common peak detection parameters (see “Common peak detection areas” on page 48) and the parameters used for each of the following detection algorithms: • Genesis Detection Method • ICIS Detection Method • Avalon Detection Method To open the Peak Detection Defaults view In the navigation pane for the Application Configuration mode, click Peak Detection Defaults. The Peak Detection Defaults view opens. • For detailed descriptions of detection parameters used for all detection algorithms, see “Common peak detection parameters” on page 48. • For detailed descriptions of detection parameters used for the Genesis detection algorithm, see “Genesis peak detection parameters” on page 50. • For detailed descriptions of detection parameters used for the ICIS detection algorithm, see “ICIS peak detection parameters” on page 53. • For detailed descriptions of detection parameters used for the Avalon detection algorithm, see “Avalon peak detection parameters” on page 56. To specify common detection parameters 1. In the Detector Type list, select a detector type. For detailed descriptions of the available detector types, see “Common peak detection parameters” on page 48. 2. In the Mass Tolerance area, do the following: a. Select the unit of measure that you want to use (MMU or PPM). b. In the Value box, specify the number of millimass units or parts per million to use as the upper limit. The application applies this mass tolerance to the extracted chromatograms. The default is 500 MMU. 46 TraceFinder User Guide Thermo Scientific 3 Using the Application Configuration Mode Specifying Default Peak Detection Parameters 3. In the Retention Time area, do the following: a. In the Window box, specify the width of the window (in seconds) to indicate how far around the expected retention time the system will look for a peak apex. b. In the View Width box, specify the viewable size (in minutes) of the ion chromatogram display. 4. In the Ion Ratio Parameters area, do the following: a. In the Window Type list, select Absolute or Relative as the calculation approach for determining the acceptable ion ratio range. b. In the Window box, select the acceptable ion ratio range. c. In the Ion Coelution box, select the maximum difference in retention time between a confirming ion peak and the quantification ion peak. 5. In the Peak Detection Parameters area, select one of the detection algorithms: Genesis, ICIS, or Avalon. 6. Specify the parameters for the selected detection algorithm. For detailed parameter descriptions, see one of the following: • Genesis Detection Method • ICIS Detection Method • Avalon Detection Method Thermo Scientific TraceFinder User Guide 47 3 Using the Application Configuration Mode Specifying Default Peak Detection Parameters Figure 12. Common peak detection areas Table 7. Common peak detection parameters (Sheet 1 of 2) Parameter Description Detector Type MS: Mass spectrometer that ionizes sample molecules and then separates the ions according to their mass-to-charge ratio (m/z). PDA: Photodiode array detector providing a linear array of discrete photodiodes on an integrated circuit chip. It is placed at the image plane of a spectrometer so that a range of wavelengths can be simultaneously detected. Analog: Supplemental detectors (for example, FID, ECD). When you select this detector, any reports that display a QIon value show the value as Analog and any reports that display spectra show the spectra as Not Available. A/D card: If your detector is not under data system control, you can capture the analog signal and convert it to digital using an interface box (for example, SS420X) for storage in the raw data file. UV: A UV spectrophotometer (for variable-wavelength detection) or photometer (for single-wavelength detection) equipped with a low-volume flow cell. This detector detects analytes that readily absorb light at a selected wavelength. Mass Tolerance Units • (Default) MMU (millimass units) MMU is a static calculation to the extracted mass. • PPM (parts per million) PPM is a variable calculation dependent on the actual mass. The smaller the mass, the narrower the tolerance range. The larger the mass, the wider the tolerance range. 48 TraceFinder User Guide Thermo Scientific 3 Using the Application Configuration Mode Specifying Default Peak Detection Parameters Table 7. Common peak detection parameters (Sheet 2 of 2) Parameter Description Value Upper limit of MMU or PPM. Default: 500 Range: 0.1 through 50 000 Retention Time Window (sec) Width of the window (in seconds) to indicate how far around the expected retention time the system will look for a peak apex. View Width (min) Viewable size (in minutes) of the ion chromatogram display. Changing the view width does not affect the process of peak detection; the TraceFinder application uses it only for graphical display. Ion Ratio Parameters Window Type The absolute or relative calculation approach for determining the acceptable ion ratio range. Window (+/-%) The acceptable ion ratio range. Ion Coelution (min) The maximum difference in retention time between a confirming ion peak and the quantification ion peak. Thermo Scientific TraceFinder User Guide 49 3 Using the Application Configuration Mode Specifying Default Peak Detection Parameters Genesis Detection Method The TraceFinder application provides the Genesis peak detection algorithm for backward compatibility with Xcalibur 1.0 studies. Figure 13. Genesis peak detection Table 8. Genesis peak detection parameters (Sheet 1 of 3) Parameter Description Sensitivity Specifies the Genesis peak detection algorithm. Detection Method Highest peak: Uses the highest peak in the chromatogram for component identification. Nearest RT: Uses the peak with the nearest retention time in the chromatogram for component identification. Smoothing 50 TraceFinder User Guide Determines the degree of data smoothing to be performed on the active component peak prior to peak detection and integration. The ICIS peak detection algorithm uses this value. Default: 1 Range: Any odd integer from 1 through 15 points Thermo Scientific 3 Using the Application Configuration Mode Specifying Default Peak Detection Parameters Table 8. Genesis peak detection parameters (Sheet 2 of 3) Parameter Description S/N threshold Current signal-to-noise threshold for peak integration. Peaks with signal-to-noise values less than this value are not integrated. Peaks with signal-to-noise values greater than this value are integrated. Range: 0.0 to 999.0 Enable Valley Detection Uses the valley detection approximation method to detect unresolved peaks. This method drops a vertical line from the apex of the valley between unresolved peaks to the baseline. The intersection of the vertical line and the baseline defines the end of the first peak and the beginning of the second peak. Expected Width (sec) The expected peak width parameter (in seconds). This parameter controls the minimum width that a peak is expected to have if valley detection is enabled. With valley detection enabled, any valley points nearer than the expected width/2 to the top of the peak are ignored. If a valley point is found outside the expected peak width, the TraceFinder application terminates the peak at that point. The application always terminates a peak when the signal reaches the baseline, independent of the value set for the expected peak width. Range: 0.0 to 999.0 Constrain Peak Width Constrains the peak width of a component during peak integration of a chromatogram. You can then set values that control when peak integration is turned on and off by specifying a threshold and a tailing factor. Selecting the Constrain Peak Width check box activates the Peak Height (%) and Tailing Factor options. Peak Height (%) A signal must be above the baseline percentage of the total peak height (100%) before integration is turned on or off. This text box is active only when you select the Constrain Peak Width check box. Range: 0.0 to 100.0% Tailing Factor A factor that controls how the TraceFinder application integrates the tail of a peak. This factor is the maximum ratio of the trailing edge to the leading side of a constrained peak. This text box is active only when you select the Constrain the Peak Width check box. Range: 0.5 through 9.0 Min Peak Height (S/N) For the valley detection approximation method to use the Nearest RT Peak Identification criteria, this peak signal-to-noise value must be equaled or exceeded. For component identification purposes, the TraceFinder application ignores all chromatogram peaks that have signal-to-noise values that are less than the S/N Threshold value. Range: 0.0 (all peaks) through 999.0 Thermo Scientific TraceFinder User Guide 51 3 Using the Application Configuration Mode Specifying Default Peak Detection Parameters Table 8. Genesis peak detection parameters (Sheet 3 of 3) Parameter Description Peak S/N Cutoff The peak edge is set to values below this signal-to-noise ratio. This test assumes it has found an edge of a peak when the baseline adjusted height of the edge is less than the ratio of the baseline adjusted apex height and the peak S/N cutoff ratio. When the S/N at the apex is 500 and the peak S/N cutoff value is 200, the TraceFinder application defines the right and left edges of the peak when the S/N reaches a value less than 200. Range: 50.0 to 10000.0 Valley Rise (%) The peak trace can rise above the baseline by this percentage after passing through a minimum (before or after the peak). This criteria is useful for integrating peaks with long tails. This method drops a vertical line from the apex of the valley between unresolved peaks to the baseline. The intersection of the vertical line and the baseline defines the end of the first peak and the beginning of the second peak. When the trace exceeds rise percentage, the TraceFinder application applies valley detection peak integration criteria. This test is applied to both the left and right edges of the peak. Range: 0.1 to 500.0 Valley S/N Specifies a value to evaluate the valley bottom. Using this parameter ensures that the surrounding measurements are higher. Default: 2.0 Range: 1.0 to 100.0 # Background Scans Number of background scans performed by the TraceFinder application. Report Noise As Determines if the noise used in calculating S/N values is calculated using an RMS calculation or peak-to-peak resolution threshold. Options are RMS or Peak To Peak. 52 TraceFinder User Guide Thermo Scientific 3 Using the Application Configuration Mode Specifying Default Peak Detection Parameters ICIS Detection Method The ICIS peak detection algorithm is designed for MS data and has superior peak detection efficiency at low MS signal levels. Figure 14. ICIS peak detection Table 9. ICIS peak detection parameters (Sheet 1 of 3) Parameter Description Sensitivity Specifies the ICIS peak detection algorithm. Detection Method Highest peak: Uses the highest peak in the chromatogram for component identification. Nearest RT: Uses the peak with the nearest retention time in the chromatogram for component identification. Thermo Scientific TraceFinder User Guide 53 3 Using the Application Configuration Mode Specifying Default Peak Detection Parameters Table 9. ICIS peak detection parameters (Sheet 2 of 3) Parameter Description Smoothing Determines the degree of data smoothing to be performed on the active component peak prior to peak detection and integration. The ICIS peak detection algorithm uses this value. Range: Any odd integer from 1 through 15 points Default: 1 Area Noise Factor The noise level multiplier used to determine the peak edge after the location of the possible peak. The ICIS peak detection algorithm uses this value. Range: 1 through 500 Default: 5 Peak Noise Factor The noise level multiplier used to determine the potential peak signal threshold. The ICIS peak detection algorithm uses this value. Range: 1 through 1000 Default: 10 Baseline Window The TraceFinder application looks for a local minima over this number of scans. The ICIS peak detection algorithm uses this value. Range: 1 through 500 Default: 40 Constrain Peak Width Constrains the peak width of a component during peak integration of a chromatogram. You can then set values that control when peak integration is turned on and off by specifying a peak height threshold and a tailing factor. Selecting the Constrain Peak Width check box activates the Peak Height (%) and Tailing Factor options. Peak Height (%) A signal must be above the baseline percentage of the total peak height (100%) before integration is turned on or off. This text box is active only when you select the Constrain Peak Width check box. Range: 0.0 to 100.0% Tailing Factor A factor that controls how the TraceFinder application integrates the tail of a peak. This factor is the maximum ratio of the trailing edge to the leading side of a constrained peak. This text box is active only when you select the Constrain the Peak Width check box. Range: 0.5 through 9.0 Min Peak Height (S/N) For the valley detection approximation method to use the Nearest RT Peak Identification criteria, this peak signal-to-noise value must be equaled or exceeded. For component identification purposes, the TraceFinder application ignores all chromatogram peaks that have signal-to-noise values that are less than the S/N Threshold value. Range: 0.0 (all peaks) through 999.0 54 TraceFinder User Guide Thermo Scientific 3 Using the Application Configuration Mode Specifying Default Peak Detection Parameters Table 9. ICIS peak detection parameters (Sheet 3 of 3) Parameter Description Noise Method The options are INCOS or Repetitive. INCOS: Uses a single pass algorithm to determine the noise level. The ICIS peak detection algorithm uses this value. Repetitive: Uses a multiple pass algorithm to determine the noise level. The ICIS peak detection algorithm uses this value. In general, this algorithm is more accurate in analyzing the noise than the INCOS Noise algorithm, but the analysis takes longer. Min Peak Width The minimum number of scans required in a peak. The ICIS peak detection algorithm uses this value. Range: 0 to 100 scans Default: 3 Multiplet Resolution The minimum separation in scans between the apexes of two potential peaks. This is a criteria to determine if two peaks are resolved. The ICIS peak detection algorithm uses this value. Range: 1 to 500 scans Default: 10 Area Tail Extension The number of scans past the peak endpoint to use in averaging the intensity. The ICIS peak detection algorithm uses this value. Range: 0 to 100 scans Default: 5 Area Scan Window The number of allowable scans on each side of the peak apex. A zero value defines all scans (peak-start to peak-end) to be included in the area integration. Range: 0 to 100 scans Default: 0 RMS Thermo Scientific Specifies that the TraceFinder application calculate noise as RMS. By default, the application uses Peak To Peak for the noise calculation. RMS is automatically selected if you manually determine the noise region. TraceFinder User Guide 55 3 Using the Application Configuration Mode Specifying Default Peak Detection Parameters Avalon Detection Method The Avalon peak detection algorithm is designed for UV data. The Avalon peak detection algorithm also supports negative peaks. You can edit the Event values from the “Avalon Event List.” Figure 15. Avalon peak detection Table 10. Avalon peak detection parameters Parameter Description Sensitivity Specifies the Avalon peak detection algorithm. Detection Method Highest peak: Uses the highest peak in the chromatogram for component identification. Nearest RT: Uses the peak with the nearest retention time in the chromatogram for component identification. Smoothing Determines the degree of data smoothing to be performed on the active component peak prior to peak detection and integration. The ICIS peak detection algorithm uses this value. Default: 1 Range: Any odd integer from 1 through 15 points Time/Event/Value Displays the events specified in the Avalon Event List dialog box. Initially displays only the default events that cannot be edited or deleted. Edit Opens the Avalon Event List dialog box where you can edit the Time/Event/Value parameters. See “Avalon Event List.” 56 TraceFinder User Guide Thermo Scientific 3 Using the Application Configuration Mode Specifying Default Peak Detection Parameters Avalon Event List The event list includes both user-defined and noneditable default events. The application displays the default events when you choose Avalon sensitivity. You cannot delete these events or change their time or values. For a detailed list of events and value ranges, see Event types. Figure 16. Avalon Event List dialog box Table 11. Avalon Event List dialog box parameters Thermo Scientific Parameter Description Time (Min) Specifies the start time of the event. Event Specifies the type of event. For a detailed list of events and value ranges, see “Event types.” Value Specifies the value of the event. Add Adds a new event to the list with the current Time/Event/Value parameters. Delete Removes the selected Time/Event/Value parameter from the event list. Change Applies the current parameter values. Cancel Closes the dialog box without making any changes. Any additions, deletions, or changes revert to their original state. Apply Closes the dialog box. TraceFinder User Guide 57 3 Using the Application Configuration Mode Specifying Default Peak Detection Parameters Figure 17. Event types Table 12. Event type descriptions (Sheet 1 of 2) 58 TraceFinder User Guide Event type Description Start Threshold Specifies the threshold at the start of a peak. The Start Threshold is directly related to the RMS noise in the chromatogram. Range: 0 to 999 999 999 End Threshold Specifies the threshold at the end of a peak. The End Threshold is directly related to the RMS noise in the chromatogram. Range: 0 to 999 999 999 Area Threshold Controls the area cutoff. Any peaks with a final area less than the area threshold will not be detected. This control is in units of area for the data. Range: 0 to 999 999 999 P-P Threshold The peak-to-peak resolution threshold controls how much peak overlap must be present before two or more adjacent peaks create a peak cluster. Peak clusters have a baseline drop instead of valley-to-valley baselines. Specified as a percent of peak height overlap. Range: 0.1 to 99.99 Negative Peaks Permits detection of a negative going peak. Automatically resets after finding a negative peak. Valid values: On or Off Bunch Factor Specifies the number of points grouped together during peak detection. This event controls the bunching of chromatographic points during integration and does not affect the final area calculation of the peak. A high bunch factor groups peaks into clusters. Range: 0 to 999 Thermo Scientific 3 Using the Application Configuration Mode Specifying Default Peak Detection Parameters Table 12. Event type descriptions (Sheet 2 of 2) Thermo Scientific Event type Description Tension Controls how closely the baseline should follow the overall shape of the chromatogram. A lower tension traces the baseline to more closely follow changes in the chromatogram. A high baseline tension follows the baseline less closely, over longer time intervals. Range: 0 to 999.99 minutes Tangent Skim Using this event, you can tangent skim any peak clusters. By default, it chooses the tallest peak in a cluster as the parent. You can also identify which peak in the cluster is the parent. Tangent skim peaks are detected on either side (or both sides) of the parent peak. Tangent skim automatically resets at the end of the peak cluster. Range: 0 to 1 Shoulders On Allows peak shoulders to be detected (peaks which are separated by an inflection rather than a valley) Sets a threshold for the derivative. Shoulders Off Disables peak shoulder detection. Range: 0 to 50 Force Cluster On Force the following peaks to be treated as a cluster (single peak). Force Cluster Off End the forced clustering of peaks. Disable Cluster On Prevent any peaks from being clustered. Disable Cluster Off Permit clusters to occur again. TraceFinder User Guide 59 3 Using the Application Configuration Mode Specifying Adducts Configuration Specifying Adducts Configuration An adduct ion is formed from a precursor ion and contains all of the constituent atoms of that ion and additional atoms or molecules. Adduct ions are often formed in the mass spectrometer ion source. Adducts can be either positive or negative. Use the Adducts Configuration page to specify the adducts that will be available for you to use in method development. Follow these procedures: • To open the Adducts Configuration view • To add an adduct • To remove an adduct To open the Adducts Configuration view In the navigation pane for the Application Configuration mode, click Adducts. The Adducts Configuration view opens, displaying the default positive and negative adducts. To add an adduct 1. In the Positive Adducts or Negative Adducts pane, click the Add New Adduct icon, . The application adds an empty row in the Adducts list. 60 TraceFinder User Guide Thermo Scientific 3 Using the Application Configuration Mode Specifying Adducts Configuration 2. Type the formula for the new adduct ion. The formula syntax is alphanumeric and case sensitive. It can include parentheses and brackets. The formula specifies the difference between the neutral molecule and the charged ion that you expect to see in the results. For example, a sodium adduct has [M+Na]+ as the expected charged ion (where M is the neutral molecule), so you would type “Na” for the formula. A water adduct has [M+H+H2O]+ as the expected charged ion, so you would type “H3O” for the formula. IMPORTANT When you create an adduct formula, you can type both uppercase and lowercase letters; however, the TraceFinder application interprets all uppercase input as single-letter elements and all lowercase input as two-letter elements. For example, it interprets the string “inau” as In Au and “COSI” as C O S I. 3. In the Gain/Loss column, select Gain or Loss. This indicates if the adduct is a loss or gain to the calculated neutral mass. The application calculates the neutral mass value for the adduct. These adducts are available for you to select in the Compound Database view of the Method Development mode when you specify parameter values for target peaks. See “Editing Compounds in the Database” on page 251. Thermo Scientific TraceFinder User Guide 61 3 Using the Application Configuration Mode Specifying Adducts Configuration To remove an adduct 1. In the Positive Adducts or Negative Adducts pane, select the adduct that you want to remove. 2. Click the Delete Selected Adduct icon, . You can delete only adducts that you added to the adducts list. You cannot delete default adducts defined by the TraceFinder installation. 62 TraceFinder User Guide Thermo Scientific 3 Using the Application Configuration Mode Activating Optional Features Activating Optional Features In the Optional Features view of the Application Configuration mode, you can activate the following features: • User Security • ToxID • Quick Acquisition • Delay Calibration Calculation • Batch Wizard Style • Multiplexing • Intelligent Sequencing • Acquisition Submission Options • Screening Library To open the Optional Features view In the Application Configuration mode, click Optional Features. The Optional Features view opens. Thermo Scientific TraceFinder User Guide 63 3 Using the Application Configuration Mode Activating Optional Features User Security When user security is activated, you must log in to the TraceFinder application, which gives you access to only those modes assigned to your user role. See “Choosing User Roles” on page 75. To turn on user security 1. Select the User Security check box. You must now log in to the TraceFinder application to access the modes assigned to your user role. See “Choosing User Roles” on page 75. When user security is activated, only users in the LabDirector or ITAdmin roles can access the Application Configuration mode. When this check box is cleared, you are not required to log in to the TraceFinder application. All modes are available to all users when the application starts; however, you cannot see the User Administration view in the Application Configuration mode unless you are assigned the LabDirector or ITAdmin role. IMPORTANT If you are the administrator logging in with user security activated, you can use Administrator/Password as the username/password. 2. Click Apply. 3. When prompted to restart the application, click Restart Now. ToxID You must activate the ToxID option before you can generate ToxID reports. To activate ToxID 1. Select the ToxID check box. 2. Click Apply. 3. When prompted to restart the application, click Restart Now. For a list of available ToxID reports, see “Reports” on page 41. Quick Acquisition The quick acquisition option activates the Quick Acquisition feature in the Acquisition, Analysis, or Method Development mode. Note The Quick Acquisition feature is not available when you activate Multiplexing. See “Multiplexing” on page 66. 64 TraceFinder User Guide Thermo Scientific 3 Using the Application Configuration Mode Activating Optional Features To activate quick acquisition 1. Select the Quick Acquisition (EnviroLab/ToxLab/QuanLab Forms) check box. 2. Click Apply. 3. When prompted to restart the application, click Restart Now. For a description of the Quick Acquisition features, see “Working with Master Methods” on page 83. Delay Calibration Calculation You can determine when the application calculates the calibration curve, using the Delay Calibration Calculation... option. Delaying the recalibration until the application processes the last calibration sample in a batch is faster but less responsive than recalibration after each calibration sample. To delay calculation of a calibration curve 1. Select the Delay Calibration Calculation... check box. 2. Click Apply. 3. When prompted to restart the application, click Restart Now. Batch Wizard Style Use the Batch Wizard Style option to choose one of two styles for your batch wizard. To select a wizard style 1. In the Batch Wizard Style list, select a wizard style: • Acquisition Batch Wizard: Adds the Acquisition mode to the navigation pane. This mode is similar to the Acquisition mode in the TraceFinder 1.1 application. See Chapter 5, “Using the Acquisition Mode.” When you activate multiplexing, the application automatically activates this wizard style. • Batch Template Wizard: The default wizard style that is similar to the acquisition wizard in the EnviroLab Forms, ToxLab Forms, and QuanLab Forms applications. See “Creating a Batch Using the Batch Wizard” on page 379. Note The Batch Template Wizard is not available when you activate Multiplexing. See Multiplexing. 2. Click Apply. 3. When prompted to restart the application, click Restart Now. Thermo Scientific TraceFinder User Guide 65 3 Using the Application Configuration Mode Activating Optional Features Multiplexing The Multiplexing options are available only when you install the Multiplexing Power Module. See “Installing the Power Modules” on page 15. Note Multiplexing is not available when you activate Intelligent Sequencing. See Intelligent Sequencing. To specify multiplexing features 1. Select the Multiplexing check box. 2. Select 2 Channels or 4 Channels: • For 2 channels, select a 1- or 2-arm Autosampler Arm Configuration. The 1 arm configuration activates channels 1 and 3; the 2 arm configuration activates channels 2 and 4. • For 4-channels, autosampler 1 uses channels 1 and 3 and autosampler 2 uses channels 2 and 4. 3. Click Apply. 4. When prompted to restart the application, click Restart Now. The application uses multiplexing features in the Acquisition mode when you specify channels for a sample in a batch (see “Defining the Sample List” on page 298) or monitor an acquisition (see “Devices Page” on page 326). Note When you activate multiplexing, the following optional features are not available: • Quick Acquisition • Batch Template Wizard • Single Sample Submission (Intelligent Sequencing) Intelligent Sequencing The Intelligent Sequencing option is available only when you install the Intelligent Sequencing Power Module. See “Installing the Power Modules” on page 15. Use Intelligent Sequencing for single-sample submission. When you submit a batch, the autosampler begins preparing for one sample injection at a time. Higher priority batches can interrupt the sample sequence in the currently acquiring batch. To activate the intelligent sequencing feature 1. Select the Intelligent Sequencing check box. Note Intelligent Sequencing is not available when you activate Multiplexing. See “Multiplexing” on page 66. 66 TraceFinder User Guide Thermo Scientific 3 Using the Application Configuration Mode Activating Optional Features The Acquisition Submission Options default to Single Sample Submission. The Full Sequence Submission option is not available when you select the Intelligent Sequencing option. 2. Click Apply. 3. When prompted to restart the application, click Restart Now. Acquisition Submission Options To control acquisitions, you can activate full-sequence or single-sample submission options. When you submit batches from the Acquisition mode, development batches from the Method Development mode, or Quick Acquisition batches from any mode, they run in first-in-last-out order. The last batch submitted is the first batch to run unless you submit a batch as a priority batch in Acquisition mode. • When you use Full Sequence Submission, priority batches always run immediately after the currently acquiring batch is completed. • When you use Single Sample Submission, priority batches always run immediately after the currently acquiring sample is completed. To specify acquisition submission features 1. Select either the Full Sequence Submission or the Single Sample Submission option: • Full Sequence Submission: Supports look-ahead features of the autosampler. When the instrument method specifies the look-ahead feature, the Tracefinder application functions like a multiplex driver and feeds the autosampler the next vial position. When you submit a batch, the autosampler begins preparing for all sample injections when the pre-run condition begins. All samples in the batch must be completed before other batches (even higher priority batches) can begin. Note The Full Sequence Submission feature is not available when you activate Intelligent Sequencing. • Single Sample Submission: Supports intelligent-sequencing features. When you submit a batch, the autosampler begins preparing for one sample injection at a time. Higher priority batches can interrupt the sample sequence in the currently acquiring batch. Note The Single Sample Submission feature is not available when you activate Multiplexing. See “Multiplexing” on page 66. 2. Click Apply. 3. When prompted to restart the application, click Restart Now. Thermo Scientific TraceFinder User Guide 67 3 Using the Application Configuration Mode Activating Optional Features Screening Library Use the screening library specified here for identification and confirmation when you specify Library Manager as the Library Search Type for a method. See “Editing the General Page” on page 107. The application searches the screening library to identify or confirm a sample compound, matches the fragment ion spectrum in the library to the compound’s ion spectrum, and returns the highest score (best match). The application performs either a forward library search or a reverse library search. A forward search compares the mass spectrum of an unknown compound to a mass spectral library entry, while a reverse search compares a library entry to an unknown compound. In a target screening master method, you can specify the library search to either identify or confirm library matches and set a score threshold to minimize poor matches. See “To specify identification and confirmation settings” on page 216. • Identify or Confirm: The application identifies or confirms the sample compound by searching the specified search library and returning the highest score (as a percentage value) for the fragment ion spectrum in that library that matches the compound’s ion spectrum. • Score Threshold: The resulting score from a library search match must be higher than the threshold value to identify or confirm the presence of a compound. IMPORTANT To use a library search for identification or confirmation, the application requires meeting these conditions: • The raw data file contains HCD (higher energy collision-induced dissociation), source CID (source collision-induced dissociation), or AIF (all ions fragmentation) ion spectra. • The spectra exist at a time point within the compound’s elution time range. 68 TraceFinder User Guide Thermo Scientific 3 Using the Application Configuration Mode Managing User Administration Managing User Administration In the User Administration view of the Application Configuration mode (when user security is activated), in either the LabDirector or ITAdmin role, you can add, remove, or edit user accounts and permissions. For detailed descriptions of each user role and the permissions and responsibilities for each role, see “Choosing User Roles” on page 75. To open the User Administration view 1. Click the Application Configuration icon, window. , in the upper right corner of any The Application Configuration navigation pane opens. Available only to users in the LabDirector or ITAdmin role Note The User Administration option is available only when you activate user security. Follow the instructions “To turn on user security” on page 64. 2. Click User Administration. The User Administration view opens. See “User Administration view” on page 73. This section includes instructions for the following tasks: • Editing User Information • Choosing User Roles Thermo Scientific TraceFinder User Guide 69 3 Using the Application Configuration Mode Managing User Administration Editing User Information When user security is activated, in either the LabDirector or ITAdmin role, you can assign each user to one of the defined roles. Follow these procedures: • To add a user • To edit user information • To change a user password • To remove a user For a list of all parameters in the User Administration view, see “User Administration view parameters” on page 74. To add a user 1. Click the Add User icon, . The application activates the parameters in the User area at the bottom of the view. 2. Type a unique name in the Username box. The user name is case insensitive. 3. Select a role from the Role list. For detailed information about the permissions allowed for each role, see “Choosing User Roles” on page 75. 4. Type the user’s password and type it again to confirm it. The password is case sensitive. Note Make sure to communicate the password to the user. 5. (Optional) Type the user’s full name, account number, phone number, and e-mail address. 6. To activate this user login, select the Enabled check box. You can disable a user login without deleting the user’s information. Follow the instructions “To edit user information” on page 71. 70 TraceFinder User Guide Thermo Scientific 3 Using the Application Configuration Mode Managing User Administration 7. Do one of the following: When all the user information is correct, click the Save Changes icon, . The TraceFinder application adds the new user to the User Listing table, and the parameters in the User area are unavailable. –or– To discard all information and not create a new user from the parameter values you entered, click the Cancel Changes icon, . The application discards all information, and the parameters in the User area are unavailable. To edit user information 1. In the User Listing table, select a user. Note Clicking anywhere in the row selects the user. The user information populates the parameter fields in the User area of the User Administration view. 2. Click the Edit User icon, . The application activates the parameter fields in the User area. 3. Edit any of the parameter values. IMPORTANT You must have an ITAdmin or LabDirector role to access the user administration features. If you are the only user in the ITAdmin or LabDirector role, you cannot remove your user name, clear the Enabled check box, or change your role to anything other than ITAdmin or LabDirector. At least one activated user must be assigned to the ITAdmin or LabDirector role so that there is a least one user who can access the User Administration page. Thermo Scientific TraceFinder User Guide 71 3 Using the Application Configuration Mode Managing User Administration 4. Do one of the following: When all the user information is correct, click the Save Changes icon, . The TraceFinder application adds the new parameter values to the User Listing, and the parameters in the User area are unavailable. –or– To discard all changes and not save the edits, click the Cancel Changes icon, . All changes are discarded, and the parameters in the User area are unavailable. To change a user password 1. In the User Listing table, select a user. The user information populates the parameter fields in the User area. 2. Click the Edit User icon, . The application activates the fields in the User area. 3. Click Reset Password. The application makes the password and confirming password visible as a string of asterisks ******. 4. In the Password box, select ****** and type a new password. 5. In the Confirm Password box, select ****** and retype the new password. 6. Click the Save Changes icon, . Make sure to communicate the new password to the user. 72 TraceFinder User Guide Thermo Scientific 3 Using the Application Configuration Mode Managing User Administration To remove a user 1. In the User Listing table, select a user. Note Clicking anywhere in the row selects the user. The user information populates the parameter fields in the User area. 2. Click the Remove User icon, . If you select your current user name, the Remove User icon is unavailable. You cannot remove yourself. 3. When prompted, confirm that you want to remove this user. If the user is currently logged in to the TraceFinder application, the user’s current session is not affected. 4. Click OK. Note Rather than completely removing the user, you can make the user login unavailable without removing all the user information from the system. Follow the instructions “To edit user information” on page 71. Figure 18. User Administration view Thermo Scientific TraceFinder User Guide 73 3 Using the Application Configuration Mode Managing User Administration Table 13. User Administration view parameters Parameter Description Security Groups All permission levels defined in the TraceFinder application. For detailed descriptions of user permissions, see “Choosing User Roles” on page 75. User Listing Username User login name. Role Security group that defines user permissions. Account Number User account number. Phone Number User telephone number. Email Address User e-mail address. Enabled Available or unavailable status for the user account. User Username Login name for the current user. Role Security group that defines the current user’s permissions. Password Login password for the current user. Full Name The current user’s actual name. Account Number Optional account number for the current user. Phone Number Optional telephone number for the current user. Email Address E-mail address for the current user. Used to notify user of a randomly generated password. Enabled Allows or disallows access for this user. When this user is currently logged in, disallowing takes effect after the user logs off. Reset Password Makes the password visible as a string of asterisks that you can select and change. Icon Function Add User Activates the fields in the User area where you can enter information for a new user. Remove User Deletes all information for the selected user. Edit User Activates the User area where you can edit any of the parameters for the selected user. Save Changes Adds the new parameter values to the User Listing table and disables the parameters in the User area. Cancel Changes Discards all new or edited information. 74 TraceFinder User Guide Thermo Scientific 3 Using the Application Configuration Mode Managing User Administration Choosing User Roles This section describes the responsibilities for five different user roles when user security is activated: LabDirector, ITAdmin, Supervisor, Technician, and QAQC. IMPORTANT User roles are in effect only when user security is activated. When user security is not activated, all users have access to all modes. TraceFinder Mode Access A user in either the LabDirector or ITAdmin role assigns you to a role that gives you access to specific modes of the TraceFinder application. When you log in, the navigation pane displays links to only the modes that you can access. Table 14. User roles and mode access User role Method Development Acquisition Analysis Application Configuration LabDirector ITAdmin Supervisor Technician QAQC LabDirector In the LabDirector role, you review graphically applicable data and manipulate data, batches, methods, and instruments. A laboratory director is responsible for these tasks: • Creating or editing methods for new levels of detection or adding new compounds to the existing database • Reviewing data from the mass spectrometer • Running samples and reviewing data collected by others • Reporting the data • Understanding the results and giving final approval of the released data before archiving ITAdmin In the ITAdmin role, you set security, manage users into their roles, and manipulate the various databases. You are responsible for adding compounds into the various compound databases. An IT administrator is responsible for these tasks: • Handling the databases • Applying roles to users • Understanding security, users, and groups Thermo Scientific TraceFinder User Guide 75 3 Using the Application Configuration Mode Managing User Administration • Creating local users and network groups Supervisor In the Supervisor role, you are responsible for setting up the instrument samples and using previously built sequences and methods for processing and acquiring data. You also develop and edit methods for processing and acquiring data, review the data, and distinguish between the need to rerun samples or pass reports up to the lab manager for final review. On a daily basis, you establish the priority for a list of samples to run and create the sequence of events. A supervisor is responsible for these tasks: • Submitting samples • Creating and submitting batches • Reporting the data to management • Creating or editing methods for new levels of detection or adding new compounds to the existing database • Reviewing data from the mass spectrometer • Understanding the results, who ran the batch, and who passed along the results before giving intermediate approval and sending the data to management • Modifying new compounds or adjusting methods for specific result sets Technician In the Technician role, you are responsible for setting up the instrument samples and using previously built sequences and methods for processing and acquiring data. You also edit existing methods for processing and acquiring data, review collected data, and distinguish between the need to rerun samples or pass reports up to the supervisor. On a daily basis, you are responsible for gathering the list of samples to run and creating the sequence of events. A technician is responsible for these tasks: • Submitting samples • Creating and submitting batches • Creating data to be reviewed by management • Receiving instructions for new sets of samples for the TraceFinder application to analyze after finishing the current analysis • Reviewing data from the mass spectrometer • Understanding the resulting data, making integration changes, and passing those changes up for further approval 76 TraceFinder User Guide Thermo Scientific 3 Using the Application Configuration Mode Managing User Administration QAQC In the QAQC role, you review graphically applicable data and interpret the data, but you do not manipulate the data. A QAQC technician is responsible for these tasks: • Reviewing data from the mass spectrometer • Understanding the results and who ran and passed along the results before giving intermediate approval and sending the data to management • Receiving instructions for new sets of samples for the TraceFinder application to analyze after finishing the current analysis Note In the QAQC role, you have access only to the Analysis mode. Thermo Scientific TraceFinder User Guide 77 4 Using the Method Development Mode This chapter includes method development tasks assigned to the Supervisor or LabDirector role when user security is activated. Contents • Working with Master Methods • Working with the Compound Database • Working with Instrument Methods • Working with Development Batches • Using Quick Acquisition From the Method Development mode, you can create a quantitative or screening master method, an instrument method, or a simple development batch to test your instrument method. You can also use the Quick Acquisition feature to quickly submit a single sample from any view in the Method Development mode. To access the Method Development mode Click Method Development in the navigation pane. The Method Development navigation pane opens. Thermo Scientific TraceFinder User Guide 79 4 Using the Method Development Mode For descriptions of all the features on the Method Development navigation pane for a quantitation method, see “Method Development navigation pane for quantitation methods.” For descriptions of all the features on the Method Development navigation pane for a screening method, see “Method Development navigation pane for screening methods” on page 82. 80 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Figure 19. Method Development navigation pane for quantitation methods Available only when you select the Acquisition Batch Wizard as your wizard style in the Application Configuration mode. Table 15. Method Development navigation pane commands for quantitation methods Command Description Method View Displays the Method View for the master method. See “Working with Master Methods” on page 83. General Displays the General page of the Method View. See “Editing the General Page” on page 107. Compounds Displays the Compounds page of the Method View. See “Editing the Compounds Page” on page 114. QAQC Displays the QAQC page of the Method View. See “Editing the QAQC Page” on page 174. Groups Displays the Groups page of the Method View. See “Editing the Groups Page” on page 183. Intel Seq Displays the Intelligent Sequencing page of the Method View. See “Editing the Intelligent Sequencing Page” on page 185. Reports Displays the Reports page of the Method View. See “Editing the Reports Page” on page 189. Compound Database See “Working with the Compound Database” on page 239. Instrument View See “Working with Instrument Methods” on page 269. Development Batch See “Working with Development Batches” on page 275. Thermo Scientific TraceFinder User Guide 81 4 Using the Method Development Mode Figure 20. Method Development navigation pane for screening methods Available only when you select the Acquisition Batch Wizard as your wizard style in the Application Configuration mode. Table 16. Method Development navigation pane commands for screening methods Command Description Method View Displays the Method View for the master method. See “Working with Master Methods” on page 83. General Displays the General page of the Method View. See “Editing the General Page” on page 107. Reports Displays the Reports page of the Method View. See “Editing the Reports Page” on page 189. Screening Displays the Screening page of the Method View. See “Editing the Screening Page” on page 212 Peak Detection Displays the Peak Detection page of the Method View. See “Editing the Peak Detection Page” on page 221 Compound Database See “Working with the Compound Database” on page 239. Instrument View See “Working with Instrument Methods” on page 269. Development Batch See “Working with Development Batches” on page 275. 82 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Working with Master Methods The TraceFinder application uses a master method to specify the nature and types of acquisition, processing, and reporting that occur with a batch of samples. When you are testing for compounds in an assay, you can create a method designed specifically for that type of application. A quantitation master method contains a list of compounds and settings for detecting, processing, and reporting those compounds. A target screening master method contains compound databases, identification and confirmation criteria used in detecting and processing, and settings for reporting compounds. When you create a master method, the TraceFinder application uses the method to determine how the software works with a set of samples to provide a set of meaningful results. The application uses an instrument method to define how raw data is acquired. The rest of the master method defines how the raw data is processed, how the flags information evaluates the results, and how the reporting functionality defines the output for your data and results. The TraceFinder application applies your master method to a batch, which is a list of one or more samples to be processed and reported. Together, the master method and batch provide a workflow-oriented approach to the data processing and information reporting for batches of samples. To speed up the creation of master methods, you can create a method template. Using a method template helps you to develop methods faster because the TraceFinder application saves all of your commonly used method settings in a template, such as the number of confirming ions or the use of data-dependent scans. This section includes instructions for the following tasks: • Creating a New Master Method • Editing a Quantitation Master Method • Editing a Target Screening Master Method • Creating a Method Template • Importing Published Master Methods • Exporting SRM Data Thermo Scientific TraceFinder User Guide 83 4 Using the Method Development Mode Working with Master Methods Creating a New Master Method Use any of the following procedures to start a method in the specific way indicated. Then, use the common features of the Method View to complete and save it as a master method. Choose File > New > Master Method from the main menu. The Create Master Method dialog box opens. Select from five different procedures (or techniques) in the Create Master Method dialog box: • Creating a New Method with Method Forge • Importing an Xcalibur Master Method • Creating a Blank Quantitation Method • Selecting Compounds from the Compound Database • Creating a Screening Method Figure 21. Create Master Method dialog box 84 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Creating a New Method with Method Forge With Method Forge, you can create a new master method by manually selecting peaks, selecting multiple compounds, renaming peaks, or comparing mass spectra from the library searches. You can also choose to let the TraceFinder application automatically create a master method for you. For detailed descriptions of all the Method Forge parameters, see “Method Forge dialog box parameters” on page 93. When the TraceFinder application automatically creates a master method for you, it performs the following functions: • Reviews your raw data file and identifies compounds that are present in your sample. • Uses your mass spectral reference libraries to assign compound names and CAS numbers. • Uses mass spectral information to select potential quantification and confirming ions and a reference mass spectrum for the compound. Note When the identified peak is from an analog trace, the application does not perform a library search and does not identify any confirming ions. Follow these procedures: • To automatically select compounds to create a new method • To manually select compounds to create a new method To automatically select compounds to create a new method 1. From the File menu, choose New > Master Method. The Create Master Method dialog box opens. To view all available ways to create a master method, see “Create Master Method dialog box” on page 84. 2. Select the Use Method Forge option and click OK. The Method Forge dialog box opens. For detailed descriptions of all the features on the Method Forge dialog box, see “Method Forge dialog box” on page 93. Use Method Forge to create a master method from an existing raw data file or to create a new raw data file to use for the master method. Each method requires a processing method template. The application displays all saved method templates in the template list. Thermo Scientific TraceFinder User Guide 85 4 Using the Method Development Mode Working with Master Methods 3. To select a processing method template, do one of the following: • Click Open Method Template Editor to create and save a new method template. See “Creating a Method Template” on page 224. • Select a method template from the template list, and click Open Method Template Editor to edit and save the method template. • Select a method template from the template list. The selected template is now selected by default each time you open the Method Forge dialog box until you restart the TraceFinder application. To view the parameters for each available method template, hold your cursor over the template name. Figure 22. Example method template parameters 86 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods 4. Select the Name the Master Method check box and type a name for your master method. You can enter a new method name, or you can enter an existing method name to overwrite when you create the method. If you do not select this option, the method is named for the raw data file used to create the method. IMPORTANT When the Name the Master Method check box is selected, you must enter a method name. To let the application name the method with the raw data file name, clear the Name the Master Method check box. 5. Select the Automatically Create the Master Method check box. 6. Specify a raw data file by doing one of the following: a. In the Raw File Selection area, choose Use an Existing Raw Data File. b. Click the browse button and locate a raw data file to use for the method. c. Go to step 8. –or– a. In the Raw File Selection area, choose Acquire a New Raw Data File. b. From the Instrument method list, select a method (.meth) file to use for acquiring the data. c. In the Raw Filename box, type the name of the file where the TraceFinder application will write the raw data file. d. In the Path box, type a path or click the browse button and locate a folder where the application will save the raw data file. e. (Optional) Type a comment about the acquired sample or the data file. 7. To acquire a new raw data file, do one of the following: Select Manual Injection. –or– Specify the autosampler settings: a. Select Use Autosampler. b. In the Vial Position box, type a vial position. c. In the Injection Volume box, type an injection volume. Range: 0.1 to 2000 μL Thermo Scientific TraceFinder User Guide 87 4 Using the Method Development Mode Working with Master Methods 8. To automatically create the master method, click OK (or Overwrite). As the Method Forge creates the method, it displays the following status bars: • For analog peaks, the Method Forge displays the detected peak as [email protected](RT)Analog. The Method Forge does not perform a library search for peaks found in analog traces. • For mass spectral peaks, the Method Forge process searches the associated libraries and displays the identified compound names instead of the peak times. When the acquisition is completed, Method Forge performs peak detection, library searching (except for analog peaks), and identification of characteristic ion and reference spectra. Method Forge then loads this information into a new master method. This process occurs immediately if you selected a previously acquired raw data file. 9. From the Instrument Method list, select an instrument method. 10. From the Qualitative Peak Processing Template list, select a method template for performing peak detection on quantitative samples following target compound analysis. 11. From the Background Subtraction Range Option list, select how you want the background subtraction range determined from one of these options: • Before Peak: Averages and subtracts a specified number of scans before the apex of the peak. • After Peak: Subtracts a specified number of scans following the apex of the peak. • Both Sides of Peak: Subtracts a specified number of scans from each side of the apex of the peak. 12. To save the new method, choose File > Save from the main menu. For a detailed description of how to modify all the parameters in a master method, see “Editing a Quantitation Master Method” on page 106. 88 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods To manually select compounds to create a new method 1. From the File menu, choose New > Master Method. The Create Master Method dialog box opens. See “Create Master Method dialog box” on page 84. 2. Select the Use Method Forge option and click OK. The Method Forge dialog box opens. For detailed descriptions of all the features on the Method Forge dialog box, see “Importing an Xcalibur Master Method” on page 95. Each method requires a qualitative peak processing template. The application displays all saved method templates in the template list. 3. To select a qualitative peak processing template, do one of the following: • Click Open Method Template Editor to create and save a new method template. See “Creating a Method Template” on page 224. • Select a method template from the template list, and click Open Method Template Editor to edit and save the method template. The application saves the methods to the following folder: C:\Thermo\TraceFinder\3.0\Forensic\Templates\Methods • Select a method template from the template list. The selected template is now selected by default each time you open the Method Forge dialog box until you restart the TraceFinder application. Thermo Scientific TraceFinder User Guide 89 4 Using the Method Development Mode Working with Master Methods To view the parameters for each available method template, hold your cursor over the template name. For example: 4. Select the Name the Master Method check box and type a name for your master method. You can enter a new method name, or you can enter an existing method name and overwrite it when you create the method. If you do not select this option, the method is named for the raw data file used to create the method. IMPORTANT When the Name the Master Method check box is selected, you must enter a method name. To let the application name the method with the raw data file name, clear the Name the Master Method check box. 5. Ensure that the Automatically Create the Master Method check box is cleared. 90 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods 6. To select a raw data file, browse to the file location. 7. To manually create the master method, click OK (or Overwrite). The method forge results view opens, listing all peaks found in the raw data file. For each peak listed in the RT column, the application displays a list of possible matches in the Libraries pane. The TraceFinder application selects the best match, displays the name in the Compound Name list, and displays the peak spectrum for that compound in the first Libraries pane. Best match compound spectra Peaks found in raw data file Thermo Scientific Best match compound name Possible matches TraceFinder User Guide 91 4 Using the Method Development Mode Working with Master Methods 8. (Optional) To use a library compound other than the compound chosen by the TraceFinder application, do the following: a. Select the peak in the RT column. b. In the Libraries pane, scroll to the spectrum for the compound that you want to use. c. Select the check box in the header of the spectrum pane. Selected compound d. Repeat these steps for each peak that you want to replace. 9. In the Compound Name list, use the CTRL or SHIFT keys to select each compound that you want to include in the method compound. Note When you select multiple compounds, the method forge results view does not display any spectrum panes. 10. (Optional) To exit the method forge results view without creating a method, click Cancel. The method forge results view closes and the application returns to the Method View without creating a method. Note To return to the method forge results view to create a method from the same results, choose Method View > View Method Forge Results from the main menu. 11. Click Create. The TraceFinder application uses all selected compounds to create the method and displays the General page of the Method View. For detailed descriptions of all the features on the General page, see “General page for a quantitation method” on page 111. Note To return to the method forge results view, choose Method View > View Method Forge Results from the main menu. 12. From the Instrument Method list, select an instrument method. 13. To save the new method, choose File > Save from the main menu. For a detailed description of how to modify a master method, see “Editing a Quantitation Master Method” on page 106. 92 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Figure 23. Method Forge dialog box Table 17. Method Forge dialog box parameters (Sheet 1 of 2) Parameter Description Method template selection Open Method Template Editor Opens the Method Template Editor, where you can edit the currently selected method template. See “Creating a Method Template” on page 224. Template Method template to use to create this master method. All methods require a method template. To view the parameters of each template, hold your cursor over the method name. See “Example method template parameters” on page 86. Name the Master Method The name for the new master method. If you do not specify a method name, the application uses the raw data file name for the method. Automatically Create the Master Method When the acquisition is completed, Method Forge performs peak detection, library searching, and identification of characteristic ion and reference spectra. This information is loaded into a new master method. This process occurs immediately when you specify an existing raw data file. Raw file selection Use an Existing Raw Data File Thermo Scientific Activates the Raw Filename box where you can select a raw data file used in creating the master method. TraceFinder User Guide 93 4 Using the Method Development Mode Working with Master Methods Table 17. Method Forge dialog box parameters (Sheet 2 of 2) Parameter Description Acquire a New Raw Data File Activates functions to acquire data to create a raw data file used in creating the master method. Instrument Method The saved method (.meth) file used for acquiring the data. Raw Filename The file name where the TraceFinder application writes the raw data. Path The location where the TraceFinder application saves the raw data file. Sample Comment (Optional) A comment about the acquired sample or the data file. Manual Injection Performs a manual acquisition. Use Autosampler Performs an autosampler acquisition. Vial Position The tray vial number used for the autosampler acquisition. Injection Amount The volume (in milliliters) injected by the autosampler acquisition. Check Instruments Opens the Submit to Acquisition dialog box that prompts you to prepare the instrument before you acquire the sample used to create a method. Available only when you select the Acquire a New Raw Data File option. Function button Overwrite Overwrites the specified master method name. This function is activated only when the specified master method name already exists. OK Creates a master method using the data and parameters that you specified. Cancel Closes Method Forge and does not create a master method. 94 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Importing an Xcalibur Master Method You can create a new master method from an existing Xcalibur processing method. To import an Xcalibur master method 1. Choose File > New > Master Method from the main menu. The Create Master Method dialog box opens. To view all available ways to create a master method, see “Create Master Method dialog box” on page 84. 2. Select the Import Xcalibur Processing Method option and click OK. The Import an Xcalibur Method dialog box opens. 3. For the Xcalibur Method to Import box, browse to the location of the Xcalibur processing method file, and open the file. The TraceFinder application imports the compound information from the Xcalibur method file. 4. (Optional) For the Raw Data File to Associate box, browse to the location of a raw data file to associate with the method (or select from the list of previously associated raw data files), and open the file. To assure that this raw data file is always available to the method (for example, if you move the method to another system), the application saves the raw data file in the method folder: C:\Thermo\TraceFinder\3.0\Forensic\Methods\MethodName Thermo Scientific TraceFinder User Guide 95 4 Using the Method Development Mode Working with Master Methods 5. (Optional) Change the number of decimal places in the Filter Precision box. You can set the number of filter precision decimal places to any integer between 2 and 5, inclusive. Note When you select a raw data file to associate, the application reads the filter precision from the file and this feature is not available. 6. (Optional) Change the number of decimal places in the Mass Precision box. You can set the number of mass precision decimal places to any integer between 2 and 6, inclusive. Note When you associate a raw data file, the application reads the filter precision from the associated file so that you cannot change the Filter Precision value. 7. Click OK. The TraceFinder application adds all compounds found in the imported Xcalibur method and displays the General page of the Method View. For detailed descriptions of the features on the General page, see “General page for a quantitation method” on page 111. 8. From the Instrument Method list, select an instrument method. 9. To save the new method, choose File > Save from the main menu. For a detailed description of how to modify a master method, see “Editing a Quantitation Master Method” on page 106. 96 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Creating a Blank Quantitation Method You can use the compounds in a previously acquired raw data file to create a new quantitation master method. To create a blank quantitation method 1. From the File menu, choose New > Master Method. The Create Master Method dialog box opens. To view all available ways to create a master method, see “Create Master Method dialog box” on page 84. 2. Select the Create Blank Quantitation Method option and click OK. The Method View for a new, unnamed method opens. This method has no associated data. You can use the compounds in a previously acquired raw data file to create a new quantitation master method. 3. From the Method View menu, choose Associate a Raw Data File. The Associate a Raw Data File dialog box opens. Browse to a data file Select a previously associated data file 4. Browse to a raw data file to associate with the method (or select from the list of previously associated raw data files) and open the file. To assure that this raw data file is always available to the method (for example, if you move the method to another system), the application saves the raw data file in the method folder: C:\Thermo\TraceFinder\3.0\Forensic\Methods Thermo Scientific TraceFinder User Guide 97 4 Using the Method Development Mode Working with Master Methods 5. Select the update options to use for creating your method: • Update Instrument/Trace Selections: Reads the Detector and Trace options from the associated raw data file. On the Detection page, only detector types and traces that are defined in the raw data file are available. For detailed descriptions of the available Detector and Trace values, see “Signal” on page 135. • Update Target Ion Ratio Values: Reads the ion ratio values from the associated raw data file. • Update Scan Filters for All Peaks: Updates all peaks with scan filters from the associated raw data file. • Automatically Set Reference Spectrum: Reads a reference spectrum from the associated raw data file. When you also select Yes, with Background Subtraction, the application uses the background subtraction range specified on the General page. See “Editing the General Page” on page 107. Options that are set to No use the standard values in the method. 6. Click OK. The TraceFinder application displays the General page of the Method View. 7. Select a qualitative peak processing template from the list. The application uses the libraries in this template to identify compounds for the method. If there is no library selected in the method template, found peaks are identified as [email protected] on the Compounds page. To specify the libraries in the qualitative peak processing template, open the template in the Method Template Editor, and then follow the instructions “To identify the peaks” on page 226. 8. Click Compounds in the navigation pane. The method must include at least one compound. 9. Click the Detection tab. The Detection page shows an empty Compound list and displays the chromatographic data for the compounds in the raw data file. 98 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods 10. Select a filter from the Filter list. 11. Select the peak in the chromatogram that represents the compound that you want to add to the method. 12. Right-click and choose Add This Peak as New Compound from the shortcut menu. The TraceFinder application performs a library search for the selected compound. The application uses the first match it finds as the compound name, the base peak of the mass spectrum as the quantitative peak, and the second and third largest ions as the confirming ion peaks. Note When the peak is from an analog trace, the application does not perform a library search and does not identify any confirming ions. Thermo Scientific TraceFinder User Guide 99 4 Using the Method Development Mode Working with Master Methods If the name of the first match is already in the library, the Add New Compound dialog box opens. 13. (Optional) Do the following: a. To use a compound other than the compound already in the library, scroll to the spectrum for that compound and select the compound name in the title bar of the spectrum pane. Selected compound b. In the Type of Compound To Add list, select a compound type. c. Click OK. 100 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods 14. Repeat this procedure for each compound that you want to add to the method. For detailed descriptions of all the features on the Detection page, see “Editing the Compounds Page” on page 114. 15. Click General in the navigation pane. The General page for the method opens. For detailed descriptions of all the features on the General page, see “General page for a quantitation method” on page 111. 16. From the Instrument Method list, select an instrument method. 17. To save the new method, choose File > Save from the main menu and name the method. For a detailed description of how to modify the parameters in a master method, see “Editing a Quantitation Master Method” on page 106. Thermo Scientific TraceFinder User Guide 101 4 Using the Method Development Mode Working with Master Methods Selecting Compounds from the Compound Database You can select compounds from the compound database to create a new master method. To select compounds form the compound database 1. Choose File > New > Master Method from the main menu. The Create Master Method dialog box opens. To view all available ways to create a master method, see “Create Master Method dialog box” on page 84. 2. Select the Select Compounds from CDB option and click OK. The Select Compounds from Database dialog box opens, listing all the compounds defined in the compound database. 3. Select the check box for each of the compounds that you want to add to the method. 102 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods 4. To select all compounds in the database, select the Compound check box at the top of the list. 5. Click Apply. The TraceFinder application adds the selected compounds to the method. 6. Click General in the navigation pane. The General page for the method opens. For detailed descriptions of all the features on the General page, see “General page for a quantitation method” on page 111. 7. From the Instrument Method list, select an instrument method. 8. To save the new method, choose File > Save from the main menu and name the method. For a detailed description of how to modify a master method, see “Editing a Quantitation Master Method” on page 106. Thermo Scientific TraceFinder User Guide 103 4 Using the Method Development Mode Working with Master Methods Creating a Screening Method You can create a new master method specifically for target screening. To create a target screening method 1. Choose File > New > Master Method from the main menu. The Create Master Method dialog box opens. To view all available ways to create a master method, see “Create Master Method dialog box” on page 84. 2. Select the Create Screening Method option and click OK. The Method View for a target screening method includes General, Reports, Screening, and Peak Detection pages. These instructions demonstrate the minimum parameters you must define to create and save a screening master method. For a detailed description of how to modify all parameters in a screening master method, see “Editing a Target Screening Master Method” on page 202. The General page for the screening method opens. 104 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods 3. From the Instrument Method list, select an instrument method. 4. Click Screening in the Method View navigation pane. The Screening page for the screening method opens. The Target Screening Settings pane displays the compound databases stored in the following folder: C:\Thermo\TraceFinder\3.0\Forensic\Databases 5. Select the Enabled check box for at least one compound database. You must select at least one compound database before you can save the method. 6. To save the new method, choose File > Save from the main menu. 7. In the Save Master Method dialog box, type a name for the method and click OK. For a detailed description of how to modify a master method, see “Editing a Target Screening Master Method” on page 202. Thermo Scientific TraceFinder User Guide 105 4 Using the Method Development Mode Working with Master Methods Editing a Quantitation Master Method You can open a master method to view or edit the compounds, method instructions, and reporting options in the method. This section includes instructions for the following tasks: • Opening a Quantitation Master Method • Editing the General Page • Editing the Compounds Page • Editing the QAQC Page • Editing the Groups Page • Editing the Intelligent Sequencing Page • Editing the Reports Page Opening a Quantitation Master Method Use the TraceFinder application to open a master method that was created and saved in the current TraceFinder application or converted from these legacy applications: previous versions of TraceFinder, EnviroLab Forms, QuanLab Forms, or ToxLab Forms. To convert legacy methods, see “Converting Legacy Data” on page 21. To open a saved master method 1. Click Method Development from the navigation pane. 2. Choose File > Open > Master Method from the main menu. The Open Master Method dialog box opens, displaying all available methods. Tip You can also open one of your most recently used master method files. Choose Files > Recent Files > MethodName. 3. Select a master method and click Open. The General page for the selected method opens. For detailed descriptions of all the features on the General page, see “General page parameters” on page 111. 106 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Editing the General Page The General page defines basic information about the master method. For detailed descriptions of all the features, see “General page parameters” on page 111. Follow these procedures: • To open the General page • To specify general information for a master method • To edit an instrument method • To select a qualitative peak processing template • To set automated background subtraction options • To specify mass tolerance • To include data-dependent filters • To enter a note for the method To open the General page Click General in the Method View navigation pane. Available only when you activate Intelligent Sequencing in the Application Configuration mode. To specify general information for a master method 1. In the Lab Name box, type the name to be displayed on the top of each printed, saved, or exported report. The default name is Default Laboratory. 2. In the Assay Type box, type the assay type to be targeted by the method. 3. From the Injection Volume box, select an injection volume (between 0.1 and 2000 μL) to be used for sample injection. Use the up/down arrows to change the volume in increments/decrements of 1 μL, or use the keyboard to enter non-integer injection volumes. IMPORTANT The TraceFinder application uses this injection volume in the master method, not the injection volume from the instrument method. Thermo Scientific TraceFinder User Guide 107 4 Using the Method Development Mode Working with Master Methods 4. From the Mass Precision box, select a precision value (between 2 and 6 inclusive) as the number of decimal places to be used in reports and in peak and spectrum displays. 5. From the Ion Range Calc Method list, select a method for calculating the ion ratio range windows. When you select Level, the TraceFinder application displays a Use Level list where you can choose a calibration level. To define the available calibration levels on the Compounds page, see “Editing the Compounds Page” on page 114. To edit an instrument method 1. From the Instrument Method list on the General page, select an instrument method. 2. To edit the selected instrument method, click Edit. The Thermo Xcalibur Instrument Setup dialog box opens. This example of an instrument setup showing multiple configured instruments. 108 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods 3. Edit the values on the instrument page for your instrument. 4. From the main menu in the Thermo Xcalibur Instrument Setup dialog box, choose File > Save and then choose File > Exit. The TraceFinder application returns you to the General page. See “General page for a quantitation method” on page 111. 5. To update any changes that were made to the instrument method after you created this master method, click Update. The Update Instrument Method? dialog box opens. 6. Choose one of the following options: • Send to Xcalibur Method: Overwrites the instrument method in the C:\Xcalibur\methods folder with the current instrument method. • Get From Xcalibur Method: Overwrites the current instrument method with the instrument method in the C:\Xcalibur\methods folder. • Cancel: Make no changes to the instrument method in the current master method. To select a qualitative peak processing template In the Qualitative Peak Processing Template list, select the template that you want to use to perform peak detection on quantitative samples after compound analysis is complete. The application lists all method templates (.pmtx files) in the following folder: C:\Thermo\TraceFinder\3.0\Forensic\Templates\Methods To set automated background subtraction options 1. In the Background Subtraction Range Option list, select how you want the subtraction range determined from the following options: • None: Subtracts no scans. • Before Peak: Averages and subtracts a specified number of scans before the apex of the peak. • After Peak: Subtracts a specified number of scans after the apex of the peak. • Both Sides of Peak: Subtracts a specified number of scans from each side of the apex of the peak. Thermo Scientific TraceFinder User Guide 109 4 Using the Method Development Mode Working with Master Methods 2. In the Number of Scans To Subtract box, enter a number. This is the number of scans that the TraceFinder application subtracts from the background after averaging. If you selected the Both Sides of Peak option, the application subtracts this number of scans from each side of the peak. 3. In the Stepoff Value box, enter a number. The TraceFinder application uses this offset value to average and subtract scans that are not adjacent to the apex of the peak. For example: If you entered 3 in the Number of Scans To Subtract box and the stepoff value is 5, the TraceFinder application ignores the first 5 scans to the left of the peak and applies the averaging and subtraction to the 6th, 7th, and 8th scans to the left of the peak. To specify mass tolerance 1. Select the units of measure that you want to use. 2. Specify the number of millimass units or parts per million to use as the m/z ± tolerance value. The application applies this mass tolerance to the extracted chromatograms. To include data-dependent filters Select the Include Data Dependent Filters option. The application includes data-dependent filters when you specify filters in the method. See “Signal” on page 135. Data-dependent filters are indicated with a “d”. Data-dependent filter When you process a sample using a data-dependent filter, the application uses the TIC trace to find all data-dependent full scans, lists them, and performs a library search against the data-dependent MS/MS or MSn scan. To enter a note for the method Type in the Notes box, or paste text from another application using CTRL+V. You can add a note to explain what makes this method unique. 110 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Figure 24. General page for a quantitation method Table 18. General page parameters (Sheet 1 of 3) Parameter Description Lab Name The laboratory name to be displayed on the top of each printed, saved, or exported report. Default: Default Laboratory To specify this default laboratory name, see “Specifying Application Defaults” on page 44. Assay Type The name for the analysis type to be targeted by the method. The assay type associates the method with the analysis of a compound or specific class of compounds (for example, you might use an assay type of PAH for the analysis of Polynuclear Aromatic Hydrocarbons). Thermo Scientific TraceFinder User Guide 111 4 Using the Method Development Mode Working with Master Methods Table 18. General page parameters (Sheet 2 of 3) Parameter Description Injection Volume The system uses the injection volume (in μL) for sample injection. For a more detailed explanation, refer to the documentation for the autosampler. The injection volume in the master method overrides the injection volume in the instrument method. The injection volume in the batch overrides the injection volume in the master method. Range: 0.1 to 2000 μL Mass Precision Number of decimal places used in reports and in peak and spectrum displays. Valid values: Integers from 2 to 6, inclusive. Ion Range Calc Method The TraceFinder application uses the selected ion range calc method to calculate the ion ratio range windows: Manual (default), Average, Level, or Weighted average. When you select Level, an additional list is displayed where you can select a calibration level amount. To define these calibration levels on the Compounds page, see “Editing the Compounds Page” on page 114. Instrument Method Instrument method used for acquiring samples. Edit Opens the Thermo Xcalibur Instrument Setup dialog box where you can edit the instrument method. Update Choose one of the following: Send to Xcalibur Method: Overwrites the Xcalibur method with the current instrument method. Get From Xcalibur Method: Overwrites the current instrument method with the Xcalibur method. Qualitative Peak Processing Template The TraceFinder application uses the qualitative peak processing template to perform peak detection on quantitative samples following compound analysis. Background Subtraction Range Option Valid values: None, Before Peak, After Peak, Both Sides of Peak Default: None Number of Scans To Subtract Valid values: Even numbered integers Default: 0 Stepoff Value Offset from the selected peak to the first subtracted peak. 112 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 18. General page parameters (Sheet 3 of 3) Parameter Description Mass Tolerance Upper limit of MMU or PPM. Default: 500 Range: 0.1 through 50 000 • (Default) MMU (millimass units): MMU is a static calculation to the extracted mass. • PPM (parts per million): PPM is a variable calculation dependent on the actual mass. The smaller the mass, the narrower the tolerance range. The larger the mass, the wider the tolerance range. Include Data Dependent Filters Available only for quantitation methods. Notes Optional notes about the method. Thermo Scientific TraceFinder User Guide 113 4 Using the Method Development Mode Working with Master Methods Editing the Compounds Page Use the Compounds page to set all parameters used to identify, detect, and quantify the target compound list. To open the Compounds page Click Compounds in the Method View navigation pane. Available only when you activate Intelligent Sequencing in the Application Configuration mode. From the Compounds page of the Method View, you can access the following pages: Acquisition List See also Acquisition List. Identification See also “Identification page parameters” on page 117. Detection See also “Detection page panes” on page 132. Calibration See also “Calibration page parameters” on page 165. Calibration Levels See also “Calibration levels page parameters” on page 167. QC Levels See also “QC levels page parameters” on page 169. Real Time Viewer See also “Real Time Viewer page parameters” on page 170. Each page on the Compounds page (except the Acquisition List and Real Time Viewer pages) uses a right-click shortcut menu. See “Using the Shortcut Menu Commands” on page 172. 114 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Acquisition List The Acquisition List page displays all compounds defined for the current method in a display similar to the Compound Database view. From the Acquisition List page, you can add additional compounds from the Compound Database or delete compounds from the method. For detailed descriptions of all the features on the Compound Database view, see “Compound Database view parameters” on page 246. To remove a compound from the method 1. Select the compound in the Compound list. 2. Click the Remove Compound icon, . 3. If you are sure you want to delete the selected compound, at the prompt, click OK. The application removes the selected compound and all its peak information. 4. To remove multiple compounds, use the CTRL or SHIFT keys. The application confirms that you want to remove the selected compounds. To add a compound to the method 1. Click the Add Compound from Compound Database icon, . The Select Compounds from Database dialog box opens, listing all the compounds defined in the compound database. This dialog box is identical to the Compound Database with the exception that you cannot edit the compound data from here; you can only choose which compounds you want to include in your method. Figure 25. Select Compounds from Database dialog box Thermo Scientific TraceFinder User Guide 115 4 Using the Method Development Mode Working with Master Methods 2. Select the compounds to add to the method. You can use the SHIFT or CTRL keys to select multiple compounds. 3. Click Add Selected Compounds to Method. The TraceFinder application adds the selected compounds to the acquisition list for the method. 116 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Identification The Identification page lists the compounds that are targeted for analysis, reporting, and other compound-specific values. For descriptions of all values on the Identification page, see “Identification page.” To filter the displayed compounds From the Show list, select the type of compounds that you want to display in the compounds list. Compound type Description Quan Compounds Displays only quantitation compounds, such as target compounds and internal standards. Target Compounds Displays only target compounds. Internal Standards Displays only internal standard compounds. Figure 26. Identification page Table 19. Identification page parameters (Sheet 1 of 2) Parameter Description RT Retention time. The time after injection when the compound elutes. The total time that the compound is retained on the column. The TraceFinder application uses the RT and Window values to determine the start and stop time for the acquisition. Range: 0.00 to 999.00 Start time = RT – (Window/2) Stop time = RT + (Window/2) Start and stop range: 0.00 to 999.00 Compound A list of identified compounds. To customize the compound names, click the cell and type a new name. To display a filtered list of compounds, use the Show list. Compound Type Compound types are Target Compound and Internal Standard. The TraceFinder application uses target compounds and internal standards in quantitative analysis. Thermo Scientific TraceFinder User Guide 117 4 Using the Method Development Mode Working with Master Methods Table 19. Identification page parameters (Sheet 2 of 2) Parameter Description Active Identifies each compound to be included in data review and reporting. By default, all added compounds are set to active. This active or inactive setting populates the Batch View and Data Review view in the Analysis mode. CAS No The Chemical Abstract Service (CAS) number that the TraceFinder application matched with each compound. To change or add a number, click the CAS No cell and enter a new number. Use as RT Reference When performing peak detection with retention time standards, the TraceFinder application first identifies those compounds identified as retention time standards and then uses their observed retention times to adjust any associated target compound. Reference Compound To be used for retention time adjustment for a compound. This list includes all compounds that are selected in the Use as RT Reference column. Shortcut menu 118 TraceFinder User Guide The Identification page uses a right-click shortcut menu. See “Using the Shortcut Menu Commands” on page 172. Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Detection Use the Detection page to customize peak detection and integration for any ions that define peaks and compounds. From the Detection page, you can access the following pages: Times See also “Times page parameters” on page 133. Signal See also “Signal page parameters” on page 141. Detect See also “Detect page parameters for Genesis” on page 146. See also “Detect page parameters for ICIS” on page 150. See also “Detect page parameters for Avalon” on page 152. Suitability See also “System Suitability dialog box” on page 156. Spectrum See also “Spectrum page shortcut menu commands” on page 161. Ratios See also “Ratios page parameters” on page 163. On the Detection page (see “Detection page” on page 131), you can configure how characteristic ions for targeted compounds are detected and integrated. You can also edit the list of characteristic ions for a specific compound. Refining these parameters in the master method for each compound and its ions can reduce the degree of manual integration that would otherwise be required. You can change the parameters used to identify a quantitative peak, mass range, or confirming ion peak. The TraceFinder application automatically uses the first match it finds as the compound name, the base peak of the mass spectrum as the quantitative peak, and the second and third largest ions as the confirming ion peaks. Follow these procedures: • To filter the displayed compounds • To change the displayed information for detected peaks • To add compounds to the method • To change the compound reference spectrum • To replace a quantitation mass • To add a mass to the existing quantitation mass ranges • To add a quantitative peak • To add a spectral peak as a new compound • To replace a quantitative peak with a confirming ion peak • To set a confirming ion peak as an additional quantitative peak • To add a trace to the Real Time Status pane • To replace a confirming ion peak • To add a mass as a new confirming ion peak • To use the cut-and-paste feature on confirming ion peaks • To save the new method Thermo Scientific TraceFinder User Guide 119 4 Using the Method Development Mode Working with Master Methods To filter the displayed compounds From the Show list, select the type of compounds that you want to display in the compounds list. Compound type Description Quan Compounds Displays only quantitation compounds, such as target compounds, internal standards, and surrogates. Target Compounds Displays only target compounds. Internal Standards Displays only internal standard compounds. To change the displayed information for detected peaks 1. Right-click the chromatogram plot for any of the quan or confirming peaks and hold the cursor over Peak Labels. 2. Choose to display labels for the peak area, peak retention time, peak height, or signal to noise. 3. To remove a label, select the label type again and clear it. The application globally applies these label settings to all quantitative peaks, confirming peaks, and internal standard peaks in the method. 120 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods To add compounds to the method Tip You can add compounds from the current raw data file (begin at step 7), or you can associate another raw data file and add compounds from that file (begin at step 1). 1. From the main menu, choose Method View > Associate a Raw Data File. The Associate a Raw Data File dialog box opens. Browse to a data file. Select a previously associated data file. 2. Browse to a raw data file to associate with the method (or click the arrow and select from the list of previously associated raw data files) and open the file. To assure that this raw data file is always available to the method (for example, if you move the method to another system), the application saves the raw data file in the method folder: C:\Thermo\TraceFinder\3.0\Forensic\Methods 3. To update the target ion ratio values when you associate this raw data file, select the Yes option. 4. To update the scan filters when you associate this raw data file, select the Yes option. 5. To set a reference spectrum, do one of the following: Select the Yes option. –or– Select the Yes, with Background Subtraction option. This feature is available only when you have set background subtraction values on the General page of the Method View. See “Editing the General Page” on page 107. 6. Click OK. Thermo Scientific TraceFinder User Guide 121 4 Using the Method Development Mode Working with Master Methods The TraceFinder application displays the chromatographic and spectrum data for the compounds in the associated raw data file. IMPORTANT While the spectra pane displays the associated raw data file, you cannot display peak information for an original compound in the Compound list. You can display peak information only for compounds in the associated raw data file. To return the display functionality for all compounds in the method, save the method. 7. Select a filter from the Filter list. 8. Click to select the peak in the chromatogram that represents the compound that you want to add to the method. 9. Right-click and choose Add This Peak as New Compound from the shortcut menu. 122 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods The TraceFinder application performs a library search for the selected compound. The application uses the first match it finds as the compound name, the base peak of the mass spectrum as the quantitative peak, and the second and third largest ions as the confirming ion peaks. • When the name of the first match does not exist in the method, the application adds this compound to the method and displays the name in the Compound list. You can now view and edit the parameters for this compound. • When the name of the first match is already in the method, the Add New Compound dialog box opens. You cannot overwrite a compound name in the method. If the selected peak already exists in the method, you must give it a new name to add it to the method. Or, you can select a different compound to add to the method, following step 10 through 12. Figure 27. Add New Compound dialog box Thermo Scientific TraceFinder User Guide 123 4 Using the Method Development Mode Working with Master Methods 10. Do one of the following: • Type a new name for the first matched compound. The application displays a red warning when the selected compound name already exists in the method. You cannot overwrite the compound name, and you cannot create a duplicate name in the method. You must type a unique name. –or– • To use a compound other than the first matched compound, scroll to the spectrum for that compound and select its corresponding check box in the title bar of the spectrum pane. Selected compound 11. In the Type of Compound To Add list, select a compound type. 12. Click OK. To change the compound reference spectrum 1. In the chromatogram pane, click a peak. The TraceFinder application displays the spectrum for the selected peak in the spectrum pane. 2. In the spectrum pane, right-click and choose Use This Spectrum for Compound Reference Spectrum from the shortcut menu. The TraceFinder application replaces the spectrum on the Spectrum page of the quantitative peak pane with this spectrum. 124 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods To replace a quantitation mass 1. Click the data pane for the quantitation mass that you want to replace. 2. In the spectrum pane, hold the cursor over a peak. The red box indicates the selected peak. 3. Right-click and choose Set This Spectral Peak as Quan Value from the shortcut menu. 4. Choose either Don’t Update Ion Ratios or Update Ion Ratios Using This Spectrum. You can see the updated ion ratios on the Ratios page for the confirming ion peaks. See “Ratios” on page 162. To add a mass to the existing quantitation mass ranges 1. In the spectrum pane, hold the cursor over a peak. The red box indicates the selected peak. 2. Right-click and choose Add This Spectral Peak to Existing Quan Ranges from the shortcut menu. 3. Choose either Don’t Update Ion Ratios or Update Ion Ratios Using This Spectrum. The TraceFinder application adds the selected mass to the existing quantitation mass ranges to increase the signal. If you chose to update the ion ratios, you can see the updated ion ratios on the Ratios page for the confirming ion peaks. See “Ratios” on page 162. Thermo Scientific TraceFinder User Guide 125 4 Using the Method Development Mode Working with Master Methods To add a quantitative peak 1. In the spectrum pane, hold the cursor over a peak. The red box indicates the selected peak. 2. Right-click and choose Add This Spectral Peak as New Quan Peak from the shortcut menu. The application adds a new quantitative peak to the compound. You can use the shortcut menu in the spectrum pane for this new quantitative peak to perform any of the tasks that you would perform on the original quantitative peak. 126 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods To add a spectral peak as a new compound 1. In the raw data file spectrum pane, hold the cursor over a peak. The red box indicates the selected peak. 2. Right-click and choose Add This Spectral Peak as New Compound from the shortcut menu. The TraceFinder application performs a library search for the selected compound. The application uses the first match it finds as the compound name, the base peak of the mass spectrum as the quantitative peak, and the second and third largest ions as the confirming ion peaks. When there are multiple matches, the Add New Compound dialog box opens. If the name of the first match is already in the library, the dialog box opens with the matching compound selected. Figure 28. Add New Compound dialog box 3. (Optional) Make any of the following changes: • Change the name for the compound in the Name of New Compound box. Thermo Scientific TraceFinder User Guide 127 4 Using the Method Development Mode Working with Master Methods • Use a compound other than the compound chosen by the TraceFinder application by scrolling to the spectrum for that compound and selecting the compound name in the title bar of the spectrum pane. Selected compound • In the Type of Compound To Add list, select a compound type. 4. Click OK. To replace a quantitative peak with a confirming ion peak 1. When you have multiple quantitative peaks, select the quantitative peak that you want to replace. 2. Right-click the header bar for the confirming ion peak that you want to use as the quantitative peak, and choose Swap with Quan Peak from the shortcut menu. The application swaps the quantitative peak and the confirming ion peak. The application replaces all information for the quantitative peak with information for the confirming ion. This includes the expected retention time that the confirming ion inherited from the original quantitative peak. The original quantitative peak replaces the confirming ion peak. The application recalculates the ratios for all confirming ion peaks. To set a confirming ion peak as an additional quantitative peak Right-click the header bar for the confirming ion peak and choose Promote to Separate Quan Peak from the shortcut menu. The application creates a new quantitative peak, using information from the confirming ion peak. This includes the expected retention time that the confirming ion peak inherited from the original quantitative peak. The application removes all references to the confirming ion peak from the method. 128 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods To add a trace to the Real Time Status pane Right-click the header bar for the quantitative peak or confirming ion peak that you want to add to the Real Time Status pane and choose Display in Real Time Viewer from the shortcut menu. The application moves the peak to the Traces To Display in Real Time Viewer pane on the Real Time Viewer page. See “Real Time Viewer” on page 170. Trace m/z 465.36 added to Real Time Viewer When you acquire samples with this method, the application displays the m/z 311.09 trace in addition to the TIC in the Real Time Status pane. Trace m/z 311.09 added to Real Time Status display Thermo Scientific TraceFinder User Guide 129 4 Using the Method Development Mode Working with Master Methods To replace a confirming ion peak 1. Click the pane for the confirming ion peak that you want to replace. 2. In the raw data file spectrum pane, hold the cursor over a peak. The red box indicates the selected peak. 3. Right-click and choose Set This Spectral Peak as Confirming from the shortcut menu. The TraceFinder application replaces the confirming ion peak with the selected mass. To add a mass as a new confirming ion peak 1. In the spectrum pane, hold the cursor over a peak. The red box indicates the selected peak. 2. Right-click and choose Add This Spectral Peak as New Confirming from the shortcut menu. The TraceFinder application adds the confirming ion peak to the quantitative peak. You can use the shortcut menu in the spectrum pane for this new confirming ion peak to perform any of the tasks that you would perform on the original confirming ion peaks. To use the cut-and-paste feature on confirming ion peaks 1. Right-click the header bar for the confirming ion peak that you want to remove and choose Cut Confirming Peak from the shortcut menu. 2. Right-click the header bar for the confirming ion peak that you want to replace and choose Paste Confirming Peak from the shortcut menu. The application pastes the confirming ion peak that you removed. You can paste a deleted peak back to the quantitative peak from which it was removed, or you can paste the confirming ion peak that was deleted to another quantitative peak for this compound. To save the new method 1. Choose File > Save. The Save Master Method dialog box opens. 2. Type a new name for the master method and click OK, or select a method name to overwrite and click Overwrite. The TraceFinder application saves the new method data in the following folder: …\Thermo\TraceFinder\3.0\Forensic\Methods 130 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Figure 29. Detection page Selected compound data Chromatogram pane Spectrum pane Selected compound Thermo Scientific TraceFinder User Guide 131 4 Using the Method Development Mode Working with Master Methods Table 20. Detection page panes Pane Description Compound Lists all compounds in the master method. The Compound list uses a right-click shortcut menu. See “Using the Shortcut Menu Commands” on page 172. QuanPeakn Displays a chromatogram for the quantitative peak and its confirming ion peaks. The quantitative peak and confirming peak panes include additional pages for retention time, signal, detection, spectrum, and ratio parameters for the selected compound. Trace Displays a combination of the Detector and Trace values used for the raw data file. Do not confuse this Trace parameter with the Trace parameter on the Signal page. This Trace parameter combines both the Detector and Trace values specified on the Signal page. See “Signal page for a mass spectrometer detector” on page 140. Note When you select a detector option other than MS or PDA, the spectrum pane reports “Not Available.” Filter Displays the filter used for the raw data file. Available only when you set the Trace parameter to MS. Reference Chromatogram and Spectra Displays a reference chromatogram and spectra for the raw data file. When you view an analog trace, there is no spectra display. To close the spectra pane and use the full width to display the chromatogram, click . Additional pages Times Defines the retention time and window for a quantitative peak. See “Times” on page 133. Signal Defines the detector and detection parameters used to display each chromatogram trace. See “Signal” on page 135. Detect Defines the peak detection algorithm and its options. See “Detect” on page 144. Spectrum Defines a reference mass spectrum for a quantitative peak or compound. See “Spectrum” on page 157. Ratios Defines the criteria for evaluating, confirming, or qualifying ions. See “Ratios” on page 162. 132 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Times Use the Times page to define the expected retention time or a retention time range for a quantitative peak. Figure 30. Times page Parameters for single RT detection types Parameters for RT range detection types Table 21. Times page parameters (Sheet 1 of 2) Parameter Description Detection Type Single - Detected: (Default) Specified as a centered retention time window. The application integrates a distinct peak. In reports, the application displays the expected retention time and actual retention time values as Method RT and Detected RT, respectively. Range - Detected: Specified as a retention time start/end range. Range - Integrated: Specified as a retention time start/end range. The application integrates all peaks within the specified time range. Expected RT (min) Expected retention time for a single peak. Available only for the Single - Detected detection type. Window (sec) Width of the window (in seconds) to indicate how far around the expected retention time the system looks for a peak apex. Available only for the Single - Detected detection type. Thermo Scientific TraceFinder User Guide 133 4 Using the Method Development Mode Working with Master Methods Table 21. Times page parameters (Sheet 2 of 2) Parameter Description Start/End RT (min) Beginning and ending retention time window that can encompass multiple peaks. Available only for the Range - Detected and the Range - Integrated detection types. When you change from a Single - Detected detection type, these values default to the previous beginning and ending time calculated from the Expected RT and Window values. View Width (min) Viewable size of the ion chromatogram display. Changing the view width does not affect the peak detection process; the TraceFinder application uses it only for graphical display. When you select either Range - Detected or Range - Integrated as the detection type, you cannot select a View Width value less than the retention time range (end time minus start time). Shortcut menu Set Peak Windows Copies the View Width and Window values to all quantitative peaks for the compound and Settings to All Peaks in updates the compound. Compound Available only when a compound has multiple quantitative peaks. Set Peak Windows Copies the View Width and Window values to all quantitative peaks for the method and Settings to All Peaks in updates the method. Method 134 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Signal Use the Signal page to define the detector and filters as you display each chromatogram trace. For detailed descriptions of all the features on the Signal page, see “Signal page parameters” on page 141. The TraceFinder application can use both analog detectors and mass spectrometer detectors. See “Signal page for a mass spectrometer detector” on page 140 or “Signal page for an analog detector” on page 141. Follow these procedures: • To specify ranges of ions for detection and integration • To specify an XIC filter • To specify an MS filter To specify ranges of ions for detection and integration 1. Select MS from the Detector list. 2. Select Mass Range from the Trace list. 3. In the Ranges area, click Edit. Note The Ranges area is available only when you set the Detector parameter to MS and the Trace parameter to Mass Range. The Edit Mass Ranges dialog box opens where you can define mass ranges using a center of mass or start and end values. Figure 31. Edit Mass Ranges dialog box 4. Enter a value in the Center Mass box and click Add. A new row with this value opens under Ranges. Center mass values are listed in the Start m/z column. The application uses a range of one amu centered on this value. 5. Enter values in the Start m/z and End m/z columns and click Add. The application adds a row with these start and end values. Thermo Scientific TraceFinder User Guide 135 4 Using the Method Development Mode Working with Master Methods 6. Add as many ranges as you want. When you process a batch with this method, the application sums the multiple ions specified by these ranges. 7. Click Apply. The application applies the parameters to the list of ranges. To specify an XIC filter 1. Select MS from the Detector list. 2. Select Mass Range from the Trace list. 3. Select the XIC option. Note The XIC option is available only when you set the Detector parameter to MS and the Trace parameter to Mass Range. 4. Click the Filter browse button. The XIC Filter dialog box opens. See XIC Filter dialog box. 5. Specify your filter options. 6. Click OK. The application updates the chromatogram data using the specified XIC filter options. The Filter box indicates the parameters of the specified XIC filter. For example: MassAnalyzerFTMS analyzer Positive polarity MS2 order Full scan mode Data-dependent filter 136 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Figure 32. XIC Filter dialog box Table 22. XIC Filter dialog box parameters (Sheet 1 of 2) Parameter Description Mass Analyzer Any: Allows any mass analyzer. Type FTMS: Fourier Transform Mass Spectrometer ITMS: Ion Trap Mass Spectrometer Sector: Static electric or magnetic sectors, or a combination of the two SQMS: Single Quad Mass Spectrometer TOFMS: Time-of-Flight Mass Spectrometer TQMS: Triple Quad Mass Spectrometer Thermo Scientific MSX Any: Allows both MSX and non-MSX scans. On: Allows only MSX scans. Off: Allows only non-MSX scans. Data Dependent Any: Allows both data-dependent and non-data-dependent filters. On: Allows only data-dependent filters. Off: Allows only non-data-dependent filters. MS Order Any: Allows any MS order. MS: Single mass spec stage MS2-MS3: Multiple mass spec stages Polarity Any: Allows both positive and negative. Positive Negative TraceFinder User Guide 137 4 Using the Method Development Mode Working with Master Methods Table 22. XIC Filter dialog box parameters (Sheet 2 of 2) Parameter Description Scan Mode Any: Allows any scan mode. Full: Full-scan mode SIM: Selective ion monitoring SRM: Selective reaction monitoring CRM: Consecutive reaction monitoring Q1MS: MS using quadrupole 1 Q3MS: MS using quadrupole 3 Activations Any: Allows any activation method. CID: Collision-induced dissociation MPD: Multiple photodissociation ECD: Electron capture dissociation PQD: Pulsed dissociation ETD: Electron transfer dissociation HCD: Higher energy collision-induced dissociation SAactivation: PTRactivation: NETDactivation: Negative electron-transfer dissociation activation NPTRactivation: This parameter is available only when the MS Order is set to MS2 or MS3. First Precursor This parameter is available only when the MS Order is set to MS2 or MS3. Second Precursor 138 TraceFinder User Guide This parameter is available only when the MS Order is set to MS3. Thermo Scientific 4 Using the Method Development Mode Working with Master Methods To specify an MS filter 1. Select the Filter option. 2. Select MS from the Detector list. 3. Select a trace type from the Trace list. 4. Select a filter from the Filter list. The application applies the selected filter to the quantitative or confirming ion peak. 5. To apply this same filter to other peaks, right-click and choose one of the following from the shortcut menu: • Set Filter Options on All Peaks in This Compound: Applies this filter to all other peaks in the compound. • Set Filter Options on All Compounds: Applies this filter to all peaks in the method. Thermo Scientific TraceFinder User Guide 139 4 Using the Method Development Mode Working with Master Methods Figure 33. Signal page for a mass spectrometer detector 140 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Figure 34. Signal page for an analog detector Table 23. Signal page parameters (Sheet 1 of 3) Parameter Description XIC Available only when you select the MS detector. Specifies an Extracted Ion Chromatogram experiment type that uses a single, full-scan mass filter that is post-processed to extract a peak for the ions of interest. Filter Available only when you select the MS detector. Select from the list of mass filters to use for processing the compound. Thermo Scientific TraceFinder User Guide 141 4 Using the Method Development Mode Working with Master Methods Table 23. Signal page parameters (Sheet 2 of 3) Parameter Description Detector Options are determined by the detection options used to create the method. The method can use the standard options (all the listed options) or only the detection options used to acquire an associated raw data file. MS: Mass spectrometer that ionizes sample molecules and then separates the ions according to their mass-to-charge ratio (m/z). PDA: Photodiode array detector providing a linear array of discrete photodiodes on an integrated circuit chip. It is placed at the image plane of a spectrometer to allow a range of wavelengths to be simultaneously detected. Analog: Supplemental detectors (for example, FID, ECD). When you select this detector, any reports that display a QIon value show the value as Analog and any reports that display spectra show the spectra as Not Available. A/D card: If you have a detector not under data system control, you can capture the analog signal and convert it to digital using an interface box (for example, SS420X) for storage in the raw data file. UV: A UV spectrophotometer (for variable-wavelength detection) or photometer (for single-wavelength detection) equipped with a low-volume flow cell. This detector detects analytes that readily absorb light at a selected wavelength. Trace Represents a specific range of the data. The TraceFinder application uses the trace to identify the characteristic ions for a compound. MS detector options: Mass Range, TIC, or Base Peak. When you select Mass Range, you are prompted to enter the start and end m/z values for the ranges. PDA detector options: Spectrum Maximum, Wavelength Range, or Total Scan. Analog detector options: Analog 1, Analog 2, Analog 3, or Analog 4. You can configure these channel names in your instrument configuration. A/D Card detector options: AD Card ch1, AD Card ch2, AD Card ch3, or AD Card ch4. You can configure these channel names in your instrument configuration. UV detector options: Channel A, Channel B, Channel C, or Channel D. You can configure these channel names in your instrument configuration. Filter Available only when you select the MS detector. Represents a particular data acquisition channel. For example, the filter option + c Full ms [35.00-500.00] represents a positive ion centroid signal acquired in single-stage, full-scan mode from m/z 35 to 500. Ranges Available only when you select the Mass Range trace for an MS detector. 142 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 23. Signal page parameters (Sheet 3 of 3) Parameter Description Edit Opens the Edit Mass Ranges dialog box where you can specify a range of ions for detection and integration. See “Edit Mass Ranges dialog box” on page 135. Start m/z End m/z Specifies ranges of ions for detection and integration. The application sums the multiple ions specified by these ranges. Ranges specified by a center mass value are listed as a single value in the Start m/z column. The application uses a range of one amu centered on this value. Thermo Scientific TraceFinder User Guide 143 4 Using the Method Development Mode Working with Master Methods Detect Use the Detect page to define the peak detection algorithm (sensitivity) and its options and to determine the area under a curve. There are three sensitivity modes: Genesis, ICIS, and Avalon. The Genesis and Avalon sensitivity modes are used for mass spectrometry detection. The ICIS sensitivity mode is used primarily for analog detection. On this page, you can specify how you want each mode to run. See the following for detailed descriptions of all the features on the Detect page: • For Genesis sensitivity, see “Detect page parameters for Genesis” on page 146. • For ICIS sensitivity, see “Detect page parameters for ICIS” on page 150. • For Avalon sensitivity, see “Detect page parameters for Avalon” on page 152. 144 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Figure 35. Detect page for Genesis Thermo Scientific TraceFinder User Guide 145 4 Using the Method Development Mode Working with Master Methods Table 24. Detect page parameters for Genesis (Sheet 1 of 3) Parameter Description Sensitivity Specifies the Genesis peak detection algorithm. Detection Method Highest peak: Uses the highest peak in the chromatogram for component identification. Nearest RT: Uses the peak with the nearest retention time in the chromatogram for component identification. Smoothing Determines the degree of data smoothing to be performed on the active component peak prior to peak detection and integration. Default: 1 Range: Any odd integer from 1 through 15 points S/N Threshold Current signal-to-noise threshold for peak integration. Peaks with signal-to-noise values less than this value are not integrated. Peaks with signal-to-noise values greater than this value are integrated. Range: 0.0 to 999.0 Enable Valley Detection Uses the valley detection approximation method to detect unresolved peaks. This method drops a vertical line from the apex of the valley between unresolved peaks to the baseline. The intersection of the vertical line and the baseline defines the end of the first peak and the beginning of the second peak. Expected Width (sec) The expected peak width parameter (in seconds). This parameter controls the minimum width that a peak is expected to have if valley detection is enabled. With valley detection enabled, any valley points nearer than the expected width/2 to the top of the peak are ignored. If a valley point is found outside the expected peak width, the TraceFinder application terminates the peak at that point. The application always terminates a peak when the signal reaches the baseline, independent of the value set for the expected peak width. Range: 0.0 to 999.0 Constrain Peak Width Constrains the peak width of a component during peak integration of a chromatogram. You can then set values that control when peak integration is turned on and off by specifying a peak height threshold and a tailing factor. Selecting the Constrain Peak Width check box activates the Peak Height (%) and Tailing Factor options. Peak Height (%) A signal must be above the baseline percentage of the total peak height (100%) before integration is turned on or off. This text box is active only when you select the Constrain Peak Width check box. Range: 0.0 to 100.0% Tailing Factor A factor that controls how the TraceFinder application integrates the tail of a peak. This factor is the maximum ratio of the trailing edge to the leading side of a constrained peak. This text box is active only when you select the Constrain the Peak Width check box. Range: 0.5 through 9.0 146 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 24. Detect page parameters for Genesis (Sheet 2 of 3) Parameter Description Min Peak Height (S/N) For the valley detection approximation method to use the Nearest RT Peak Identification criteria, this peak signal-to-noise value must be equaled or exceeded. For component identification purposes, the TraceFinder application ignores all chromatogram peaks that have signal-to-noise values that are less than the S/N Threshold value. Range: 0.0 (all peaks) through 999.0 Available only for quantitation methods. Peak S/N Cutoff The peak edge is set to values below this signal-to-noise ratio. This test identifies an edge of a peak when the baseline adjusted height of the edge is less than the ratio of the baseline adjusted apex height and the peak S/N cutoff ratio. When the S/N at the apex is 500 and the peak S/N cutoff value is 200, the TraceFinder application defines the right and left edges of the peak when the S/N reaches a value less than 200. Range: 50.0 to 10000.0 Valley Rise (%) The peak trace can rise above the baseline by this percentage after passing through a minimum (before or after the peak). This method drops a vertical line from the apex of the valley between unresolved peaks to the baseline. The intersection of the vertical line and the baseline defines the end of the first peak and the beginning of the second peak. When the trace exceeds rise percentage, the TraceFinder application applies valley detection peak integration criteria. The TraceFinder application applies this test to both the left and right edges of the peak. The rise percentage criteria is useful for integrating peaks with long tails. Range: 0.1 to 500.0 Valley S/N Specifies a value to evaluate the valley bottom. Using this parameter ensures that the surrounding measurements are higher. Default: 2.0 Range: 1.0 to 100.0 # Background Scans Number of background scans performed by the TraceFinder application. Report Noise As Determines if the noise used in calculating S/N values is calculated using an RMS calculation or a peak-to-peak resolution threshold. Options are RMS or Peak to Peak. Shortcut menu Apply to All Peaks in Method Thermo Scientific Updates all compounds in the method with the current settings on the Detect page. These updates apply to both quantitative and confirming ion peaks. TraceFinder User Guide 147 4 Using the Method Development Mode Working with Master Methods Table 24. Detect page parameters for Genesis (Sheet 3 of 3) Parameter Description Apply to All Peaks with Uses the current settings on the Detect page to update all compounds in the method that Like Sensitivity Setting use the Genesis sensitivity mode. These updates apply to both quantitative and confirming ion peaks that use the Genesis sensitivity mode. Apply to All Peaks in Compound 148 TraceFinder User Guide Updates all peaks in the current compound with the current settings on the Detect page. These updates apply to both quantitative and confirming ion peaks. Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Figure 36. Detect page for ICIS Thermo Scientific TraceFinder User Guide 149 4 Using the Method Development Mode Working with Master Methods Table 25. Detect page parameters for ICIS (Sheet 1 of 2) Parameter Description Sensitivity Specifies the ICIS peak detection algorithm, used primarily with analog detectors. Detection Method Highest peak: Uses the highest peak in the chromatogram for component identification. Nearest RT: Uses the peak with the nearest retention time in the chromatogram for component identification. Smoothing Determines the degree of data smoothing to be performed on the active component peak prior to peak detection and integration. Default: 1 Range: Any odd integer from 1 through 15 points Area Noise Factor The noise level multiplier used to determine the peak edge after the location of the possible peak. Default: 5 Range: 1 through 500 Peak Noise Factor The noise level multiplier used to determine the potential peak signal threshold. Default: 10 Range: 1 through 1000 Baseline Window The TraceFinder application looks for a local minima over this number of scans. Default: 40 Range: 1 through 500 Constrain Peak Width Constrains the peak width of a component during peak integration of a chromatogram. You can then set values that control when peak integration is turned on and off by specifying a peak height threshold and a tailing factor. Selecting the Constrain Peak Width check box activates the Peak Height (%) and Tailing Factor options. Peak Height (%) A signal must be above the baseline percentage of the total peak height (100%) before integration is turned on or off. This text box is active only when you select the Constrain Peak Width check box. Range: 0.0 to 100.0% Tailing Factor A factor that controls how the TraceFinder application integrates the tail of a peak. This factor is the maximum ratio of the trailing edge to the leading side of a constrained peak. This text box is active only when you select the Constrain the Peak Width check box. Range: 0.5 through 9.0 Min Peak Height (S/N) For the valley detection approximation method to use the Nearest RT Peak Identification criteria, this peak signal-to-noise value must be equaled or exceeded. For component identification purposes, the TraceFinder application ignores all chromatogram peaks that have signal-to-noise values that are less than the S/N Threshold value. Range: 0.0 (all peaks) through 999.0 Available only for quantitation methods. 150 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 25. Detect page parameters for ICIS (Sheet 2 of 2) Parameter Description Noise Method The options are INCOS or Repetitive. INCOS: Uses a single pass algorithm to determine the noise level. Repetitive: Uses a multiple pass algorithm to determine the noise level. In general, this algorithm is more accurate in analyzing the noise than the INCOS Noise algorithm, but the analysis takes longer. Min Peak Width The minimum number of scans required in a peak. Default: 3 Range: 0 to 100 scans Multiplet Resolution The minimum separation in scans between the apexes of two potential peaks. This is a criterion to determine if two peaks are resolved. Default: 10 Range: 1 to 500 scans Area Tail Extension The number of scans past the peak endpoint to use in averaging the intensity. Default: 5 Range: 0 to 100 scans Area Scan Window The number of allowable scans on each side of the peak apex. A zero value defines all scans (peak-start to peak-end) to be included in the area integration. Default: 0 Range: 0 to 100 scans RMS Specifies that the TraceFinder application calculate noise as RMS. By default, the application uses Peak To Peak for the noise calculation. RMS is automatically selected if you manually determine the noise region. Shortcut menu Apply to All Peaks in Compound Updates all peaks in the current compound with the current settings on the Detect page. These updates apply to both quantitative and confirming ion peaks. Apply to All Peaks in Method Updates all compounds in the method with the current settings on the Detect page. These updates apply to both quantitative and confirming ion peaks. Apply to All Peaks with Uses the current settings on the Detect page to update all compounds in the method that Like Sensitivity Setting use the ICIS sensitivity mode. These updates apply to both quantitative and confirming ion peaks that use the ICIS sensitivity mode. Thermo Scientific TraceFinder User Guide 151 4 Using the Method Development Mode Working with Master Methods Figure 37. Detect page for Avalon Table 26. Detect page parameters for Avalon (Sheet 1 of 2) Parameter Description Sensitivity Specifies the Avalon peak detection algorithm. Detection Method Highest Peak: Uses the highest peak in the chromatogram for component identification. Nearest RT: Uses the peak with the nearest retention time in the chromatogram for component identification. 152 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 26. Detect page parameters for Avalon (Sheet 2 of 2) Parameter Description Smoothing Determines the degree of data smoothing to be performed on the active component peak prior to peak detection and integration. Default: 1 Range: Any odd integer from 1 through 15 points Autocalc Initial Events Automatically calculates the events in the Event list. Edit Opens the Avalon Event List dialog box. See “Avalon Event List” on page 57. Shortcut menu Apply to All Peaks in Compound Updates all peaks in the current compound with the current settings on the Detect page. These updates apply to both quantitative and confirming ion peaks. Apply to All Peaks in Method Updates all compounds in the method with the current settings on the Detect page. These updates apply to both quantitative and confirming ion peaks. Apply to All Peaks with Uses the current settings on the Detect page to update all compounds in the method that Like Sensitivity Setting use the Avalon sensitivity mode. These updates apply to both quantitative and confirming ion peaks that use the Avalon sensitivity mode. Thermo Scientific TraceFinder User Guide 153 4 Using the Method Development Mode Working with Master Methods Suitability Use the Suitability page to determine if the column is degrading and to identify suspicious peaks eluting at the same time as the target compound. Suspicious peaks caused by highly retained compounds from a previous injection tend to have a broader than expected peak profile. Tailing peaks frequently indicate a degrading column. The Suitability page displays the parameter values that the application uses to check the suitability of chromatographic peaks during processing. You can edit these parameters in the System Suitability dialog box. 154 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods To set system suitability parameters 1. Click Edit. The System Suitability dialog box opens. See “System Suitability dialog box” on page 156. 2. To perform symmetry testing, do the following: a. Select the Symmetry Parameters check box. b. Type a peak height for symmetry testing in the Peak Height box. c. Type a threshold for symmetry testing in the Symmetry Threshold box. 3. To carry out classification tests, do the following: a. Select the Peak Classification Parameters check box. b. To adjust Xcalibur peak width testing thresholds, type parameters in the Detect Peak Width area. • To enter a peak height for the test, type a value in the Peak Height box. • To enter a minimum peak width threshold, type a value in the Min Peak Width box. c. To adjust the Xcalibur peak tailing test, type parameters in the Detect Tailing area. • To enter a peak height for the test, type a value in the Peak Height box. • To enter a threshold limit for peak tailing, type a value in the Failure Threshold box. d. To adjust the Xcalibur column overload test, type parameters in the Detect Column Overload area. • To enter a peak height for the test, type a value in the Peak Height box. • To enter a threshold limit for peak tailing, type a value in the Failure Threshold box. e. To adjust the Xcalibur baseline clipping test, type parameters in the Detect Baseline Clipping area. To define the test window, type a value in the Number of Peak Widths for Noise Detection box. 4. To save your settings, click OK. Thermo Scientific TraceFinder User Guide 155 4 Using the Method Development Mode Working with Master Methods Figure 38. System Suitability dialog box 156 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Spectrum Use the Spectrum page to store a reference mass spectrum for a quantitative peak or compound. For detailed descriptions of all the shortcut menu commands on the Spectrum page, see “Spectrum page shortcut menu commands” on page 161. Follow these procedures: • To update confirming ion ratios • To change the quantitation mass used for a quantitative peak • To add ions together to get an accumulated signal • To add a quantitative peak to an existing compound • To add one or more confirming ions to an existing compound • To zoom in on the chromatogram or spectrum displays To update confirming ion ratios 1. Click a peak in the quantitative peak chromatogram pane. The mass spectrum for the peak is displayed in the Spectrum pane. 2. Right-click the Spectrum pane and choose Update Confirming Ion Ratios with This Spectrum from the shortcut menu. To change the quantitation mass used for a quantitative peak 1. Click a peak in the chromatogram pane. The mass spectrum for the peak is displayed in the Spectrum pane. 2. In the Spectrum pane, hold the cursor over the mass-to-charge value for an ion. A red box around the ion’s m/z value indicates that the ion is selected. 3. Right-click and choose one of the following commands from the shortcut menu: • Set This Mass as Quan Mass > Don’t Update Ion Ratios • Set This Mass as Quan Mass > Update Ion Ratios Using This Reference Spectrum The following examples show an original quantitative peak and a quantitative peak with an updated quantitation mass. Thermo Scientific TraceFinder User Guide 157 4 Using the Method Development Mode Working with Master Methods Figure 39. Original quantitative peak mass example Original quantitative peak mass The TraceFinder application replaces the original quantitation mass with the selected mass. Figure 40. Updated quantitative peak mass example New quantitative peak mass 158 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods To add ions together to get an accumulated signal 1. Hold the cursor over the m/z value for an ion in the Spectrum pane. A red box around the ion’s m/z value indicates that the ion is selected. 2. Right-click and choose Add This Mass to Existing Quan Mass Range from the shortcut menu. You can now update the ion ratios to adjust the confirming ion comparisons to the new summed quantitative peak signal. To add a quantitative peak to an existing compound 1. Click the peak in the Quan Peak chromatogram pane. The mass spectrum for the peak is displayed in the Spectrum pane. 2. In the Spectrum pane, hold the cursor over the m/z value for an ion. A red box around the ion’s m/z value indicates that the ion is selected. 3. Right-click and choose Set This Mass as New Quan Peak from the shortcut menu. The TraceFinder application adds this ion as a new quantitative peak. New quantitative peak mass Thermo Scientific TraceFinder User Guide 159 4 Using the Method Development Mode Working with Master Methods To add one or more confirming ions to an existing compound 1. Click the quantitative peak in the chromatogram pane. The mass spectrum for the peak is displayed in the Spectrum pane. 2. In the Spectrum pane, hold the cursor over the m/z value for an ion. A red box around the ion’s m/z value indicates that the ion is selected. 3. Right-click and choose to Add This Mass as New Confirming Ion from the shortcut menu. The TraceFinder application adds the selected mass as a confirming peak for this quantitative peak. To zoom in on the chromatogram or spectrum displays 1. Drag the cursor to delineate a rectangle. The display zooms in on the specified rectangle. 2. To return to the original display, right-click and choose Reset Scaling from the shortcut menu. 160 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Figure 41. Spectrum page Table 27. Spectrum page shortcut menu commands Command Description Update Confirming Ion Ratios With This Spectrum Updates the confirming ion ratios using the selected peak. Set This Mass as Quan Mass Adds the quantitation mass of the selected ion to the quantitation mass used for the quantitative peak. You can choose to update the ion ratios or not update the ion ratios using this reference spectrum. Add This Mass to Existing Quan Mass Range Adds the selected mass to your existing quantitation mass range. You can choose to update the ion ratios to adjust the confirming ion comparisons to the new summed quantitative peak signal. Set This Mass as New Quan Peak Adds a new quantitative peak to an existing compound. Add This Mass as New Confirming Ion Adds one or more confirming ion peaks to an existing compound. Reset Scaling Returns the chromatogram or spectrum display to its original size. Copy to Clipboard Copies the graphic display to the Clipboard. Thermo Scientific TraceFinder User Guide 161 4 Using the Method Development Mode Working with Master Methods Ratios Use the Ratios page (see “Ratios page” on page 163) to define the criteria for evaluating the confirming or qualifying ions. The TraceFinder application detects compounds that have confirming ion values outside their acceptable window and flags them in the Acquisition mode and on reports. For detailed descriptions of all the features on the Ratios page, see “Ratios page parameters” on page 163. To specify ion ratio criteria 1. Select the Enable check box to activate the confirming ion. 2. In the Target Ratio box, select the theoretical ratio of the confirming ion’s response to the quantification ion’s response. 3. In the Window Type list, select Absolute or Relative as the calculation approach for determining the acceptable ion ratio range. 4. In the Window (+/-%) box, select the acceptable ion ratio range. 5. In the Ion Coelution box, select the maximum difference in retention time between a confirming ion peak and the quantification ion peak. In the following example • The target ratio is expected to be 61.02% and the window is Absolute 20%, so the acceptable window for this confirming ion peak is 41.02–81.02%. • However, if the window type is Relative, the plus or minus value is 20% of 61.02% (or 12.20%), so the acceptable window for this confirming ion peak is 48.82–73.22%. 162 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Figure 42. Ratios page Table 28. Ratios page parameters Parameter Description Enable Makes the ion ratio criteria available. Target Ratio (%) The theoretical ratio of the confirming ion’s response to the quantification ion’s response. Window Type The absolute or relative calculation approach for determining the acceptable ion ratio range. Window (+/-%) The acceptable ion ratio range. Ion Coelution (min) The maximum difference in retention time between a confirming ion peak and the quantification ion peak. Shortcut menu Set Ion Ratio to All Confirming Peaks in Compound Copies the Window Type, Window, and Ion Coelution values to all confirming ion peaks for the compound and updates the compound. Available only when a compound has multiple confirming ion peaks. Set Ion Ratio to All Confirming Peaks in Method Copies the Window Type, Window, and Ion Coelution values to all quantitative peaks for the method and updates the method. Thermo Scientific TraceFinder User Guide 163 4 Using the Method Development Mode Working with Master Methods Calibration Use the Calibration page to set or edit the mathematical model used for preparing the initial calibration evaluation for one or more calibration standards. Each target compound can have its own initial calibration settings, independent of the other compounds. You can modify the calibration approach on this page or in Acquisition mode when you view the results of an actual calibration batch. Typically, general quantitation uses a measured response (area or height) to determine the amount of a compound contained in a sample. The application compares the response of an unknown, target compound to the response of a calibration sample that contains a known amount of the compound by building a calibration curve to interpolate the amount in the target compound. To use a semi-quantitative process, you specify the compound’s standard type as Estimated and then identify another compound as the linked compound. Instead of using the target compound to create a calibration curve, the application uses a calibration curve from the linked compound to calculate the amount in the target compound. For detailed descriptions of all the features on the Calibration page, see Calibration page parameters. To specify an internal standard for a compound 1. On the Identification page, specify at least one compound in the method as an internal standard compound type. See “Identification” on page 117. 2. On the Calibration page, do the following: a. In the Standard Type column, select Internal. b. In the ISTD column, select the compound that you want to use as the internal standard for this compound. The application lists only compounds specified as internal standards on the Identification page. To view the internal standard peak in the Analysis mode, see “Compound Details” on page 437. Figure 43. Calibration page 164 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 29. Calibration page parameters Parameter Description RT Retention time. The time after injection when the compound elutes. The total time that the compound is retained on the column. Compound The compound name. Compound Type Displays the compound type as a Target Compound or Internal Standard. Standard Type Specifies Internal, External, or Estimated standards. Response Via The use of area or height. When you set the standard type to Estimated, this column is inactive. Curve Type Specifies Linear, Quadratic, or AverageRF curve types. When you set the standard type to Estimated, this column is inactive. Origin The origin treatment is Ignore, Include, or Force. The Origin and Weighting columns are available only when you use Linear or Quadratic curve types. When you set the standard type to Estimated, this column is inactive. Weighting Specifies the weighting as Equal, 1/X, 1/X^2, 1/Y, or 1/Y^2. When you set the standard type to Estimated, this column is inactive. Units The units to be displayed with the calculated values. ISTD The internal standard (ISTD) for a target compound or surrogate. The list displays all compounds with the compound type of Internal Standard. This column is available only when you set the standard type to Internal. Amount The amount of the internal standard for ISTD compounds. When you set the standard type to Estimated, this column is inactive. Linked Compound This column is available only when the standard type is set to Estimated. The list of available compounds to be linked does not include any compounds whose standard type is set to Estimated. Estimation Method This column is unavailable for editing when the standard type is set to Estimated. • When the compound type for the associated linked compound is Target Compound, the estimation method is automatically set to Ext Curve. • When the compound type for the associated linked compound is Internal Standard, the estimation method is automatically set to Ratio. Shortcut menu Thermo Scientific The Calibration page uses a right-click shortcut menu. See “Using the Shortcut Menu Commands” on page 172. TraceFinder User Guide 165 4 Using the Method Development Mode Working with Master Methods Calibration Levels On the Calibration levels page (see “Calibration Levels page” on page 167) for a master method, you can define the standards for calibration. You can edit calibration levels and concentrations for master methods only. The contents of this page are read-only when you are editing a local method. For detailed descriptions of all the features on the Calibration Levels page, see “Calibration levels page parameters” on page 167. To specify calibration levels and concentrations 1. Select the compound whose calibration levels and concentrations you want to define. 2. In the Manage Calibration Levels area, type a value for the first calibration level. The application adds a new, empty calibration level row beneath the edited row. 3. Continue adding calibration levels. When you finish adding calibration levels, you can specify the concentrations for each compound at each level. 4. To enter the concentrations to the table, do the following: a. Select the first calibration level table cell. b. Click the cell again to make it editable. c. Type a concentration value. 5. Repeat Step 4 for all calibration levels associated with the first compound. 6. To specify the same concentration values for all compounds, select the value that you want to copy, right-click, and choose Copy Down from the shortcut menu. 166 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Figure 44. Calibration Levels page Table 30. Calibration levels page parameters Parameter Description RT Retention time. The time after injection when the compound elutes. The total time that the compound is retained on the column. Compound The compound name. Cal1-Caln User-defined calibration levels for the compound. Manage Calibration Levels Defines values for each of the calibration level values for the selected compound. Shortcut menu The Calibration Levels page uses a right-click shortcut menu. See “Using the Shortcut Menu Commands” on page 172. QC Levels Use the QC levels page for a master method to define the standards for QC levels. See “QC Levels page” on page 169. You can edit QC levels for master methods only. The contents of this page are read-only when you are editing a local method. For detailed descriptions of all the features on the QC Levels page, see “QC levels page parameters” on page 169. To specify QC levels and concentrations 1. Select the compound whose QC levels, percentage test values, and concentrations that you want to define. Thermo Scientific TraceFinder User Guide 167 4 Using the Method Development Mode Working with Master Methods 2. In the QC Levels area, type a name for the first QC level. The TraceFinder application adds a new, empty QC level row beneath the edited row. 3. Type a value for the % Test. The % Test is the acceptable difference (as a percentage) between the known amount and the calculated (measured) amount of each QC level. 4. Continue adding QC levels and values for the percentage test. When you finish adding QC levels, you can specify the concentrations for each level for each compound. 5. To enter the concentration values to the table, do the following: a. Select the first QC level table cell. b. Click the cell again to make it editable. c. Type a concentration value. 6. Repeat Step 5 for all QC levels associated with the first compound. 7. To specify the same concentration values for all compounds, select the value that you want to copy, right-click, and choose Copy Down from the shortcut menu. 168 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Figure 45. QC Levels page Table 31. QC levels page parameters Parameter Description RT Retention time. The time after injection when the compound elutes. The total time that the compound is retained on the column. Compound The compound name. QC1–QCn User-defined quality control levels for the compound. QC levels Level User-defined quality control level names. % Test A value for the acceptable difference (as a percentage) between the known amount and calculated (measured) amount of each QC level. Shortcut menu Thermo Scientific The QC Levels page uses a right-click shortcut menu. See “Using the Shortcut Menu Commands” on page 172. TraceFinder User Guide 169 4 Using the Method Development Mode Working with Master Methods Real Time Viewer Use the Real Time Viewer page to specify which traces display in the Real Time Status pane when you perform acquisition in the Acquisition mode or when you acquire a development batch in the Method Development mode. See “Real Time Status Pane” on page 323. Figure 46. Real Time Viewer page Table 32. Real Time Viewer page parameters (Sheet 1 of 2) Parameter Description Show Quan Peaks Only Displays only quantitative peaks in the compounds list. Quantitative peaks are indicated with a black dot in the Quan Peak column. Displayable Traces Quan Peak Dots indicate quantitative peak traces. Unmarked traces indicate confirming ion peaks. Compound Name Names of all compounds in the method. Trace Lists the simple mass or precursor mass for all traces—both quantitative peak and confirming ion peak—for each compound. 170 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 32. Real Time Viewer page parameters (Sheet 2 of 2) Parameter Description Moves the selected trace to the Traces to Display in Real Time Viewer pane. Moves the selected trace to the Displayable Traces pane. Moves all traces to the Displayable Traces pane. To move multiple traces to the Traces to Display... pane, hold down the SHIFT key, select multiple traces, and then click . Traces to Display in Real Time Viewer (n/25) List the traces to be displayed and the display order used in the real-time display in the Acquisition mode. See “Real-Time Trace Display” on page 335. Maximum number of traces is 25. Move to Top Moves the selected trace to the top of the Traces to Display... list and the second position in the real-time display. The TIC is always the first position in the real-time display in the Acquisition mode. Move Up Moves the selected trace up one position in the list. Move Down Moves the selected trace down one position in the list. Move to Bottom Moves the selected trace to the bottom of the list. Thermo Scientific TraceFinder User Guide 171 4 Using the Method Development Mode Working with Master Methods Using the Shortcut Menu Commands Each page on the Compounds page (except the Acquisition List and Real Time Viewer pages) uses right-click shortcut menu commands to display or hide the retention column, remove compounds from the method, copy and paste data, or save the compound list to a .csv file. Table 33. Compounds page shortcut menu commands (Sheet 1 of 2) Command Description Copy Down Copies the value in the selected row to all rows below it. This command is available only when you have selected a value that can be copied down. See Appendix B, “Using Copy Down and Fill Down.” Display Retention Time Displays or hides the RT column in the compound list. Column Delete Compound From Removes the selected compound from the current master Method method. 172 TraceFinder User Guide Copy Copies the data in the selected rows or columns to the Clipboard. Use this command to copy compound information to another application, such as an Excel spreadsheet. You cannot paste this data back into the method development compound list. Copy With Headers Copies the data in the selected rows or columns and the associated column headers to the Clipboard. Use this command to copy sample information to another application, such as an Excel spreadsheet. You cannot paste this data back into the method development compound list. Paste Pastes a single column of copied data from another application, such as an Excel spreadsheet, into the selected column. The pasted data must be valid data for the selected column. Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 33. Compounds page shortcut menu commands (Sheet 2 of 2) Command Description Undo Last Paste Removes the last pasted item in the method development compound list. Export to CSV File Opens the Save As dialog box where you can save the current compound list to a CSV file. Sort by Compound Name Sorts the compounds alphabetically from A to Z. Sort by Retention Time Sorts the compounds from shortest retention time to longest retention time. Add This Compound to Adds the selected compound to the compound database. When CDB the compound already exists in the compound database, the TraceFinder application updates the compound database with the current compound information. Add All Compounds to CDB Thermo Scientific Adds all compounds in the current method to the compound database. When any of these compounds already exist in the compound database, the TraceFinder application updates the compound database with the current compound information. TraceFinder User Guide 173 4 Using the Method Development Mode Working with Master Methods Editing the QAQC Page Use the QAQC page to set limits and ranges so that the TraceFinder application can review the data and results as an aid to final approval. To open the QAQC page Click QAQC in the Method View navigation pane. Available only when you activate Intelligent Sequencing in the Application Configuration mode. From the QAQC page of the Method View, you can access these additional pages: • Limits • Calibration • QC Check • Negative • ISTD • Solvent Blank • Hydrolysis 174 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Limits Use the Limits page to define levels of review for quantified results. Quantified results appear on printed and electronic reports. You can also define when a quantified value is reported instead of reporting less than a particular limit. Figure 47. Limits page Table 34. Limits page parameters Parameter Description RT Retention time. The time after injection when the compound elutes. The total time that the compound is retained on the column. Compound The compound name. LOD (Detection Limit) Limit of detection. The lowest amount that can be detected. Usually derived from a method detection limit (mdl) study. LOQ (Quantitation Limit) Limit of quantitation. The lowest amount that can be confidently and accurately quantitated. This is usually the lowest calibration amount. Cutoff Also called limit of reporting (LOR) in some industries. This is the lowest amount that can be reported, as determined by each laboratory’s standard operating practices. ULOL (Linearity Limit) Upper limit of linearity. This is usually the highest calibrator amount. Carryover Limit The highest amount of a substance that does not leave a residual amount in the instrument. If a substance has a carryover limit of 5, amounts higher than 5 usually dirty the instrument and leave residue behind, tainting the following sample. A carryover limit of less than 5 does not leave any residual amounts of the substance. Thermo Scientific TraceFinder User Guide 175 4 Using the Method Development Mode Working with Master Methods Calibration Use the Calibration page to define acceptable criteria for initial calibration. The TraceFinder application makes the evaluation by comparing the initial calibration results for each compound found in the sample to the values defined on this page. On the Calibration report, the application flags the calculated values for internal standard compounds that exceed these limits. Figure 48. Calibration page Table 35. Calibration page parameters Parameter Description RT Retention time. The time after injection when the compound elutes. The total time that the compound is retained on the column. Compound The compound name. R^2 Threshold The minimum correlation coefficient (r2) for an acceptable calibration (when in linear or quadratic mode). Max RSD (%) The maximum relative standard deviation (RSD) for an acceptable calibration (when in average RF mode). Min RF The minimum average response factor (RF) for an acceptable calibration (when in average RF mode). Max Amt Diff (%) The maximum deviation between the calculated and theoretical concentrations of the calibration curve data points (when in linear or quadratic mode). CV Test (%) Coefficient of Variance test. The coefficient of variance percentage is the standard deviation of the multiple samples of one level, multiplied by 100, and then divided by the average of the multiple samples of that level. This calculation is based on the areas of the peaks. 176 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods QC Check Use the QC Check page to review the calibration on an ongoing basis. The TraceFinder application makes the evaluation by comparing the quality check standard results for each compound in the sample to the initial calibration using values defined on this page. On the Quality Control report, the TraceFinder application flags the calculated values for internal standard compounds that exceed these limits. For linear and quadratic modes, the maximum difference for the calculated concentration in the QC sample versus the theoretical value is set on the QC Levels page of the Compounds page. Figure 49. QC Check page Table 36. QC Check page parameters Thermo Scientific Parameter Description RT Retention time. The time after injection when the compound elutes. The total time that the compound is retained on the column. Compound The compound name. Max RF Diff (%) The maximum deviation between the response factor (RF) of the QC sample and the average response factor from the calibration (when in average RF mode). Min RF The minimum response factor for the QC sample (when in average RF mode). CV Test (%) Coefficient of Variance test. The coefficient of variance percentage is the standard deviation of the multiple samples of one level, multiplied by 100, and then divided by the average of the multiple samples of that level. This calculation is based on the areas of the peaks. TraceFinder User Guide 177 4 Using the Method Development Mode Working with Master Methods Negative Use the Negative page to define acceptable levels of target compounds in blank samples. The TraceFinder application makes the evaluation by comparing the calculated concentration for each compound in the sample to the maximum concentration defined on this page. You can enter the maximum concentration as a percentage of a flag value or as a specified value. For detailed descriptions of all the features on the Negative page, see Negative page parameters. On the Negative report, the application flags the calculated values for target compounds that exceed these limits. To specify the maximum concentration as a percentage 1. From the Method column list, select one of the following methods: • % of LOD • % of LOQ • % of LOR 2. In the Percentage column, type a percentage value. To specify the maximum concentration 1. From the Method column list, select Concentration. 2. In the Max Conc column, type an absolute value. Figure 50. Negative page Table 37. Negative page parameters Parameter Description RT Retention time. The time after injection when the compound elutes. The total time that the compound is retained on the column. Compound The compound name. Method The evaluation process used for comparing the calculated concentration. You can specify no maximum, a specific concentration, or a percentage of the LOR, LOD, or LOQ. Percentage The percentage of the LOR, LOD, or LOQ if you are using the percentage approach. Max Conc The maximum concentration if you are using an absolute value. 178 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods ISTD Use the ISTD page to review the response and retention time of internal standards (when available). The TraceFinder application makes the evaluation by comparing the area and retention time results for each internal standard compound in the sample to a specified range. If all of your target compounds are set to external calibration mode or if you have not identified any compounds as internal standards, this page does not show any values. Figure 51. ISTD page Table 38. ISTD page parameters Parameter Description RT Retention time. The time after injection when the compound elutes. The total time that the compound is retained on the column. Compound The compound name. Min Recovery (%) The minimum and maximum percent recoveries for the internal standards to define an acceptable range. For check standards, the TraceFinder application compares the response of each internal standard in each sample to a range around the average of the responses of that compound in all of the calibration standards. For all other samples, the application calculates the comparison range around the check standard responses if a check standard is available in the batch. If no check standard is available, the application tests against the initial calibration. Max Recovery (%) Min RT (–min) Max RT (+min) CV Test (%) Thermo Scientific The minimum and maximum drift (in minutes) for the internal standards to define an acceptable range. For check standards, the TraceFinder application compares the retention time of each internal standard in each sample to a range around the average of the retention times of that compound in all of the calibration standards. For all other samples, the application calculates the comparison range around the check standard retention times if a check standard is available in the batch. If no check standard is available, the application tests against the initial calibration. Coefficient of Variance test. The coefficient of variance percentage is the standard deviation of the multiple samples of one level, multiplied by 100, and then divided by the average of the multiple samples of that level. This calculation is based on the areas of the peaks. TraceFinder User Guide 179 4 Using the Method Development Mode Working with Master Methods Solvent Blank Use the Solvent Blank page to view or edit QC values for solvent reporting. The application makes the evaluation by comparing the calculated response for each compound in the sample to the maximum response defined on this page. On the Solvent Blank report, the TraceFinder application flags the calculated values for target compounds that exceed these limits. Figure 52. Solvent Blank page Table 39. Solvent Blank page parameters 180 TraceFinder User Guide Parameter Description RT Retention time. The time after injection when the compound elutes. The total time that the compound is retained on the column. Compound The compound name. Method The evaluation process to use as a response for the quantitation ion only (Quan Ion RT) or as a summed response for the quantitation ion and any confirming ions (All Ion RT). To deactivate the solvent blank test for a specific compound, select None. Upper Limit Specifies an upper limit for each compound in the sample when you select an evaluation process. These values are not concentrations; they are raw response values. Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Hydrolysis Use the Hydrolysis page to specify the hydrolysis checks for compounds. Figure 53. Hydrolysis page Table 40. Hydrolysis page parameters (Sheet 1 of 2) Parameter Description RT Retention time. The time after injection at which the compound elutes. The total time that the compound is retained on the column. Compound The compound name. Method The evaluation process to use, specified as either a lower threshold or a range. To deactivate the hydrolysis test for a specific compound, select None. Threshold/Lower Limit For compounds using the Threshold method, this specifies the threshold value for the hydrolysis test. Values below this threshold are flagged in the Hydrolysis report. For compounds using the Range method, this specifies the lower limit of the range. Upper Limit For compounds using the Range method, this parameter specifies the upper limit of the range. Shortcut menu Copy Down Copies the selected column value to all rows in that column. For detailed instructions about using the Copy Down command, see Appendix B, “Using Copy Down and Fill Down.” Display Retention Time Column Displays or hides the RT column in the compound list. Delete Compound From Removes the selected compound from the current master method. Method Copy Copies the data in the selected rows or columns to the Clipboard. Use this command to copy compound information to another application, such as an Excel spreadsheet. You cannot paste this data back into the method development compound list. Copy With Headers Copies the data in the selected rows or columns and the associated column headers to the Clipboard. Use this command to copy compound information to another application, such as an Excel spreadsheet. Thermo Scientific TraceFinder User Guide 181 4 Using the Method Development Mode Working with Master Methods Table 40. Hydrolysis page parameters (Sheet 2 of 2) Parameter Description Paste Pastes a single column of copied data from another application, such as an Excel spreadsheet, into the selected column. The pasted data must be valid data for the selected column. Undo Last Paste Removes the last pasted item in the method development compound list. Export to CSV File Opens the Save As dialog box where you can save the current compound list to a CSV file. 182 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Editing the Groups Page Use the Groups page of the Method View (see ““Groups page” on page 184”) to organize compounds into functional or logical groups. You can use these groups for creating a subset of target compounds. For detailed descriptions of all the features on the Groups page, see “Groups page parameters.” For quantitative processing, the TraceFinder application processes all compounds in the method and stores the complete result set, but only those in the selected group are visible in the Acquisition mode. Limiting the displayed compounds to those in the selected group can be useful when working with a master method containing a large list of compounds, only some of which are required for analysis in certain samples. In that case, the application requires only a single method and can reduce the results. To display only those compounds to be used in quantitative processing, select Quan Compounds from the Show list. You can create multiple groups and include the same compound in more than one group. To open the Groups page Click Groups in the Method View navigation pane. Available only when you activate Intelligent Sequencing in the Application Configuration mode. To create a group 1. At the bottom of the Groups area, click Add Group. The Add a New Group dialog box opens. 2. Type a name for the new group and click OK. The new group appears in the Groups area. 3. Drag a compound from the Compounds area onto a group name (as if you were moving files into a folder). Thermo Scientific TraceFinder User Guide 183 4 Using the Method Development Mode Working with Master Methods 4. To remove all the compounds from a group, rename the group, or delete it, right-click the group name and choose from the shortcut menu. 5. To remove a single compound, right-click the compound name in the group and choose Remove from Group from the shortcut menu. Figure 54. Groups page Table 41. Groups page parameters Parameter Description Compounds Lists all available compounds. Groups Lists all available groups. Add Group Opens the Add a New Group dialog box where you can create a new group. Shortcut menu 184 TraceFinder User Guide Empty Group Removes all compounds from the selected group. Rename Group Changes the name of the selected group. Delete Group Removes the selected group and all the compounds in it. Remove From Group Removes the selected compound from its group. Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Editing the Intelligent Sequencing Page Use the Intelligent Sequencing page to specify the actions you want the application to take when there are acquisition failures with each sample type. The Intelligent Sequencing page is available only when you activate Intelligent Sequencing in the Application Configuration mode. See “Intelligent Sequencing” on page 66. To open the Intelligent Sequencing page Click Intel Seq in the Method View navigation pane To specify actions for sample acquisition failures 1. In the Sample Types list, select a sample type. Each sample type has a specific set of failure flags. See “Sample-Specific Failure Flags” on page 188. 2. For each failure flag, select a failure action. The failure action choices are the same for each failure flag except flags for Solvent or Negative sample types. The Solvent and Negative sample types do not have Auto Sample or Auto Sample and Reinject failure actions. Thermo Scientific TraceFinder User Guide 185 4 Using the Method Development Mode Working with Master Methods Each Failure Action requires one or more of the following values: • Sample Type • Priority • Max Action Count • Failure Continuation For a detailed description of each of these parameters, see “Actions” on page 187. 3. Select a sample type to use for the failure action. This value is available only for Auto Sample and Auto Sample and Reinject failure actions. When you create your samples list on the Auto Samples page, you must include at least one sample with this sample type for the autosampler to use when it encounters this error condition. See “Auto Samples Page” on page 376. 4. In the Priority column, type a priority value for this action. The priority value can be any positive or negative integer. • The application performs the failure action for the highest priority failure it encounters and ignores all others. • When you assign the same priority to two or more failures, the application performs the failure action for the first failure it encounters and ignores all others. 5. In the Max Action Count column, type a value for the maximum number of times the application should repeat a sample. 6. In the Failure Continuation column, do one of the following: • Select the check box to skip this sample and continue to the next sample when this sample exceeds the Max Action Count value. • Clear the check box to stop the batch when this sample exceeds the Max Action Count value. 186 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Actions Use the Actions pane to specify what action the application takes when it encounters a submission failure for the type of failure flag associated with each sample type. Table 42. Actions parameters (Sheet 1 of 2) Parameter Description Flag Flag (error) types specific to each sample type. See Sample-Specific Failure Flags. Each flag type has a set of user-specified actions that the application follows when it encounters this error. Failure Action In the event of a failed sample, the application does one of the following: • Continue: Continues to the next sample in the batch. • Stop: Stops the batch. • Auto Sample: Injects the sample type specified for the Auto Sample Type parameter and continues to the next sample. • Reinject: Reinjects the current sample by inserting a “reinject” sample in the batch. • Auto Sample and Reinject: Injects the sample type specified for the Auto Sample Type parameter and then reinjects the failed sample. Sample Type Specifies either a Solvent or Negative sample type to use for the auto sample injection. Default: Solvent Priority The priority value can be any positive or negative integer. When two or more failures have the same priority, the application performs the failure action for the first failure it encounters and ignores all others. The application performs the failure action for the highest priority failure and ignores all others. Thermo Scientific TraceFinder User Guide 187 4 Using the Method Development Mode Working with Master Methods Table 42. Actions parameters (Sheet 2 of 2) Parameter Description Max Action Count Specifies the maximum number of times the application should repeat a sample before it continues to the next sample or stops the sequence, as determined by the value in the Failure Continuation parameter. Default: 1 Failure Continuation When this check box is selected, samples that exceed the value specified for the Max Action Count parameter cause the application to skip the sample and continue to the next sample. Default: Selected When this check box is cleared, samples that exceed the value specified for the Max Action Count parameter cause the application to stop the batch. Sample-Specific Failure Flags Each sample type has a specific set of failure flags. Sample Type 188 TraceFinder User Guide Flag Negative • Negative Calibrator • Cal Out of Range • Ion Ratio Failure • Carryover QC • Ion Ratio Failure • Out of Range Hydrolysis • Ion Ratio Failure • Hydrolysis Solvent • Solvent Flag Unextracted • Ion Ratio Failure Specimen • Ion Ratio Failure • Carryover Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Editing the Reports Page Use the Reports page to specify how you want to save or print your reports. For detailed descriptions of the features on the Reports page, see “Reports page parameters” on page 190. For the quantitation report types, you can modify quantitation limits flags, user interface options, and quantitation flag options on the Quan Report Settings page. For ToxID report types, you can modify default report options, semi-quantitative results options, ion ratio calculation methods, the exact mass window, and Exactive™ options on the Target Screening Export Settings page. This section includes instructions for the following tasks: • Specifying Report Formats • Specifying Quan Report Settings • Specifying Target Screening Export Settings (for ToxID Reports) Specifying Report Formats • For each Standard report type, you can create a hardcopy printout, a PDF file, or an XML file. • For each Custom report type, you can create a hardcopy printout or an Excel Macro-Enabled Workbook (.xlsm) file. • For each ToxID report type, you can create a hardcopy printout or a PDF file. To open the Reports page Click Reports in the Method View navigation pane. Available only when you activate Intelligent Sequencing in the Application Configuration mode. The Reports page opens with a list of all configured reports. To configure which reports are available when you create a master method or which reports create a batch-level report, see “Specifying the Reports Configuration” on page 39. Thermo Scientific TraceFinder User Guide 189 4 Using the Method Development Mode Working with Master Methods To specify report types and output formats 1. To edit the Report Title, double-click the name and type your new custom title. The TraceFinder application uses this title for all reports that use this master method. You cannot edit the Report Title from other report views. 2. To specify the type of report output to create for each report type, select the check box in the appropriate column. 3. To duplicate an output type for all reports, click the cell to select it, and then right-click and choose Copy Down from the shortcut menu. All check boxes in the column below the selected cell duplicate the selected or cleared state of the selected cell. This action applies only to reports where this output format is available. By default, all report types are cleared. Figure 55. Reports page Table 43. Reports page parameters Parameter Description Example Opens a PDF that displays an example of the report type. Report Name The name of a report. Report Title The user-defined description to be used on a report. Report Type The type of report: Standard, Custom, or ToxID. Print Sends reports to the printer. Available for all report types. Create PDF Saves reports as PDF files. Available only for Standard and ToxID report types. Create XML Exports reports in XML format. Available only for Standard report types. Create XLSM Exports reports in Excel Macro-Enabled Workbook (.xlsm) format. Available only for Custom report types. Batch Level Rather than creating separate reports for each sample, the application uses a composite of the data from all the appropriate samples to create a single report for the entire batch. Batch-level reports are prepended with a B to differentiate them. You cannot select this option from the Reports page. You must select the Batch Level option for the report in the report configuration. See “Specifying the Reports Configuration” on page 39. 190 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Specifying Quan Report Settings Use the options on the Quan Report Settings page to choose parameters for flagging values and displaying information in standard report types. Follow these procedures: • To specify quantitation limits • To specify user interface options • To specify quantitation flag options • To specify the concentration calculation method • To track the use of the tune file To specify quantitation limits 1. To report the calculated concentration at all times or only when the quantified value exceeds LOD, LOQ, or LOR, choose the appropriate value from the Report Concentration list. For a description of concentration limits, see “Editing the QAQC Page” on page 174. 2. To select the number of decimal places to report for calculated concentrations, set the value in the Decimal Places to be Reported box. 3. To include a chromatogram of the sample in the Quantitation Report, select the Show Chromatogram on Quantitation Report check box. 4. To display only valid compounds, select the Display Compounds Above Set Limit check box. Thermo Scientific TraceFinder User Guide 191 4 Using the Method Development Mode Working with Master Methods To specify user interface options 1. To shade a compound row on any of the reports if a value fails one of the criteria used for evaluation, select the Shade Row when Sample is Outside of Evaluation Criteria check box. 2. To separate the ion overlay pane from the confirming ion plots, select the Separate Ion Overlay Display check box. 3. To use an alternate format for the Calibration Report designed to print more concisely and limit the report to a maximum of seven calibration standards, select the Use Alternate Calibration Report Format check box. 4. To display flags and a legend on high density reports, select the Display Quan Flags and Legend check box. To specify quantitation flag options Select the values that you want to display in the report. Values are above or below the limits defined on the Quan page. These flags appear on a variety of reports and are defined in “Quan Report Settings page parameters” on page 194. 192 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods To specify the concentration calculation method In the Calculate Concentration As box, select Rounded or Truncated. • Rounded: Rounds the calculated amount to the nearest value using the number of decimal places specified in the Quan Limits Flags area. • Truncated: Truncates the calculated amount at the number of decimal places specified in the Quan Limits Flags area. See “To specify quantitation limits” on page 191. To track the use of the tune file 1. Select the Enable Tune Time Tracking check box. This option tracks the number of hours between the last instrument tune and each sample acquisition. 2. In the Tune File Lifetime box, enter the number of hours that you want to allow between the last instrument tune and a sample acquisition. Any sample acquired outside this maximum allowable time is flagged on the Batch report. Thermo Scientific TraceFinder User Guide 193 4 Using the Method Development Mode Working with Master Methods Figure 56. Quan Report Settings page Table 44. Quan Report Settings page parameters (Sheet 1 of 2) Parameter Description Quan Limits Flags Report Concentration Reports the concentration at all times or only when the quantified value exceeds either the limit of detection (LOD), the limit of quantitation (LOQ), or the limit of reporting (LOR). Report concentration: Always, >LOD, >LOQ, or >LOR. Decimal Places to be Reported Number of decimal places to be included in the report. Maximum value is 6. Show Chromatogram on Quantitation Report Displays a chromatogram (TIC trace) of the sample on the quantitation report. Display Compounds Above Set Limit Prints reports for only the compounds that are found in a sample. If a compound is above the specified Quan Flag Options limits, the TraceFinder application reports the compound. This prevents generating “empty” reports for the compounds that are not found. User Interface Options Shade Row When Sample is Outside of Evaluation Criteria Shades a compound row on any of the reports if a value fails one of the criteria used for evaluation. Separate Ion Overlay Display Separates the ion overlay pane from the confirming ion plots in an analysis. Use Alternate Calibration Report Format Uses an alternate format for the Calibration Report that is designed to print more concisely (this report is limited to a maximum of seven calibration standards). Display Quan Flags and Legend Displays manual flags, confirming manual flags, quantitation flags, and a legend on high-density reports. 194 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 44. Quan Report Settings page parameters (Sheet 2 of 2) Parameter Description Quan Flag Options Values that are above or below limits defined on the Limits page. These flags appear on a variety of reports. Flag Values Below LOD Flags values below the limit of detection (LOD). Flag Values Below LOQ Flags values below the limit of quantitation (LOQ). Flag Values Above LOR Flags values above the limit of reporting (LOR). Flag Values Above ULOL Flags values above the upper limit of linearity (ULOL). Flag Values Above Carryover Flags values above the carryover limit. Flag Values Between LOD and LOQ Flags values between the limit of detection and the limit of quantitation known as the J flag. Calculated Amount Option Calculate Concentration As Specifies the Rounded or Truncated method for reporting concentration amounts. Tune Time Tracking Options Enable Tune Time Tracking Tracks the number of hours between the last instrument tune and each sample acquisition. Tune File Lifetime Specifies the maximum number of hours between the last instrument tune and a sample acquisition. Any sample acquired outside this maximum allowable time is flagged on the Batch report. Thermo Scientific TraceFinder User Guide 195 4 Using the Method Development Mode Working with Master Methods Specifying Target Screening Export Settings (for ToxID Reports) Use the options on the Target Screening Export Settings page to set the parameters required to produce ToxID reports. For detailed descriptions of the features on the Target Screening Export Settings page, see “Target Screening Export Settings page parameters” on page 200. The TraceFinder application uses these parameters to process a raw data file and create a report similar to a ToxID report. Note The Target Screening Export Settings page is available only when you activate the ToxID features. See “ToxID” on page 64. Follow these procedures: • To specify the default parameters • To calculate and report semi-quantitative results • To specify the ion ratio calculation method • To specify the exact mass window • To specify the Exactive parameters To specify the default parameters 1. Click the Processing Configuration File browse button and select a configuration file (.csv). 2. From the Screening Method list, select one of these compound screening methods. • (Default) Auto Detect • Based on Full MS2 scans • Based on SRM and MS2 scans • Based on MS2 and MS3 scans 196 TraceFinder User Guide Thermo Scientific 4 • • • • Using the Method Development Mode Working with Master Methods Based on MS3 scans Based on accurate mass scans Based on SRM scans Based on Exactive screening method 3. Type the name of the company to print on the report. 4. Type the name of the laboratory to print on the report. 5. Click the Company Logo browse button and select a graphic file (.jpg, .gif, or .bmp) to print on the report. 6. In the m/z Window box, enter a value for the window above and below the m/z value for the compounds. 7. In the RT Window box, enter a value for the window above and below the retention time value for the compounds. 8. In the MS2 Search Library boxes, type the names of as many as three search libraries for searching MS/MS spectra. 9. In the MS3 Search Library boxes, type the names of as many as three search libraries for searching MS3 spectra. 10. Select the Use Full MS Scan to Confirm check box if you want to confirm library search results with parent ion peak detection in the full scan. When the application does not detect a peak in the full scan, the compound is not reported as a hit. To calculate and report semi-quantitative results 1. In the Semi Quantitative area, do the following: a. Select the Report Semi-Quantitative Result check box. b. Type the measurement units. The measurement units are used only for labeling purposes. 2. Select either the Scan Intensity or the Peak Area option. • Scan Intensity: The application measures the intensity of the MS/MS peak without performing background subtraction. • Peak Area: The application measures the peak area of the reconstructed full-scan chromatogram peak of the parent ion. When you select Peak Area, the Use Full MS Scan to Confirm check box is automatically selected. Thermo Scientific TraceFinder User Guide 197 4 Using the Method Development Mode Working with Master Methods To specify the ion ratio calculation method 1. Select the Use Scan at Peak Apex or the Use Average Scan option. • Use Scan at Peak Apex: The application calculates the ion ratio based on the peak apex scan spectrum. • Use Average Scan: The application calculates the ion ratio based on the average scan spectrum over the range of the peak’s half height. The relative intensity in the configuration file must use the selected scan method. 2. In the Ion Ratio Window (%) box, type the acceptable percentage of the intensity of the qualifier ion to the quantitation ion. For example, when the Ion Ratio Window is 20% and the quantitation ion has an intensity/height of 100, the specified confirming ion/mass must have a height of at least 80 to be considered found. To specify the exact mass window Type a total window width value in parts per million for the Exact Mass Window. For example, when you expect a mass of 50 with a window of 2, the algorithm creates an XIC based on the responses of all masses from 49 to 51. To specify the Exactive parameters 1. Type values for Adduct 1, Adduct 2, and Adduct 3. These values identify the adducts listed in and applied throughout the configuration file. Adducts are polarity sensitive. For negative ionization, enter negative adduct values. These values default to H+, NH4+, and Na+, respectively. To add or remove adducts from the default lists, see “Specifying Adducts Configuration” on page 60. 198 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods 2. To search the entire raw data file for the specified peak, do the following: a. Select the No Specified Retention Time check box. b. Select either the First Peak or the Highest Peak option. When the search finds more than one m/z match in the raw data file, the application uses the specified peak for processing. 3. Select the Report All Compounds Listed in Configuration File check box to report all compounds in the configuration file whether or not matches are found for them. The default reports on only those compounds where matches are found in the raw data file. This option applies to the Exactive experiment only. Thermo Scientific TraceFinder User Guide 199 4 Using the Method Development Mode Working with Master Methods Figure 57. Target Screening Export Settings page Table 45. Target Screening Export Settings page parameters (Sheet 1 of 2) Parameter Description Processing Configuration File Specifies a configuration file (.csv). Screening Method Specifies one of the following screening methods: • (Default) Auto Detect • Based on Full MS2 scans • Based on SRM and MS2 scans • Based on MS2 and MS3 scans • Based on MS3 scans • Based on accurate mass scans • Based on SRM scans • Based on Exactive screening method Note Using the Auto Detect method, the ToxID application can identify the screening experiment implemented in the acquired data file. Company Name Specifies the name of the company to print on the report. Laboratory Name Specifies the name of the laboratory to print on the report. Company Logo Specifies a graphic file (.jpg, .gif, or .bmp) to print on the report. m/z Window (mu) Specifies a value for the window above and below the m/z value for the compounds. RT Window (min) Specifies a value for the window above and below the retention time value for the compounds. MS2 Search Library Specifies the names of as many as three search libraries for searching MS/MS spectra. MS3 Search Library Specifies the names of as many as three search libraries for searching MS3 spectra. 200 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 45. Target Screening Export Settings page parameters (Sheet 2 of 2) Parameter Description Use Full MS Scan to Confirm Specifies that the application confirms library search results with parent ion peak detection in the full scan. When the application does not detect a peak in the full scan, the compound is not reported as a hit. Semi Quantitative Report SemiQuantitative Result Includes the semi-quantitative results in the target screening reports. Measurement Unit Units used for labeling purposes. Calculation Based On Specifies one of the following calculation methods: • Scan Intensity: Specifies that the application measures the intensity of the MS/MS peak without performing background subtraction. • Peak Area: Specifies that the application measures the peak area of the reconstructed full-scan chromatogram peak of the parent ion. When you select Peak Area, the Use Full MS Scan to Confirm check box is automatically selected. Ion Ratio Calculation Method (In SRM Experiment) Use Scan at Peak Apex Specifies that the application calculates the ion ratio based on the peak apex scan spectrum. Use Average Scan Specifies that the application calculates the ion ratio based on the average scan spectrum over the range of the peak’s half height. The relative intensity in the configuration file must use the selected scan method. Ion Ratio Window(%) Specifies the acceptable ion ratio range. Accurate Mass Experiment Exact Mass Window Specifies a value in parts per million for the accurate mass experiment. Exactive Adduct 1–n Specifies the adducts listed in and applied throughout the configuration file. Adducts represent a gain or loss to the neutral mass. For negative ionization, enter negative adduct values. Defaults: Adduct 1: H+, Adduct 2: NH4+, and Adduct 3: Na+ No Specified Retention Specifies either First Peak or Highest Peak to use for processing when the search finds more Time than one m/z match in the raw data file. Report All Compounds Specifies that in an Exactive experiment, the application reports all compounds in the Listed in Configuration configuration file whether or not matches are found for them. File Default: Reports only those compounds where matches are found in the raw data file. Thermo Scientific TraceFinder User Guide 201 4 Using the Method Development Mode Working with Master Methods Editing a Target Screening Master Method You can open a target screening master method to specify method instructions, reporting options, peak filter settings, screening databases, identification and confirmation settings, and peak detection parameters. This section includes instructions for the following tasks: • Opening a Target Screening Master Method • Editing the General Page • Editing the Reports Page • Editing the Screening Page • Editing the Peak Detection Page Opening a Target Screening Master Method For target screening methods, you select which databases to use in the Compound Databases area of the Target Screening Settings pane. The available databases are the compound databases stored in C:\Thermo\TraceFinder\3.0\Forensic\Databases\filename.cdb The target screening method uses only the target list of compounds in the selected compound databases to identify the compounds in the samples. To open a saved master method 1. Click Method Development from the navigation pane. 2. Choose File > Open > Master Method from the main menu. The Open Master Method dialog box opens, displaying all available methods. Tip You can also open one of your most recently used master method files. Choose Files > Recent Files > MethodName. 202 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods 3. Select a target screening master method and click Open. The General page for the selected method opens in the Method View. For detailed descriptions of all the features on the General page, see “General page parameters” on page 206. The Method View for a target screening method includes General, Reports, Screening, and Peak Detection pages. Editing the General Page Use the General page to define basic information about the master method. To edit the parameters on the General page 1. Click General in the Method View navigation pane. The General page for the screening method opens. See “General page for a screening method” on page 206. 2. In the Lab Name box, type the name to be displayed on the top of each printed, saved, or exported report. The default name is Default Laboratory. 3. In the Assay Type box, type the assay type to be targeted by the method. 4. From the Injection Volume box, select the injection volume (in μL) to be used for sample injection. Range: 0.1 to 2000 μL Use the up/down arrows to change the volume in increments/decrements of 1 μL, or use the keyboard to enter non-integer injection volumes. IMPORTANT The TraceFinder application uses this injection volume in the master method, not the injection volume in the instrument method. 5. From the Mass Precision box, select the number of decimal places to be used in reports and in peak and spectrum displays. Valid values: Integers from 2 to 6, inclusive Thermo Scientific TraceFinder User Guide 203 4 Using the Method Development Mode Working with Master Methods 6. From the Instrument Method list, select an instrument method. 7. To edit the instrument method, click Edit. The Thermo Xcalibur Instrument Setup dialog box opens. This example of an instrument setup shows multiple configured instruments. 8. Edit the values on the instrument page for your instrument. 9. From the main menu in the Thermo Xcalibur Instrument Setup dialog box, choose File > Save and then choose File > Exit. The TraceFinder application returns you to the General page of the Method View. 10. Select the units of measure that you want to use. • (Default) MMU (millimass units): A static calculation to the extracted mass. • PPM (parts per million): A variable calculation dependent on the actual mass. The smaller the mass, the narrower the tolerance range. The larger the mass, the wider the tolerance range. 204 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods 11. From the Mass Tolerance box, select the number of millimass units or parts per million to use as the m/z ± tolerance value. Use the up/down arrows to change the volume in increments/decrements of 1 unit, or use the keyboard to enter non-integer tolerances. The application applies this mass tolerance to the extracted chromatograms. 12. From the Library Search Type list, select the type of library to use for target screening. • NIST: Uses the NIST library that you installed with the TraceFinder application. See “Installing the NIST and QED Libraries” on page 16. Note Because the NIST library is large, using this library can slow sample processing. • Library Manager: Uses the library that you specified in the Application Configuration mode. See “Screening Library” on page 68. The application searches the library to identify or confirm the sample compound, matches the fragment ion spectrum in the library to the compound’s ion spectrum, and returns the highest score (best match). 13. To display all compounds specified in the method, including those that are not found in the sample, select the Show All Compounds check box. 14. Type in the Notes box, or paste text from another application using CTRL+V. You can add a note to explain what makes this method unique. Thermo Scientific TraceFinder User Guide 205 4 Using the Method Development Mode Working with Master Methods Figure 58. General page for a screening method Table 46. General page parameters (Sheet 1 of 2) Parameter Description Lab Name The laboratory name to be displayed on the top of each printed, saved, or exported report. Default: Default Laboratory To specify this default laboratory name, see “Specifying Application Defaults” on page 44. Assay Type The name for the analysis type to be targeted by the method. The assay type associates the method with the analysis of a compound or specific class of compounds (for example, you might use an assay type of PAH for the analysis of Polynuclear Aromatic Hydrocarbons). Injection Volume The system uses the injection volume (in μL) for sample injection. For a more detailed explanation, refer to the documentation for the autosampler. The injection volume in the master method overrides the injection volume in the instrument method. The injection volume in the batch overrides the injection volume in the master method. Range: 0.1 to 2000 μL Mass Precision Number of decimal places used in reports and in peak and spectrum displays. Valid values: Integers from 2 to 6, inclusive. Instrument Method Instrument method used for acquiring samples. 206 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 46. General page parameters (Sheet 2 of 2) Parameter Description Edit Opens the Thermo Xcalibur Instrument Setup dialog box where you can edit the instrument method. Update Choose one of the following: Send to Xcalibur Method: Overwrites the Xcalibur method with the current instrument method. Get From Xcalibur Method: Overwrites the current instrument method with the Xcalibur method. Mass Tolerance Upper limit of MMU or PPM. Default: 500 Range: 0.1 through 50 000 • (Default) MMU (millimass units): A static calculation to the extracted mass. • PPM (parts per million): A variable calculation dependent on the actual mass. The smaller the mass, the narrower the tolerance range. The larger the mass, the wider the tolerance range. Library Search Type Specifies the type of library to use for target screening. • NIST: Uses the NIST library that you installed with the TraceFinder application. See “Installing the NIST and QED Libraries” on page 16. • Library Manager: Uses the library that you specified in the Application Configuration mode. See “Screening Library” on page 68. Show All Compounds Display all compounds specified in the method, including those that are not found in the sample. Notes Optional notes about the method. Thermo Scientific TraceFinder User Guide 207 4 Using the Method Development Mode Working with Master Methods Editing the Reports Page Use the Reports page to specify the reports and report output formats that you want to create for the method. You can also specify options for exporting compounds to Excel spreadsheets or CSV files. Follow these procedures: • To open the Reports page • To specify report types and output formats • To specify options for exporting compounds to an Excel worksheet • To specify options for exporting compounds to a CSV file • To specify report options To open the Reports page Click Reports in the Method View navigation pane. The Reports page for the screening method opens. See “Reports page for a target screening method” on page 210. The reports list displays only the Target Screening report types. For information about configuring the Target Screening Summary Report or Target Screening High Density Sample Report when you create a target screening method, see “Specifying the Reports Configuration” on page 39. To specify report types and output formats 1. To edit the Report Title, double-click the name and type your new title. The TraceFinder application uses this title for all reports that use this master method. You cannot edit the Report Title from other report views. 2. To specify the type of report output to create for each report type, select the check box in the appropriate column. 3. To duplicate an output type for all reports, click the cell to select it, and then right-click and choose Copy Down from the shortcut menu. All check boxes in the column below the selected cell duplicate the selected or cleared state of the selected cell. This action applies only to reports where this output format is available. By default, all report types are cleared. 208 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods To specify options for exporting compounds to an Excel worksheet 1. In the Excel Export Settings area on the Target Screening Export/Report Settings page, select one of the following worksheet formats: Multiple Worksheets: Writes one sample to each Excel worksheet tab. Single Worksheet: Write all samples to a single Excel worksheet tab. The application uses the selected worksheet format when you export a batch compound list to an Excel spreadsheet file. For instructions about exporting a compound list from the Analysis mode, see “To export compounds to an Excel spreadsheet” on page 459. 2. In the Peaks area, select the type of peaks to export: All Peaks, Confirmed Only, or Identified and Confirmed. For detailed descriptions of the criteria used to identify and confirm peaks, see “To specify identification and confirmation settings” on page 216. For detailed descriptions of the Format and Peaks parameters, see Reports page parameters. To specify options for exporting compounds to a CSV file 1. In the CSV Export Settings area on the Target Screening Export/Report Settings page, select one of the following file formats: Multiple Files: Writes one sample to each file. Single Rile: Write all samples to a single file. The application uses the selected file format when you export a batch compound list to a CSV file. For instructions about exporting a compound list from the Analysis mode, see “To export compounds to a CSV file” on page 459. 2. In the Peaks area, select the type of peaks to export: All Peaks, Confirmed Only, or Identified and Confirmed. For detailed descriptions of the criteria used to identify and confirm peaks, see “To specify identification and confirmation settings” on page 216. To specify report options Use the Report Options on the Target Screening Export/Report Settings pane to specify the compounds to use in reports: all compounds in the method or only the compounds found in the sample. These settings affect all reports created with this method. Thermo Scientific TraceFinder User Guide 209 4 Using the Method Development Mode Working with Master Methods Figure 59. Reports page for a target screening method Table 47. Reports page parameters Parameter Description Report list columns Example This option is not available for target screening reports. Report Name The name of a report. Report Title The user-defined description to be used on a report. Report Type In a target screening method, all reports are the Target Screening report type. Print Sends reports to the printer. Create PDF Saves reports as PDF files. Create XML Exports reports as XML files. Create XLSM This option is not available for target screening reports. Batch Level This option is not available for target screening reports. 210 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Figure 60. Target Screening Export/Report Settings page for a target screening method Table 48. Target Screening Export/Report Settings page parameters Parameter Description Excel Export Settings Format Specifies one of the following formats for exporting reports to an Excel spreadsheet file: • Multiple Worksheets: Writes one sample to each Excel worksheet tab. • Single Worksheet: Writes all samples to a single Excel worksheet tab. Peaks Specifies one of the following options for reporting peaks: • All Peaks: All peaks found in the sample data. • Identified and Confirmed: Reports peaks that are considered identified and peaks that are considered confirmed. • Confirmed Only: Reports only peaks that are considered confirmed. CSV Export Settings Format Specifies one of the following formats for exporting reports to a comma-separated-value (.csv) file: • Multiple Files: Writes one sample to each file. • Single File: Writes all samples to a single file. Peaks Specifies one of the following options for reporting peaks: • All Peaks: All peaks found in the sample data. • Identified and Confirmed: Reports peaks that are considered both identified and confirmed. • Confirmed Only: Reports only peaks that are considered confirmed. Report Options Include All Compounds Reports all compounds in the method, including those that are not found in the sample. Include Only Found Compounds Reports only compounds that are found in the sample. Thermo Scientific TraceFinder User Guide 211 4 Using the Method Development Mode Working with Master Methods Editing the Screening Page Use the Screening page to specify peak filter settings, screening databases, and identification and confirmation settings for a screening method. To open the screening page Click Screening in the Method View navigation pane. The Screening page for the screening method opens. See “Screening page for a target screening method” on page 218. This section includes instructions for the following tasks: • Specifying Peak Filter Settings • Specifying Compound Databases • Specifying Identification and Confirmation Settings Specifying Peak Filter Settings The Peak Filter Settings pane displays parameters for limiting unwanted data. To specify peak filter settings 1. To set a retention time range that excludes searching for peaks outside the range, do the following: a. Select the Use RT Limits check box. The application activates the Search From and To options. b. In the Search From box, enter the lower limit; in the To box, enter the upper limit. 2. To use one or more negative samples for subtraction to filter the resulting peaks, do the following: a. Select the Use Matrix Blank check box. The application activates the Amplifier option. 212 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods During automatic processing, the TraceFinder application subtracts the areas of the peaks in the negative samples from the matching areas in the specimen samples. To determine the pair of peaks to subtract from each other, the application selects the two peaks with the mass and the retention time that are closest to each other (as defined in the compound database), within the mass tolerance specified in the method. When the same compound peak (same mass and retention time within the predefined tolerance windows) is in multiple selected negative samples, the application subtracts only the one with the highest area. When a compound peak in one negative sample has the same primary ion as another peak in a different negative sample but has different adducts, the application uses all the adducts from both these peaks for subtraction purposes. For example, if a compound has the M+H and M+Na ions in one negative sample, and this same compound has the M+H and M+NH4 ions in another negative sample, the application uses for subtraction the area that results from all of these ions. When no negative sample exists in the sequence, or if one or more negative samples exist but you do not select the Use Matrix Blank check box, then subtraction does not occur. If subtraction occurs and the subtracted area is less than 0, the application sets the subtracted area to 0. b. In the Amplifier box, type an amplifier value. Use the up/down arrows to change the value in increments/decrements of 1 unit, or use the keyboard to enter non-integer values. The TraceFinder application multiplies a negative area by this value before performing subtraction. The larger the amplifier value, the more peaks the application filters from the final results. In the Batch View for sequences created with this method, you can select which negative samples to use for subtraction. See “Blank Subtraction in Target Screening Batches” on page 348. 3. In the Chromatogram View Width box, type a value to define the chromatogram viewing range in the Data Review view. 4. To use source CID scans for target screening confirmation (fragment ion or library search), select the Use Source CID Scans check box. When you select this check box, the TraceFinder application uses the source CID scans when they are available in the data file. If they are not available, then the application uses AIF or MS/MS scans when available. Thermo Scientific TraceFinder User Guide 213 4 Using the Method Development Mode Working with Master Methods Specifying Compound Databases The Target Screening Settings pane displays the compound databases stored in the following folder: C:\Thermo\TraceFinder\3.0\Forensic\Databases To specify compound databases 1. Select the Enabled check box for at least one compound database. 2. (Optional) To edit a database, click Open and do the following: a. Edit the database. See “Editing Compounds in the Database” on page 251. b. When you finish editing the database, click Screening in the Method View navigation pane to return to the Screening page. 214 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Specifying Identification and Confirmation Settings The TraceFinder application automatically uses the mass-to-charge ratio (m/z) for filtering compound peaks. In the Identification and Confirmation Settings area, you can select additional criteria to help increase confidence using either of the following: • Compound identification for identifying a sample compound as a minimum requirement for a match to be displayed in the results. To identify a compound, the application searches within the specified RT window (or the RT window override if specified in the method) and compares the measured m/z of the sample peak against the calculated (expected) m/z of the target compound. When the sample peak’s m/z is within the default ±5 ppm tolerance of the target compound’s m/z, the application considers that this target compound is identified. • Compound confirmation for confirming a sample compound and to increase confidence in the match results. To confirm a compound, the application searches the entire raw data file and compares the measured m/z of the sample peak against the calculated (expected) m/z of the target compound. When the sample peak’s m/z is within the tolerance of the target compound’s m/z, the application considers that this target compound is confirmed. Thermo Scientific TraceFinder User Guide 215 4 Using the Method Development Mode Working with Master Methods To specify identification and confirmation settings 1. To set a target threshold override and include only peaks with areas above this designated threshold, do the following: a. Select the Threshold Override check box. b. In the associated box, type the threshold as an area value. This threshold overrides the Response Threshold value set in the compound database. The application ignores the peaks with areas below your specified threshold. c. To include only peaks with signal-to-noise ratios (S/Ns) that are above a specified value, in the S/N Ratio Threshold box, type the threshold as a ratio value. The application ignores the peaks with S/Ns that are below the specified threshold. 2. To specify the Retention Time option, do the following: a. Select either the Identity or Confirm check box. b. Select the Window Override check box and type the window value. This window overrides the RT Window value that was set in the compound database and includes only peaks within this designated window. The application identifies or confirms the presence of a compound only when its measured retention time matches the target compound’s expected retention time within the specified Window Override retention time. 3. To specify the Fragment Ions option, do the following: a. Select either the Identity or Confirm check box. b. In the Max. # of Fragments box, type the maximum number of fragments to use to identify or confirm the presence of a compound. 4. To specify the Isotopic Pattern option, do the following: a. Select either the Identity or Confirm check box. b. In the Fit Threshold box, type the fit threshold percentage. To identify or confirm the presence of a compound, the resulting score percentage from isotopic pattern matching must be higher than the specified fit threshold percentage. c. In the Allowed Intensity Deviation box, type a value to specify the allowed intensity deviation of the mass spectrometer relative to the monoisotopic ion, as a percentage of the base peak height. The TraceFinder isotopic pattern algorithm considers an isotope peak as not found if its intensity, relative to the monoisotopic ion’s intensity, is more than the deviation percentage from the theoretical relative intensity of the isotope ion. For best results, set this value to a number that causes up to 98% of all intensity deviations to be smaller than the allowed intensity deviation value. 216 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods d. To specify that isotopic pattern calculations use internal mass calibration instead of external mass calibration, select the Use Internal Mass Calibration check box. When this check box is selected, the application applies a requirement that an isotope’s m/z must be closer to its theoretical value to avoid a score penalty. 5. To specify the Library Search option, do the following: a. Select either the Identity or Confirm check box. b. Type the threshold value in the Score Threshold box. The resulting score percentage from a library search match must be higher than your entered threshold value to identify or confirm the presence of a compound. Thermo Scientific TraceFinder User Guide 217 4 Using the Method Development Mode Working with Master Methods Figure 61. Screening page for a target screening method Table 49. Screening page parameters (Sheet 1 of 3) Parameter Description Peak Filter Settings Use RT Limits 218 TraceFinder User Guide Specifies a lower and upper limit for searches. Ranges: 0.00 to 999.99 minutes Default: 0.00 minutes for lower limit; 999.00 minutes for upper limit Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 49. Screening page parameters (Sheet 2 of 3) Parameter Description Use Matrix Blank Specifies that during automatic processing, the TraceFinder application subtracts the areas of the peaks in the selected negative samples from the matching areas in the specimen samples. Amplifier The application multiplies a negative area by this value before performing subtraction. The larger the amplifier value, the more peaks the application filters from the final results. Range: .01 to 1000.00 Default: 1.00 Chromatogram View Width Specifies a a window width to define the chromatogram viewing range in the Data Review view. Range: 0.10 to 999.00 minutes Default: 0.75 minutes Use Source CID Scans Specifies that the application use the source CID scans when they are available in the data file. If they are not available, then the application uses AIF or MS/MS scans when available. Compound Databases Enabled Specifies databases to use for target screening processing. Database Name Lists available databases in the Databases folder. Identification and Confirmation Settings Peaks Specifies that the application use the mass-to-charge ratio (m/z) for filtering compound peaks. Threshold Override This threshold overrides the Response Threshold value set in the compound database. The application ignores the peaks with areas below this specified threshold. Range: 1000 to 1 000 000 000 Default: 5000 S/N Ratio Threshold Includes only peaks with signal-to-noise ratios (S/Ns) above the specified value. Range: 1.0 to 100 000 Default: 5.0 Retention Time Specifies either the Identify or Confirm option for a retention time search. To identify a compound, the application searches the specified RT window for a match. To confirm a compound, the application searches the entire raw data file. Window Override Specifies the number of seconds to override the RT Window value set in the compound database and include only peaks within this designated window. The application identifies or confirms the presence of a compound only when its measured retention time matches the target compound’s expected retention time within the specified Window Override retention time. Range: 0 to 999 seconds Default: 30 seconds Fragment Ions Specifies either the Identify or Confirm option for a fragment ion match. To identify a fragment, the application searches the specified RT window for a match. To confirm a fragment, the application searches the entire raw data file. Thermo Scientific TraceFinder User Guide 219 4 Using the Method Development Mode Working with Master Methods Table 49. Screening page parameters (Sheet 3 of 3) Parameter Description Max. # of Fragments Specifies the maximum number of fragments to use to identify or confirm the presence of a compound. Range: 1 to 5 Default: 1 Isotopic Pattern Specifies either the Identify or Confirm option for an isotopic pattern match. To identify a compound, the application searches the specified RT window for a match. To confirm a compound, the application searches the entire raw data file. Fit Threshold (%) To identify or confirm the presence of a compound, the resulting score percentage from isotopic pattern matching must be higher than the specified fit threshold percentage. Default: 90% Allowed Intensity Deviation Specifies the allowed intensity deviation of the mass spectrometer, relative to the monoisotopic ion, as a percentage of the base peak height. The TraceFinder isotopic pattern algorithm considers an isotope peak as not found if its intensity relative to the monoisotopic ion’s intensity is more than this deviation percentage from the theoretical relative intensity of the isotope ion. For best results, set this value to a number that causes up to 98% of all intensity deviations to be smaller than the allowed intensity deviation value. Default: 10% Use Internal Mass Calibration Specifies that the application require an isotope’s m/z to be closer to its theoretical value to avoid a score penalty. Allowed Mass Deviation Specifies the allowed mass deviation in the spectrum data. The TraceFinder isotopic pattern algorithm considers an isotope peak as found if its measured m/z is less than this amount away from its expected m/z. For best results, set this value to a number that causes up to 98 percent of all mass deviations to be smaller than the allowed mass deviation value. Range: 3 to 100 ppm Default: 3 ppm Library Search Specifies either the Identify or Confirm option for a library search. To identify a compound, the application searches the specified RT window for a match. To confirm a compound, the application searches the entire raw data file. Score Threshold The resulting score percentage from a library search match must be higher than your specified threshold value to identify or confirm the presence of a compound. Default: 80% 220 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Editing the Peak Detection Page The TraceFinder application can use any of the following peak detection algorithms: Genesis, ICIS, or Avalon. To specify peak detection parameters 1. Click Peak Detection in the Method View navigation pane. The Peak Detection page for the screening method opens. 2. Select a detection algorithm: Genesis, ICIS, or Avalon. • The Genesis peak detection algorithm is provided for backward compatibility with Xcalibur 1.0 studies. • The ICIS peak detection algorithm is designed for MS data and has superior peak detection efficiency at low MS signal levels. • The Avalon peak detection algorithm is designed for integrating UV/Vis and analog chromatograms. 3. Specify the peak detection parameters for your method. Figure 62. Parameters on the Genesis peak detection page for a target screening method Genesis peak detection parameters for screening methods are the same as for quantitation methods. See “Detect page parameters for Genesis” on page 146. Thermo Scientific TraceFinder User Guide 221 4 Using the Method Development Mode Working with Master Methods Figure 63. Parameters on the ICIS peak detection page for a target screening method ICIS peak detection parameters for screening methods are the same as for quantitation methods. See “Detect page parameters for ICIS” on page 150. 222 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Figure 64. Parameters on the Avalon peak detection page for a target screening method Avalon peak detection parameters for screening methods are the same as for quantitation methods. See “Detect page parameters for Avalon” on page 152. Thermo Scientific TraceFinder User Guide 223 4 Using the Method Development Mode Working with Master Methods Creating a Method Template In the TraceFinder application, you can create a processing method using a method template that contains common settings. The application uses the settings in the method template to identify the data to display in the Qualitative View. See “Qualitative View” on page 416. Only quantitation methods use method templates. Target screening methods do not use method templates. Follow these procedures: • To open the Method Template Editor • To specify peak criteria • To identify the peaks • To specify confirming ions • To calibrate the compounds • To enter a note for the method • To save the method template To open the Method Template Editor 1. Click Method Development in the navigation pane. The Method Development navigation pane opens. 2. Click Method View. 3. From the main menu, choose File > New > Method Template. The Method Template Editor opens. For a complete description of the features on the Method Template Editor, see “Method Template Editor dialog box” on page 231. 224 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods To specify peak criteria 1. In the Find the Peaks area, select a sensitivity level. In selecting the degree of sensitivity, you define how extensively the peak detector algorithm searches for low-level peaks. • The Genesis peak detection algorithm is provided for backward compatibility with Xcalibur 1.0 studies. • The ICIS peak detection algorithm is designed for MS data and has superior peak detection efficiency at low MS signal levels. • The Avalon peak detection algorithm is designed for integrating UV/Vis and analog chromatograms. 2. To look for peaks only in a certain range of the entire chromatogram, select the Limit the Retention Time Range check box and specify a retention time (RT) range. 3. To indicate whether to select peaks by relative height or area and the percentage of the highest peak that results in compound selection, select the Enable Peak Threshold check box. To consider a peak for a processing method, the TraceFinder application uses the Enable Peak Threshold filter to determine which peaks meet the specified percentage of the height or area of the largest peak. 4. To display a specific number of the largest peaks by height or area, select the Only Select Top Peaks check box and enter the number of peaks to display. Thermo Scientific TraceFinder User Guide 225 4 Using the Method Development Mode Working with Master Methods To identify the peaks 1. In the Use these Libraries box, select the libraries that you want to search. All libraries loaded on your instrument are displayed in the Use these Libraries box. 2. To limit the number of hits returned when the system searches a spectrum against the selected libraries, set a value in the Limit Library Hits box. 3. To specify how to sort the library searches, select a value from the Best Match Method list. To specify confirming ions 1. To set the number of confirming ions, select the Include Confirming Ions check box and enter a value in the Number of Confirming Ions box. This value is the number of other ions in the spectrum whose ratio is compared to the quantitation ion. Using this ratio, you can then determine if it is the target compound or something else. You can set this value to integers from 1 to 10, inclusive. This value defaults to 2 because you typically perform a 3-ion experiment with one quantitation mass and two confirming ions. The system selects the most intense ion to use as the quantitation mass and uses this mass for the mathematical operations. 226 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods 2. To define the criteria for evaluating confirming or qualifying ions, select the Specify Default Ion Ratio Ranges check box and set the following values: a. To specify the maximum difference in retention time between a confirming ion peak and the quantification ion peak, set a value in the Ion Coelution (min) box. b. To specify an absolute or relative calculation approach for determining the acceptable ion ratio range, select Absolute or Relative from the Window Type list. c. To specify the acceptable ion ratio range, set a value in the Window (+/– %) box. 3. To include the peak spectrum in the processing method, select the Include Compound Peak Spectrum as Reference Spectrum check box. To calibrate the compounds 1. From the Calibration Method list, select Internal or External. 2. From the Curve Type list, select one of the following: • Linear: All other settings are available with this exception: When you select Include in the Origin list, the Weighting parameter is unavailable. • Quadratic: All other settings are available with this exception: When you select Include in the Origin list, the Weighting parameter is unavailable. • Average RF: The Weighting and Origin parameters are unavailable. 3. From the Origin list, select one of the following: • Ignore: Specifies that the origin is not included as a valid point in the calibration curve when the curve is generated. When you select Ignore, the calibration curve might or might not pass through the origin. • Force: Specifies that the calibration curve passes through the origin of the data point plot when the calibration curve is generated. • Include: Specifies that the origin is included as a single data point in the calculation of the calibration curve. When you select Include, the calibration curve might or might not pass through the origin. Thermo Scientific TraceFinder User Guide 227 4 Using the Method Development Mode Working with Master Methods 4. From the Weighting list, select one of the following: • Equal: Specifies that the origin is included as a single data point in the calculation of the calibration curve. When you select Equal, the calibration curve might or might not pass through the origin. • 1/X: Specifies a weighting of 1/X for all calibration data points during the least-squares regression calculation of the calibration curve. Calibrants are weighted by the inverse of their quantity. • 1/X^2: Specifies a weighting of 1/X^2 for all calibration data points during the least-squares regression calculation of the calibration curve. Calibrants are weighted by the inverse of the square of their quantity. • 1/Y: Specifies a weighting of 1/Y for all calibration data points during the least-squares regression calculation of the calibration curve. Calibrants are weighted by the inverse of their response (or response ratio). • 1/Y^2: Specifies a weighting of 1/Y^2 for all calibration data points during the least-squares regression calculation of the calibration curve. Calibrants are weighted by the inverse of the square of their response (or response ratio). 5. From the Response Via list, select Area or Height. • Area: Specifies that the TraceFinder application use this area value in response calculations. • Height: Specifies that the application use this height value in response calculations. 228 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods To specify qualitative peak processing 1. Select the Use Genesis Algorithm for Qual Processing check box and specify a value for internal standard matching. The application uses the Genesis algorithm to match internal standards in a range plus/minus the value that you specify. For additional information about the Genesis algorithm, see “Genesis Detection Method” on page 50. This parameter is available only when you set the Sensitivity parameter in the Find the Peaks area to ICIS or Avalon. When you select the Use Genesis Algorithm for Qual Processing check box, the application ignore the Sensitivity parameter in the Find the Peaks area. 2. Select or clear the Exclude Matching Quan Peaks check box and specify a value for the exclusion window. The application excludes quantitative peaks in a range plus or minus the value that you specify. 3. To process samples that include data-dependent scans, select the Use Data Dependent Scans check box. When you process a sample using this feature, the application uses the TIC trace to find all data-dependent full scans, lists them, and performs a library search against the data-dependent MS/MS or MSn scan. This option constrains the Data Review to only data-dependent scan spectra. See “Working in the Report View” on page 468. In addition to the peak information, the TIC Report and TIC Summary Report display information about the data-dependent filtered data. See Appendix A, “Reports.” 4. To indicate whether to select peaks above a minimum percentage of the nearest internal standard peak that results in compound selection, select the Enable ISTD Threshold check box and specify a minimum percentage. To consider a peak for a processing method, the TraceFinder application uses the Enable ISTD Threshold filter to determine which peaks meet the specified percentage of the height of the nearest internal standard peak. Thermo Scientific TraceFinder User Guide 229 4 Using the Method Development Mode Working with Master Methods When you select the Enable ISTD Threshold parameter, the method ignores values set for the Enable Peak Threshold and Only Select Top Peaks parameters. See “To specify peak criteria” on page 225. Note When you create a method with the Method Forge, the application ignores the parameters in the Qualitative Peak Processing area. To enter a note for the method Type in the Notes box, or paste text from another application using CTRL+V. You can add a note to your method template to explain what makes this template unique. To save the method template 1. Choose File > Save from the Method Template Editor menu. The Save Method Template dialog box opens. 2. Do one of the following: Type a new name for the master method and click OK. –or– Select a method name to overwrite and click Overwrite. The TraceFinder application saves the new method template in the following folder: …\Thermo\TraceFinder\3.0\Forensic\Templates\Methods Saved method templates are available when you create a method using Method Forge. See “Creating a New Method with Method Forge” on page 85. 230 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Figure 65. Method Template Editor dialog box Thermo Scientific TraceFinder User Guide 231 4 Using the Method Development Mode Working with Master Methods Table 50. Method Template Editor dialog box parameters (Sheet 1 of 3) Parameter Description Find the peaks Sensitivity Defines how extensively the peak detector algorithm searches for low-level peaks. Limit the Retention Time Range Min RT specifies the beginning of the range. Max RT specifies the end of the range. Enable Peak Threshold Specifies whether to select peaks by relative height or area and the percentage of the highest peak that results in compound selection. Only Select Top Peaks Displays a specific number of the largest peaks by height or area. Identify the peaks Use These Libraries Lists the libraries that you can search. Limit Library Hits Specifies the number of hits returned when the system searches a spectrum against the selected libraries. Best Match Method Specifies how to sort the library searches. Valid values: Search Index, Reverse Search Index, Match Probability Handle confirming ions Include Confirming Ions/ Number of Confirming Ions Specifies the number of confirming ions, which are other ions in the spectrum whose ratio is compared to the quantitation ion to identify the compound. This value defaults to 2 because you typically perform a 3-ion experiment with one quantitation mass and two confirming ions. Range: Integers from 1 to 10, inclusive. Specify Default Ion Ratio Ranges Enables the ion ratio range features. Ion Coelution specifies the maximum difference in retention time between a confirming ion peak and the quantification ion peak. Window Type specifies an Absolute or Relative calculation approach for determining the acceptable ion ratio range. Window (+/-%) specifies the acceptable ion ratio range. Include Compound Peak Spectrum as Reference Spectrum Includes the peak spectrum in the processing method. Use this setting to perform a spectra comparison in Data Review. Calibrate the compounds Calibration Method Specifies an internal or external calibration method. Curve Type Specifies a linear, quadratic, or average RF curve type. 232 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 50. Method Template Editor dialog box parameters (Sheet 2 of 3) Parameter Description Origin Specifies that the origin is ignored, forced, or included in the generated calibration curve. • Ignore: Specifies that the origin is not included as a valid point in the calibration curve when the curve is generated. When you select Ignore, the calibration curve might or might not pass through the origin. • Force: Specifies that the calibration curve passes through the origin of the data point plot when the calibration curve is generated. • Include: Specifies that the origin is included as a single data point in the calculation of the calibration curve. When you select Include, the calibration curve might or might not pass through the origin. Weighting Specifies the weighting for the calibration data points. • Equal: Specifies that the origin is included as a single data point in the calculation of the calibration curve. When you select Equal, the calibration curve might or might not pass through the origin. • 1/X: Specifies a weighting of 1/X for all calibration data points during the least-squares regression calculation of the calibration curve. Calibrants are weighted by the inverse of their quantity. • 1/X^2: Specifies a weighting of 1/X^2 for all calibration data points during the least-squares regression calculation of the calibration curve. Calibrants are weighted by the inverse of the square of their quantity. • 1/Y: Specifies a weighting of 1/Y for all calibration data points during the least-squares regression calculation of the calibration curve. Calibrants are weighted by the inverse of their response (or response ratio). • 1/Y^2: Specifies a weighting of 1/Y^2 for all calibration data points during the least-squares regression calculation of the calibration curve. Calibrants are weighted by the inverse of the square of their response (or response ratio). Response Via Specifies if the TraceFinder application uses area or height in response calculations. • Area: Specifies that the application use this peak area value in response calculations. • Height: Specifies that the application use this peak height value in response calculations. Qualitative Peak Processing Use Genesis Algorithm For Qual Processing The application uses the Genesis algorithm to match internal standards. ISTD Matching Excludes all the target compounds found in the method and does not list these compounds in the TIC Report or in the Qual Mode view in the Data Review. Exclude Matching Quan Compares the retention time of the internal standard in the method to the found retention Peaks time of the internal standard in the library search and excludes peaks outside the Exclusion Window range. Exclusion Window Thermo Scientific Defines a range plus/minus the Exclusion Window value that you specify. TraceFinder User Guide 233 4 Using the Method Development Mode Working with Master Methods Table 50. Method Template Editor dialog box parameters (Sheet 3 of 3) Parameter Description Use Data Dependent Scans Constrains the Data Review to only data-dependent scan spectra. See “Working in the Report View” on page 468. In addition to the peak information, the TIC Report and TIC Summary Report display information about the data-dependent filtered data. Enable ISTD Threshold Specifies that, when identifying a peak, qualitative peak processing use the minimum threshold specified as a percentage of the nearest internal standard peak, rather than the threshold specified in the Enable Peak Threshold and Only Select Top Peaks parameters. See Enable Peak Threshold or Only Select Top Peaks in this parameter table. % of Internal Standard 234 TraceFinder User Guide Percentage of the nearest internal standard peak to use as the minimum threshold for identifying a peak. Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Importing Published Master Methods In the TraceFinder application, you can import published methods to use for detecting, processing, and reporting. The Tracefinder installation provides the following folder of published methods: …\Thermo\TraceFinder\3.0\Forensic\Published Master Methods To import a published master method 1. Choose Method View > Import Published Method from the main menu. The Import Published Method dialog box opens. 2. Select a method to import. 3. Click Import. The application reports that the method successfully imported and saves the method in the following folder: …\Thermo\TraceFinder\3.0\Forensic\Methods You can use any of the Open Method commands to open this method just as you would a method that you created. Thermo Scientific TraceFinder User Guide 235 4 Using the Method Development Mode Working with Master Methods Exporting SRM Data In the TraceFinder application, you can export the selected reaction monitoring (SRM) data from a quantitation method to an XML file that can be read by a TSQ or Q Exactive application. You can export SRM transitions only from quantitation methods. To export SRM data to an XML file 1. Open the master method whose SRM data you want to export. If you make changes to the method, you must save it before you can export the SRM transitions. 2. To view a list of your SRM transitions, click the Acquisition List tab on the Compounds page. You do not have to display the Acquisition List to export the data, but the compounds in the Acquisition List must contain at least one SRM experiment type. For information about displaying SRM experiment types, see “Acquisition List” on page 115. For information about editing SRM experiment types, see “Editing Compounds in the Database” on page 251. 3. Choose Method View > Export SRM Data from the main menu. The application writes the transitions to the following folder, using a format compatible with your configured instrument: …\Thermo\TraceFinder\3.0\Forensic\Methods\method IMPORTANT If you have neither a TSQ nor an Exactive instrument configured, a message asks which format you want to export: Triple Quadrupole or Q Exactive. 236 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Triple Quadrupole Format The TraceFinder application writes the data in the SRM table to the following file: …\Thermo\TraceFinder\3.0\Forensic\Methods\method\method.xml The data in this file matches the TSQ XML data, which you can use in the instrument method editor of that application. Example SRM data file in TSQ format: <?xml version="1.0" encoding="utf-8" ?> - <TSQMassList> - <TSQListItem> <ParentMass>356.1</ParentMass> <ProductMass>321.1</ProductMass> <CollisionEnergy>14</CollisionEnergy> <EnergyRamp>0</EnergyRamp> <RT>0</RT> <Width>60</Width> <PreWidth>0</PreWidth> <PostWidth>0</PostWidth> <StartTime>0</StartTime> <StopTime>0.5</StopTime> <TubeLens>0</TubeLens> <S-Lens>0</S-Lens> <Polarity>0</Polarity> <Name>15-acethyldeoxynivalenol+NH4</Name> - </TSQListItem> Thermo Scientific TraceFinder User Guide 237 4 Using the Method Development Mode Working with Master Methods Q Exactive Format The TraceFinder application writes the data in the SRM table to the following file: C:\Thermo\TraceFinder\3.0\Forensic\Methods\method\method.xml.include-masses The data in this file matches the Exactive XML data, which you can use in the instrument method editor of that application. Example SRM data file in Q Exactive format: <?xml version="1.0" encoding="utf-8"?> <IncludeMasses xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" FullInternalName="Framework.IncludeMassesContainer"> <Masses FullInternalName="Framework.IncludeMasses"> <Mass id="1"> <Value unit="m/z" FullInternalName="decimal">321.1</Value> <Polarity>0</Polarity> <Start unit="min" FullInternalName="decimal">5</Start> <End unit="min" FullInternalName="decimal">5</End> <NormalizedCollisionEnergy FullInternalName="decimal">14</NormalizedCollisionEnergy> <ChargeState FullInternalName="int">0</ChargeState> <Comment /> </Mass> 238 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with the Compound Database Working with the Compound Database When user security is activated, as a user in either the LabDirector or ITAdmin role, you can manage compound definitions in the current database in the Compound Database view. This section includes the following topics: • Opening and Saving a Database • Editing Compounds in the Database • Choosing Experiment Types • Exporting and Importing Compounds For a description of all the parameters in the Compound Database view, see “Compound Database Views” on page 243. Thermo Scientific TraceFinder User Guide 239 4 Using the Method Development Mode Working with the Compound Database Opening and Saving a Database You can load a compound database that was included with your TraceFinder installation, or you can create your own database. For detailed descriptions of all parameters and functions in the Compound Database view, see “Compound Database Views” on page 243. When you save the edits for a compound, the application saves the changes to the compound database file. For instructions about editing compounds, see “Editing Compounds in the Database” on page 251. Follow these procedures: • To open the Compound Database editor • To load a compound database into the editor • To create a new compound database • To save the database to a new name To open the Compound Database editor 1. Click Compound Database in the Method Development navigation pane. The current database opens in the Compound Database view. If there is no compound database displayed in the editor, see the instructions To load a compound database into the editor. You can add compounds to the database by importing a file of compounds into the new database, or you can manually add compounds one at a time. See “To import compounds” on page 262 or “To add a compound to the database” on page 251. 240 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with the Compound Database To load a compound database into the editor 1. Choose File > Open Compound Database. The Open Compound Database dialog box opens. 2. Double-click the name of the database that you want to open. The selected database opens in the Compound Database view. See “Compound Database Views” on page 243. Note Or, you can choose File > Recent Files > filename from the main menu to load a previously opened database. To create a new compound database 1. Choose File > New Compound Database from the main menu. The New Compound Database dialog box opens. 2. Type a file name for the new database and click OK. The application stores the database as C:\Thermo\TraceFinder\3.0\Forensic\Databases\filename.cdb Thermo Scientific TraceFinder User Guide 241 4 Using the Method Development Mode Working with the Compound Database To save the database to a new name 1. Choose File > Save Compound Database As from the main menu. The Save Compound Database As dialog box opens. 2. Do one of the following: Type a file name for the new database and click OK. –or– Select the name of a database to overwrite, and click Overwrite. If you attempt to overwrite the compound database that you currently have open, the application warns that you cannot overwrite the compound database because it is being used. The application stores the database as C:\Thermo\TraceFinder\3.0\Forensic\Databases\filename.cdb 242 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with the Compound Database Compound Database Views The parameters in the compound database are different depending on which experiment type the compound uses. • Compound Database view for SRM experiments • Compound Database view for SIM experiments • Compound Database view for XIC experiments For detailed descriptions of all parameters used in the compound database, see “Compound Database view parameters” on page 246. Figure 66. Compound Database view for SRM experiments Thermo Scientific TraceFinder User Guide 243 4 Using the Method Development Mode Working with the Compound Database Figure 67. Compound Database view for SIM experiments 244 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with the Compound Database Figure 68. Compound Database view for XIC experiments Thermo Scientific TraceFinder User Guide 245 4 Using the Method Development Mode Working with the Compound Database Table 51. Compound Database view parameters (Sheet 1 of 5) Parameter Description Search Displays only compounds that match the typed text. Displays one of these experiment types that each use a different structure for the mass filter. See “Choosing Experiment Types” on page 258. • SRM: Selected Reaction Monitoring • XIC: Extracted Ion Chromatogram • SIM: Single Ion Monitoring Compound Alphabetically lists the compounds in the database followed by the experiment type. Some long names are truncated in the list. Hold your cursor over the name to display a ToolTip with the entire name. Formula Chemical formula for the compound. Used to calculate the neutral mass for the compound. Compound Detail Compound Alphanumeric name assigned to the compound. Experiment Experiment type: SRM, XIC, or SIM. For details about the differences, see “Choosing Experiment Types” on page 258. Category (Optional) Alphanumeric identifier. CAS The Chemical Abstract Service (CAS) number that the TraceFinder application matched with the compound. Formula Alphanumeric chemical identifier. Ionization Alphanumeric identifier. Valid values: None, ESI, APCI, EI, CI, or APPI Default: None Response Threshold The application integrates only peaks with a response greater than this threshold. The response threshold is a minimum response that must be met to allow peak confirmation. Used only for target screening methods. Available only for XIC experiments. Default: 5000 Range: 1000 or greater Neutral Mass 246 TraceFinder User Guide Mass calculated from the chemical formula. The neutral mass is the sum of all AMU elements in the compound. This parameter is informational only; it is not used for peak detection. Thermo Scientific 4 Using the Method Development Mode Working with the Compound Database Table 51. Compound Database view parameters (Sheet 2 of 5) Parameter Description Target Peaks Precursor Mass The mass-to-charge ratio (m/z) of a target peak. The location of the center of a target precursor-ion peak in mass-to-charge ratio units. In confirming peaks, the precursor mass is the same as the target peak precursor mass. Default: 0.0 Range: 10.000 to 2999.999 Available for all SRM experiments and for XIC experiments with the MS Order set to MS2. For mass values in XIC experiments when the MS Order set to MS1, see Extracted Mass. Product Mass The mass-to-charge ratio of the confirming peak. The location of the center of a target quan-ion peak in mass-to-charge ratio (m/z) units. Default: 0.0 Range: 10.000 to 2999.999 Available for all SRM experiments and for XIC experiments with the MS Order set to MS2. For mass values in XIC experiments when the MS Order set to MS1, see Extracted Mass. Mass Thermo Scientific The mass-to-charge ratio of the confirming peak. The location of the center of a target quan-ion peak in mass-to-charge ratio (m/z) units. Available only for SIM experiments. TraceFinder User Guide 247 4 Using the Method Development Mode Working with the Compound Database Table 51. Compound Database view parameters (Sheet 3 of 5) Parameter Description Extracted Mass The mass-to-charge ratio of the target peak. The location of the center of a target quan-ion peak in mass-to-charge ratio (m/z) units. You can enter a value for the Extracted Mass, but when you change the values for Formula, Adduct, Polarity, or Charge State, the application recalculates the Extracted Mass value, overwriting the value you entered. Default: 0.0 Range: 10.000 to 2999.999 Available only for XIC experiments with the MS Order set to MS1. For mass values in XIC experiments when the MS Order set to MS2, see Precursor Mass or Product Mass. Polarity Positive or Negative Adduct Lists the adducts specified in the configuration file. To add or remove adducts from the default lists, see “Specifying Adducts Configuration” on page 60. Adducts affect the calculated amount of the extracted mass by adding to or subtracting from the neutral mass. Adducts are polarity sensitive. Select the Polarity parameter before selecting the Adduct value. Default Positive Valid Values: Neutral, NH4, H, Na, K Default Negative Valid Values: Neutral, H, H3C2O2, HCO2 Default: Neutral Charge State Specifies the charge state of the ion (the z value in m/z). For example, a charge state of 2 with a negative polarity means that the compound has 2 more electrons than protons. Valid Values: 1 through 10 Default: 1 MS Order Specifies whether the confirming peaks come from the same scan (MS1) or are fragments from an adjacent scan (MS2). Available only for XIC experiments. Time Range Peak Specifies whether the acquisition time is specified as a window around a specified RT value or as a retention time range in minutes. This parameter is visible only when you are editing a compound. 248 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with the Compound Database Table 51. Compound Database view parameters (Sheet 4 of 5) Parameter Description Window (sec) The application uses RT and Window values to determine the start and stop time for the acquisition. Available only when the Time Range Peak option is not selected. Range: 0.00 to 499.50 Start time = RT – (Window/2) Stop time = RT + (Window/2) Start and stop range: 0.00 to 999.00 RT (min) Retention time. The application uses RT and Window values to determine the start and stop time for the acquisition. When the Time Range Peak option is selected, the RT value is specified as a range. Range: 0.00 to 999.00 Start time = RT – (Window/2) Stop time = RT + (Window/2) Start and stop range: 0.00 to 999.00 Lens Range: –400 to 400 Collision Energy The energy used when ions collide with the collision gas. Available only for SRM experiments. Range: –250.00 to 250.00 Energy Ramp Range: 0.00 to 200.00 Confirming Peaks Confirming peak parameters are used only in quantitative methods. Precursor The mass-to-charge ratio of a precursor ion. The location of the center of a target precursor-ion peak in mass-to-charge ratio (m/z) units. Available only for SRM experiments or XIC experiments with the MS Order set to MS2. Default: 0.0 Range: 10.000 to 2999.999 Product Mass The mass-to-charge ratio of the quantitation ion. The location of the center of a target quan-ion peak in mass-to-charge ratio (m/z) units. Available only for SRM experiments. Default: 0.0 Range: 10.000 to 2999.999 Mass Thermo Scientific The mass-to-charge ratio of the confirming peak. The location of the center of a target quan-ion peak in mass-to-charge ratio (m/z) units. Available only for SIM experiments. TraceFinder User Guide 249 4 Using the Method Development Mode Working with the Compound Database Table 51. Compound Database view parameters (Sheet 5 of 5) Parameter Description Extracted Mass The mass-to-charge ratio of the target peak. The location of the center of a target quan-ion peak in mass-to-charge ratio (m/z) units. Available only for XIC experiments. Default: 0.0 Range: 10.000 to 2999.999 Collision Energy The energy used when ions collide with the collision gas. Available only for SRM experiments. Range: –250.00 to 250.00 MS Order Fragments Extracted Mass Specifies whether the confirming peaks or fragments come from the same scan (MS1) or an adjacent scan (MS2). Available only for XIC experiments. Fragment parameters are used for XIC experiment types in target screening methods. The application uses fragments to define masses that are present in an adjacent scan (MS2). The mass-to-charge ratio of the target peak. The location of the center of a target quan-ion peak in mass-to-charge ratio (m/z) units. Available only for XIC experiments. Default: 0.0 Range: 10.000 to 2999.999 250 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with the Compound Database Editing Compounds in the Database In the Compound Database view, you can import compounds into the database, add or remove compounds from the database, add target or confirming peaks to a compound, or remove target or confirming peaks from a compound. Follow these procedures: • To add a compound to the database • To remove a compound • To make a compound editable • To add a target peak to a compound • To add a confirming peak to a target peak • To copy target peaks from one compound to another • To copy window values from one peak to another • To add a fragment to a target peak To add a compound to the database 1. Click the Add Compound icon, . The application adds a new, empty compound page and highlights the required parameters in red. 2. Click the Compound box, and type the required Compound name. 3. Select the Experiment type: SRM, SIM, or XIC. The required parameters are different for each experiment type. See “Choosing Experiment Types” on page 258. 4. In the Target Peaks area, do the following: • For SRM experiments, enter values for Precursor Mass and Product Mass. • For SIM or XIC experiments, enter a value for Extracted Mass. 5. In the Confirming Peaks area, do the following: • For SRM experiments, enter values for Precursor and Product Mass. • For SIM or XIC experiments, enter a value for Precursor and Extracted Mass. Thermo Scientific TraceFinder User Guide 251 4 Using the Method Development Mode Working with the Compound Database 6. Enter or edit any of the other optional parameters described in the “Compound Database view parameters” on page 246. Tip You cannot add another new compound or access the menu commands until you enter all required parameters or cancel the new compound. To remove a compound 1. In the Compound list, select the compound that you want to delete. 2. Click the Remove Compound icon, . 3. If you are sure you want to delete the selected compound, at the prompt, click OK. The application removes the selected compound and all its peak information. 4. The application supports the following methods to delete multiple compounds: • CTRL+A to select all compounds • CTRL+click to select noncontiguous compounds • SHIFT+click to select contiguous compounds To make a compound editable 1. In the Compound list, select the compound that you want to edit. 2. Click the Edit Compound icon, . The application makes the compound parameters editable and displays the Add icons, , so that you can add target peaks, confirming peaks, and fragments to the compound details. Note If you are adding a new compound, it is “editable” by default. 252 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with the Compound Database To add a target peak to a compound 1. Click the Add Peak icon in the Target Peaks header. Add Target Peak icon The application adds a new target peak to the compound. A target peak includes quantitative values for the compound. Delete Target Peak icon 2. Enter all required parameters. The required target peak values differ for each experiment type. See “Choosing Experiment Types” on page 258. For a list of required and optional parameters, see the list of “Compound Database view parameters” on page 246. Tip You cannot add another new target peak or save the compound until you enter all required peak parameters or delete the new target peak. 3. Repeat these steps to add as many as six target peaks to the compound. Thermo Scientific TraceFinder User Guide 253 4 Using the Method Development Mode Working with the Compound Database To add a confirming peak to a target peak 1. Click the Add Confirming Peak icon in the Confirming Peaks header. Add Confirming Peak icon The application adds a new confirming peak to the target peak. Delete Confirming Peak icon 2. Type the required values for the confirming peak. The required confirming peak values differ for each experiment type. See “Choosing Experiment Types” on page 258. For a list of required and optional parameters, see “Compound Database view parameters” on page 246. 3. Repeat these steps to add as many as 10 confirming peaks to the target peak. Tip You cannot add another new confirming peak or save the compound until you enter all required peak parameters or delete the new confirming peak. To copy target peaks from one compound to another 1. In the compounds list, select the compound whose target peak you want to copy. Source compound 2. When the target peak includes more than one peak, in the Target Peaks area for the selected compound, scroll to the peak you want to copy. 254 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with the Compound Database 3. In the compounds list, keep the source compound selected and use the SHIFT or CTRL keys to select the compounds that you want to copy the target peak to. Source compound IMPORTANT Be careful to keep the source compound selected. 4. In the Target Peaks area for the selected compound, right-click the target peak area and choose Add Peak 1 to N Selected Compounds from the shortcut menu. Right-click the target peak area. The application reports that the peak was copied to the specified number of compounds. The application copies the peak information to the selected compounds, adding this peak to the peaks already defined for the compounds. 5. Click OK. To copy window values from one peak to another 1. In the compounds list, select the compound with the window value that you want to copy. Source compound Thermo Scientific TraceFinder User Guide 255 4 Using the Method Development Mode Working with the Compound Database 2. In the Target Peaks area for the selected compound, identify the peak whose window you want to copy. 3. In the compounds list, keep the source compound selected and use the CTRL key to select the compounds that you want to copy the window to. Source compound IMPORTANT Be careful to keep the source compound selected. 4. In the Target Peaks area for the selected compound, right-click the target peak area and choose Set the Window for All Peaks of selectedCompounds to windowValue from the shortcut menu. Right-click the target peak area. The application reports that the retention time and window were copied to the specified number of compounds, including the source compound when it has multiple peaks. The application copies the retention time and window information to all peaks in the selected compounds and all additional peaks in the source compound, overwriting the values for these parameters. 5. Click OK. 256 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with the Compound Database To add a fragment to a target peak 1. Click the Add Fragment icon in the Fragments header. Add Fragment icon The application adds a new fragment to the target peak. Delete Fragment icon 2. Click the Extracted Mass box, and type a value between 10 and 2999.999. 3. Repeat these steps to add as many fragments as you want. Tip You cannot save the compound until you enter all required fragment parameters or delete Thermo Scientific the new fragment. TraceFinder User Guide 257 4 Using the Method Development Mode Working with the Compound Database Choosing Experiment Types The TraceFinder application uses three experiment types: SRM, SIM, and XIC. Each of these experiment types uses a different structure for the mass filter. The target peak and confirming peak parameters for each experiment type are defined in the “Compound Database view parameters” on page 246. A compound database can include multiple experiment types for a single compound; however, each compound name and experiment type combination must be unique. SRM: Selected Reaction Monitoring The SRM experiment type supports triple quadrupole LC/MS. The mass filter includes precursor mass and narrow mass ranges to identify product masses. Imported compounds with no experiment type are treated as SRM data. Confirming peaks include values for precursor mass, product mass, and collision energy. 258 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with the Compound Database SIM: Single Ion Monitoring The SIM experiment type supports single quadrupole LC/MS, GC/MS, and Exactive systems. The mass filter includes narrow mass ranges to identify product masses. Confirming peaks include an extracted mass value. Thermo Scientific TraceFinder User Guide 259 4 Using the Method Development Mode Working with the Compound Database XIC: Extracted Ion Chromatogram The mass filter is a single, full scan which is post-processed to extract a peak for the ions of interest. Confirming peaks include an extracted mass value and a choice of mass order: MS1 or MS2. 260 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with the Compound Database Exporting and Importing Compounds From the Compound Database, you can export compounds to a CSV file or import compounds from an XML, a CSV, or a CDB file. Follow these procedures: • To export compounds • To import compounds • To convert a legacy compound database to TraceFinder 3.0 format In addition to procedures for importing and exporting compound data, this section also contains the following topics: • Compound Database Names Mapped to CSV Column Names • Data Columns with Default Values To export compounds 1. Choose Compound Database > Export Compounds from the main menu. The Export Compounds dialog box opens. 2. (Optional) Click Browse and locate a different folder or file name where you want to write the exported compound database. Each parameter in the compound database editor is represented by a column of data in the spreadsheet. When you export compound data to a CSV file, each parameter is assigned to a column and each row is assigned to a compound. 3. Select one of these options: • Export Only Columns with Data: Writes only columns that contain nondefault data for at least one compound. This option does not export columns that contain only default data. See “Data Columns with Default Values” on page 267. • Export All Columns: Writes all columns to the CSV file, including columns that contain no data for any compound. 4. Click Export and Overwrite. Thermo Scientific TraceFinder User Guide 261 4 Using the Method Development Mode Working with the Compound Database The application stores the database as C:\Thermo\TraceFinder\3.0\Forensic\Databases\databaseName.csv A Microsoft Excel window opens with the compound data in spreadsheet format. Figure 69. Compound data in an Excel spreadsheet Column names in an exported Excel spreadsheet do not always match the parameter names in the compound database editor. See “Compound Database Names Mapped to CSV Column Names” on page 266. You can use the tools in the spreadsheet to edit the data in the compound database and then import the data in the CSV file back into the TraceFinder application. If you delete a column from the spreadsheet and then import the CSV file, the TraceFinder application replaces the data in that column with default values. For a list of default values, see “Data Columns with Default Values” on page 267. To import compounds 1. Choose Compound Database > Import Compounds from the main menu. The Select File to Import into the Current Compound Database dialog box opens. You can import compounds from the following file types: • ToxID Exactive CSV • ToxID MS2 CSV • TraceFinder CSV • TraceFinder MassList XML • TraceFinder 2.1 Legacy CDB • ExactFinder 2.0 CDB 262 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with the Compound Database IMPORTANT Before you import data from a CSV file, verify that the following required columns have data for each compound. These columns have no default values and must have a value before you can import .csv data into the TraceFinder compound database: • CompoundName • ExperimentType • ProductMass (target peak) • Confirm Product (confirming peak) • Fragment If you delete one of these columns from the spreadsheet and attempt to import the .csv data into the TraceFinder application, the application warns that it is unable to parse the file and identifies the missing columns. 2. Locate the CDB, CSV, or XML compounds file that you want to import and click Open. The Import Compounds dialog box opens. Note If the import file is missing required compound information, the application warns that it is unable to parse the file and identifies the missing columns. For a list of required columns, see “To convert a legacy compound database to TraceFinder 3.0 format” on page 264. 3. To select a different compound database, click Browse, locate an XML, a CSV, or a CDB compounds file, and click Open. 4. Confirm that the import file and the target database are correct. The dialog box reports the total number of compounds in the import file, the number of compounds with validation errors, and the number of compounds that already exist in the target database. Thermo Scientific TraceFinder User Guide 263 4 Using the Method Development Mode Working with the Compound Database 5. Select one of these options: • Skip: Imports only those compounds that do not already exist in the target database. • Overwrite: Replaces compounds that already exist in the target database with the imported compounds. 6. Click Import. The TraceFinder application imports the compounds from the imported file, adds them to any compounds already in the database, and alphabetically sorts them. The application reports the number of imported compounds. 7. Click OK. To convert a legacy compound database to TraceFinder 3.0 format 1. Choose File > New Compound Database from the main menu. The New Compound Database dialog box opens. 2. In the Database Name box, type a name for the new compound database that you will create. 3. Click OK. The application creates a new, empty database. 4. Choose Compound Database > Import Compounds from the main menu. 264 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with the Compound Database 5. In the Select File to Import into the Current Compound Database dialog box, select a legacy compound database CDB, CSV, or XML file to import. The Import Compounds dialog box opens. 6. Confirm that the import file and the target database are correct. The dialog box reports the total number of compounds in the import file, the number of compounds with validation errors, and the number of compounds that already exist in the target database. Because you are importing compounds into a new, empty database, the number of compounds already found should be zero. 7. Click Import. The application reports the number of imported compounds. 8. Click OK. Note You can use the Import Compounds command to add compounds from a legacy database to your current compound database. See “To import compounds” on page 262. Thermo Scientific TraceFinder User Guide 265 4 Using the Method Development Mode Working with the Compound Database Compound Database Names Mapped to CSV Column Names Column names in an Excel spreadsheet do not always match the parameter names in the compound database editor. The following table maps the parameter names to the column headings in a CSV spreadsheet. Table 52. CSV column names for compound parameters (Sheet 1 of 2) CDB parameter CSV column heading Compound Detail Compound CompoundName Experiment ExperimentType Category Category CAS CAS Formula ChemicalFormula Ionization Ionization Response Threshold (XIC only) ResponseThreshold Target Peaks 266 TraceFinder User Guide Precursor Mass (SRM only) PrecursorMass Product Mass (SRM only) ProductMass Mass (SIM only) ProductMass Extracted Mass (XIC only) Extracted Mass Product Mass Mass Extracted Mass Extracted Mass (when CDB contains any combination of SRM, XIC, and SIM experiments) Adduct Adduct Polarity Polarity Charge State ChargeState Window Window RT RT Collision Energy (SRM only) CollisionEnergy Lens Lens Energy Ramp EnergyRamp Thermo Scientific 4 Using the Method Development Mode Working with the Compound Database Table 52. CSV column names for compound parameters (Sheet 2 of 2) CDB parameter CSV column heading Confirming Peaks Precursor (SRM and XIC only) Confirm Precursor Product Mass (SRM only) Confirm Product Mass (SIM only) Confirm Product Extracted Mass (XIC only) Confirm Extracted Product Mass Mass Extracted Mass Confirm Extracted (when CDB contains any combination of SRM, XIC, and SIM experiments) Collision Energy (SRM only) Confirm Energy Fragments (XIC only) Extracted Mass Fragment Data Columns with Default Values When you export compounds to a CSV file with the Export Only Columns with Data option, the application writes only columns that contain nondefault data for at least one compound. This option does not export columns that contain only default data. When you import compounds from a CSV data file that has missing columns, the application replaces the missing columns and uses default values for all compounds. Table 53. Default values for compound parameters (Sheet 1 of 2) CDB parameter Default value Compound Detail Formula Blank CAS Blank Category Blank Ionization None Response Threshold (XIC only) 5000 Target Peaks Thermo Scientific Precursor Mass Blank Collision Energy 0 TraceFinder User Guide 267 4 Using the Method Development Mode Working with the Compound Database Table 53. Default values for compound parameters (Sheet 2 of 2) CDB parameter Default value Adduct Neutral Lens 0 Energy Ramp 0 Confirming Peaks 268 TraceFinder User Guide Precursor 0 Collision Energy Blank Thermo Scientific 4 Using the Method Development Mode Working with Instrument Methods Working with Instrument Methods An instrument method is a set of experiment parameters that define the operating settings for an autosampler, mass spectrometer, and so on. Instrument methods are saved as file type .meth. IMPORTANT Do not open the Thermo Foundation Instrument Configuration window while the TraceFinder application is running. Follow these procedures: • To open the Instrument View • To create a new instrument method • To create a new multiplexing instrument method • To open an instrument method • To import an instrument method To open the Instrument View 1. Click Method Development from the navigation pane. The Method Development navigation pane opens. 2. Click Instrument View. Thermo Scientific TraceFinder User Guide 269 4 Using the Method Development Mode Working with Instrument Methods To create a new instrument method 1. Choose File > New Instrument Method from the main menu. The Thermo Xcalibur Instrument Setup window opens. Figure 70. Example instrument setup showing multiple configured instruments 2. Click the icon for the instrument that you want to use for the method. 3. Edit the values on the instrument page. 4. From the main menu in the Thermo Xcalibur Instrument Setup window, choose File > Save As. The Save As dialog box opens. 270 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Instrument Methods 5. Select an instrument method name to overwrite, or type a new name for the instrument method, and click Save. The File Summary Information dialog box opens. 6. (Optional) Type a comment about the new instrument method. 7. Click OK. The TraceFinder application saves the new instrument method in the following folder: …\Xcalibur\methods Thermo Scientific TraceFinder User Guide 271 4 Using the Method Development Mode Working with Instrument Methods To create a new multiplexing instrument method 1. Choose File > New Instrument Method from the main menu. The Thermo Xcalibur Instrument Setup window opens. Figure 71. Example instrument setup showing a configured multiplexed instrument 2. Click the icon for the instrument that you want to use for the method. 3. Edit the values for the instrument method. For information about specifying multiplexing values, refer to the documentation for your multiplexed instrument. 4. Specify the channels that you want to use for acquisition. For example: 5. From the main menu in Thermo Xcalibur Instrument Setup window, choose File > Save As. The Save As dialog box opens. 272 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Instrument Methods 6. Select an instrument method name to overwrite or type a new name for the instrument method, and click Save. The File Summary Information dialog box opens. 7. (Optional) Type a comment about the new instrument method. 8. Click OK. The TraceFinder application saves the new instrument method in the following folder: …\Xcalibur\methods To open an instrument method 1. Click Open Instrument Method on the Instrument View navigation pane. An instrument method browser opens. 2. In the browser, do one of the following: • Select an instrument method from the list and click Open. • Click Xcalibur Instrument Method, select a method from the list of recent methods, and click Open. The selected method opens in the Thermo Xcalibur Instrument Setup window. You can edit this method and save the changes, or you can save this method with another name. Note To open Help for any of your configured instruments, click Help on the instrument page. Thermo Scientific TraceFinder User Guide 273 4 Using the Method Development Mode Working with Instrument Methods To import an instrument method 1. From the main menu, choose Instrument View > Import Published Method. The Import Published Method dialog box opens. This dialog box lists the master methods in the Published Master Methods folder. You can import instrument methods that are associated with these published master methods. 2. Select a method that includes the instrument method that you want to import. For instructions about importing the master methods, see “Importing Published Master Methods” on page 235. 3. Click Import. The Save Instrument Method dialog box opens. 4. Do one of the following: Type a new name for the instrument method and click OK. –or– Select an instrument method name to overwrite and click Overwrite. The application reports that the method successfully imported. You can use any of the Open Instrument Method commands to open this method just as you would an instrument method that you created. 274 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Development Batches Working with Development Batches In the Development Batch view, you can test your instrument method in real time by creating and acquiring test samples. Development batches let you test different instrument methods and optimize parameters, such as MS source parameters and autosampler variables, to find the best conditions for a master method. Development batches are not designed for high throughput in everyday analysis. This section includes instructions for the following tasks: • Creating a Development Batch • Editing Samples in a Development Batch • Acquiring Samples in a Development Batch Creating a Development Batch You create a development batch to test your instrument method and use it to acquire samples only once. You cannot save a development batch; you can save only the raw data files created when you acquire the samples in the batch. Follow these procedures: • To open the Development Batch view • To specify a location for development batch data • To add samples to the development batch • To insert samples into the development batch • To copy a sample To open the Development Batch view 1. Click Method Development in the navigation pane. The Method Development navigation pane opens. 2. Click Development Batch. The Development Batch view opens a new, empty batch. Note The Channel column is available only when you have activated multiplexing in the Application Configuration mode. See “Multiplexing” on page 66. Thermo Scientific TraceFinder User Guide 275 4 Using the Method Development Mode Working with Development Batches To specify a location for development batch data 1. To specify a location for the files, choose Development Batch > Select Batch Location from the main menu. By default, the TraceFinder application writes the temporary files, raw data files, and SLD method file to the following folder: …\Thermo\TraceFinder\3.0\Forensic\Temp 2. In the browser, do one of the following: Locate the folder that you want to use for the development batch files and click OK. –or– Create a new folder: a. Locate and select the folder where you want to create a new folder for the batch files. b. Click Make New Folder. The TraceFinder application creates a new folder in the selected folder. c. Right-click the New Folder name and choose Rename from the shortcut menu. d. Type the name for the folder. e. Click OK. The TraceFinder application creates all development batch files in the specified folder. To add samples to the development batch Do one of the following: Right-click and choose Add Sample from the shortcut menu. –or– To add multiple sample rows, enter the number of rows and click the Add Sample icon. The application adds the specified number of new, empty samples to the end of the sample list. To insert samples into the development batch 1. Select the sample above which you want to insert empty samples. 2. Do one of the following: Right-click and choose Insert Sample from the shortcut menu. –or– 276 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Development Batches To insert multiple sample rows, enter the number of rows and click the Insert Sample icon. The TraceFinder application inserts new, empty samples above the selected sample. Note You cannot insert samples into an empty batch. You must have at least one sample to select before you can use this icon. To copy a sample 1. Select the sample that you want to copy. 2. Right-click and choose Insert Copy Sample from the shortcut menu. The TraceFinder application adds a copy of the sample above the selected sample. Editing Samples in a Development Batch A development batch requires fewer parameters than a real batch, but the mechanism for managing the information is the same. For detailed instructions about using the Copy Down or Fill Down commands to enter column values, see Appendix B, “Using Copy Down and Fill Down.” A development batch uses the same shortcut menu features as a batch in the Batch View in the Analysis mode. For detailed descriptions of the right-click shortcut menu, see “Batch View Shortcut Menu” on page 355. Follow these procedures: • To enter column values • To resize or reorganize the columns • To remove selected samples from the list • To remove all samples from the list To enter column values 1. Double-click the Filename column and type a file name for the raw data file. 2. (Optional) Enter values for the Sample Name or Sample ID columns. 3. Enter a vial position for each sample. 4. Enter an injection volume for each sample. The minimum injection volume value allowed is 0.1 μL; the maximum injection volume value allowed is 5000 μL. Thermo Scientific TraceFinder User Guide 277 4 Using the Method Development Mode Working with Development Batches 5. To enter an instrument method for each sample, click the down arrow in the Instrument Method column and select a method from the list. This list contains all the available instrument methods. 6. To enter a channel for each sample, click the down arrow in the Channel column and select a channel from the list. You cannot specify the auto channel selection in a development batch. Note The Channel column is available only when you have activated multiplexing in the Application Configuration mode. See “Multiplexing” on page 66. Figure 72. Completed development batch To resize or reorganize the columns 1. To resize a column, drag the header separator on the right side of the column. 2. To move a column, drag the column header. You cannot move the Filename column. To remove selected samples from the list 1. Select the samples that you want to remove. Use the first column to ensure that the samples are selected. Selected samples 2. Right-click and choose Remove Selected Samples from the shortcut menu. 278 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Development Batches To remove all samples from the list 1. Choose File > New Sample List from the main menu. One of the following happens: • If the samples in the current batch have all been acquired, the list is cleared. • If the samples in the current list have not been acquired, a message confirms that you want to clear them and start a new list. 2. To create a new empty list, click Yes. Note You cannot save a development batch when you create a new one; you can only create, acquire, and discard each batch after you use it. The TraceFinder application saves only the generated raw data files in the specified batch location. Thermo Scientific TraceFinder User Guide 279 4 Using the Method Development Mode Working with Development Batches Acquiring Samples in a Development Batch In a development batch, you can submit the entire batch for acquisition or submit only selected samples. Follow these procedures: • To acquire selected samples • To acquire the batch To acquire selected samples 1. Select the samples that you want to acquire. 2. Right-click and choose Submit Selected Samples from the shortcut menu, or click the Submit Selected Samples icon, . The TraceFinder application creates a raw data file for each selected sample. It writes the raw data files and all temporary working files to the following folder: C:\Thermo\TraceFinder\3.0\Forensic\Temp When the acquisition is complete, the application deletes all the temporary working files. Only the raw data files and a MethodDevelopment.sld file remain in the folder. If you acquire a sample more than once, the application time-stamps the subsequent raw data files with the acquisition time. To acquire the batch Right-click and choose Submit Batch from the shortcut menu, or click the Submit Batch icon, . The TraceFinder application creates a raw data file for each sample in the batch and an .sld method file. The TraceFinder application writes the raw data files, the .sld method file, and all temporary working files to the specified folder. When the acquisition is complete, the application deletes all the temporary working files. Only the raw data files and a MethodDevelopment.sld file remain in the folder. If a sample is acquired more than once, the subsequent raw data files are time-stamped with the acquisition time. 280 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Working with Development Batches Viewing Raw Data Files in the Qual Browser You can view the chromatogram and spectra for completed samples in a development batch. Follow these procedures: • To open the Qual Browser • To display the last completed raw data file in the Qual Browser To open the Qual Browser From the main menu, choose Go > Launch Qual Browser. The Thermo Xcalibur Qual Browser window opens. For detailed instructions about using the Qual Browser, refer to the Qual Browser Help. Thermo Scientific TraceFinder User Guide 281 4 Using the Method Development Mode Working with Development Batches To display the last completed raw data file in the Qual Browser On the Acquisition page of the real-time viewer, right-click and choose View Last File in Qual Browser from the shortcut menu. The last completed file opens in the Qual Browser. When all samples are completed, you can view the last raw data file for the batch. 282 TraceFinder User Guide Thermo Scientific 4 Using the Method Development Mode Using Quick Acquisition Using Quick Acquisition Use the quick acquisition feature to quickly submit a single sample from any view of the Acquisition mode. Note The Quick Acquisition feature is available only when you activate it in the Application Configuration mode. See “Quick Acquisition” on page 64. To run a quick acquisition 1. Choose Go > Quick Acquire Sample from the main menu or click the Quick Acquire Sample icon, . The Quick Acquisition dialog box opens. 2. Select an instrument method. 3. Type a name for the raw data file that you acquire. Do not enter the .raw file extension. 4. For the path, browse to a folder where you want to write the acquired raw data file. 5. Select either the manual injection or the autosampler option: • To perform manual injection, do the following: i. Select the Manual Injection option. ii. Click OK. The application submits the sample to the Acquisition queue. See “Acquisition Page” on page 324. Thermo Scientific TraceFinder User Guide 283 4 Using the Method Development Mode Using Quick Acquisition • To perform autosampler injection, do the following: i. Select the Use Autosampler option. ii. In the Vial Position box, type a vial position. iii. In the Injection Volume box, type an injection volume. The minimum injection volume allowed is 0.1 μL; the maximum injection volume allowed is 5000 μL. iv. Click OK. The Quick Acquisition dialog box opens. v. Select the Use check box for the device that you want to use for this acquisition. vi. (Optional) Select the Start Device check box to indicate the device that will initiate communication with the other instruments. This is usually the autosampler. vii. (Optional) Select the Start When Ready check box, which starts all instruments together when they are all ready. When this is cleared, individual instruments can start at different times and then must wait for the last instrument to be ready. viii. (Optional) Select the Priority check box to place the sample immediately after any currently acquiring sample. ix. (Optional) Select a value for the Post-run System State: Unknown, On (default), Off, or Standby. The application sets the system to this state after it acquires the last sample. x. Click OK. The application submits the sample to the Acquisition queue. See “Acquisition Page” on page 324. 284 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode This chapter describes the tasks associated with the Acquisition mode. This mode is available only when you select the Acquisition Batch Wizard style in the Application Configuration mode. See “Batch Wizard Style” on page 65. Contents • Working with Batches • Using Quick Acquisition • Real Time Status Pane • Sample Types When you plan to work with multiple samples or use similarly designed batches, use the Acquisition mode to reduce the amount of data you must enter. Because the nature and types of batches are often similar (in some cases specified by laboratory standard practices), you can define a batch template that supplies the basic structure of a batch. Note When user security is activated, only a user in the LabDirector or Supervisor role can create a batch template. Using a master method, you can create a batch and run the samples. A batch represents one or more samples that are to be acquired, processed, reviewed, and reported as a set. After you create a batch of samples, you can submit the batch and review the results in the Analysis mode or you can go directly to viewing and printing reports. You can set up a calibration batch with known concentrations of the target compounds and compare the calibration values against samples in future batches. You can also use the Quick Acquisition feature to quickly submit a single sample from any page in the Acquisition mode. See “Using Quick Acquisition” on page 321. Thermo Scientific TraceFinder User Guide 285 5 Using the Acquisition Mode Working with Batches Working with Batches This section includes instructions for the following tasks: • Opening and Navigating the Acquisition Mode • Creating and Submitting Batches Opening and Navigating the Acquisition Mode To access the Acquisition mode Click Acquisition in the navigation pane. The navigation pane for the Acquisition mode opens. As you progress through the Acquisition mode using any of these methods for creating a batch, the task pane at the top of the view tracks your progress. As you complete each stage, you can hold your cursor over the view name in the task pane to display the parameters that you specified for the batch. See Example task pane when you have completed the Acquisition mode. 286 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode Working with Batches Figure 73. Example task pane when you have completed the Acquisition mode Hold your cursor over Batch Selection, Sample Definition, or Report Selection to view the parameters for your batch. Categories in the Sample Definition list: QC Samples: QC Calibration Samples: Calibrator Blank Samples: Negative Unknown Samples: All other samples Thermo Scientific TraceFinder User Guide 287 5 Using the Acquisition Mode Working with Batches Creating and Submitting Batches To create and submit a batch, the Acquisition mode uses a wizard-style interface to guide you through these major steps: 1. Selecting a Batch 2. Defining the Sample List 3. Selecting and Reviewing Reports 4. Submitting the Batch The Acquisition mode provides multiple techniques for creating either a batch or a batch template. • To start a new quantitative batch • To start a new screening batch • To select a prepared batch • To reinject samples in a previously acquired batch • To create a quantitative batch template • To create a screening batch template Each batch creation technique has an associated workflow, as shown in the following flowcharts. Each workflow uses a different combination of Acquisition mode views. Workflow for Creating an Original Batch Batch and Method Samples Reports Finish To create an original batch, start with the instructions “To start a new quantitative batch” on page 290 or “To start a new screening batch” on page 292. 288 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode Working with Batches Workflow for Acquiring a Prepared Batch Batch Finish Samples To acquire a prepared batch, start with the instructions “To select a prepared batch” on page 294. Workflow for Reinjecting a Previously Acquired Batch Batch Samples Finish To process a previously acquired batch, start with the instructions “To reinject samples in a previously acquired batch” on page 295. Workflow for Creating or Editing a Batch Template Template and Method Samples Finish Note When user security is activated, in either the LabDirector or ITAdmin role, you can create a batch template. To create a batch template, start with the instructions “To create a quantitative batch template” on page 296 or “To create a screening batch template” on page 297. Thermo Scientific TraceFinder User Guide 289 5 Using the Acquisition Mode Working with Batches Selecting a Batch In a Batch Selection view of the Acquisition mode, you can create a new quantitative or screening batch in any of your current projects/subprojects. Or, you can submit a batch that you previously prepared and saved, reinject the samples in a batch that you previously acquired, or create a batch template to use for future batches. Follow these procedures: • To start a new quantitative batch • To start a new screening batch • To start a new batch from a template • To select a prepared batch • To reinject samples in a previously acquired batch • To create a quantitative batch template • To create a screening batch template To start a new quantitative batch 1. Click Create a New Batch in the navigation pane. 2. Select the Quantitative Batch option. 3. Select the project and subproject where you want to create the new batch. 4. Type a name for the new batch in the Batch Name box. If the name you enter is not unique, a red warning flashes. 5. Select a method from the Method Selection list. 290 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode Working with Batches The Method Compound Data pane displays the compounds in the method. You cannot edit the compounds list from the Acquisition mode. 6. To continue to the next view, click Next. The Sample Definition view opens. See “Defining the Sample List” on page 298. Thermo Scientific TraceFinder User Guide 291 5 Using the Acquisition Mode Working with Batches To start a new screening batch 1. Click Create a New Batch in the navigation pane. 2. Select the Screening Batch option. 3. Select the project and subproject where you want to create the new batch. 4. Type a name for the new batch in the Batch Name box. If the name you enter is not unique, a red warning flashes. 5. Select a method from the Method Selection list. The Method Compound Databases pane displays the compound databases in the method. The application uses these databases to identify the compounds in the samples. You cannot edit the compound database list from the Acquisition mode. 6. To continue to the next view, click Next. The Sample Definition view opens. See “Defining the Sample List” on page 298. 292 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode Working with Batches To start a new batch from a template 1. Click Create a New Batch in the navigation pane. 2. Select either the Screening Batch or the Quantitative Batch option. The Available Templates pane displays only batch templates for the selected option. 3. In the Available Templates pane, select the template and method combination that you want to use. The system creates a batch name with the selected template name and appends the date and time stamp. You can change the default project, subproject, or method associated with this template. 4. (Optional) Select a different project and subproject where you want to create the new batch. 5. (Optional) Select a different method to use for the new batch. 6. To continue to the next view, click Next. The Sample Definition view of the Acquisition mode opens. See “Defining the Sample List” on page 298. Thermo Scientific TraceFinder User Guide 293 5 Using the Acquisition Mode Working with Batches To select a prepared batch 1. Click Submit a Prepared Batch in the navigation pane. The application displays all your unacquired, saved batches. The TraceFinder application stores all unacquired batches in the following folder: …\Thermo\TraceFinder\3.0\Forensic\Projects\projectname\subprojectname 2. Select the batch that you want to acquire. 3. To continue to the next view, click Next. The Finish view of the Acquisition mode opens. From the Finish view, you can save the batch, submit the batch for acquisition, or go to the Sample Definition view to edit the sample list for this batch. • If the batch is unreadable, the application reports that the batch file is not valid and cannot be opened. • If a sample in the batch is unreadable, the application cannot open the sample. The application creates a new sample with the same name and flags the sample. You must complete the missing information such as Sample Type, Level, and so forth, and then save the batch before you submit it for acquisition. Or, you can browse in a new raw data file to replace the corrupt file. 4. Do one of the following: • To edit the sample list, click Previous. For detailed instructions, see “Defining the Sample List” on page 298. –or– . • To prepare the batch for acquisition, click Submit, For detailed instructions, see “Submitting the Batch” on page 313. –or– • To save the batch to be acquired later, click Save, . The TraceFinder application saves your batch in the following folder: C:\Thermo\TraceFinder\3.0\Forensic\Projects\projectname\subprojectname 294 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode Working with Batches To reinject samples in a previously acquired batch 1. Click Reinject Samples in the navigation pane. 2. In the Project pane, select a project name. All subprojects included in the selected project are displayed in the Subproject pane. 3. In the Subproject pane, select a subproject name. The Batch pane displays all previously acquired batches included in the selected subproject, both quantitative and screening. 4. In the Batch pane, select the batch that you want to reacquire. 5. To continue to the next view, click Next. The Sample Definition view of the Acquisition mode opens. See “Defining the Sample List” on page 298. • If the batch is unreadable, the application reports that the batch file is not valid and cannot be opened. • If a sample in the batch is unreadable, the application creates a new sample with the same name and flags the sample. You must complete the missing information, such as Sample Type, Level, and so forth, and then save the batch before you submit it for acquisition. Or, you can browse in a new raw data file to replace the corrupt file. Thermo Scientific TraceFinder User Guide 295 5 Using the Acquisition Mode Working with Batches To create a quantitative batch template 1. Click Create or Edit a Template in the navigation pane. Note When user security is activated, this page is available only to users in the LabDirector or Supervisor role. 2. Select the Quantitative Batch option. 3. Select the project and subproject where you want to create the new batch template. 4. Type a name for the new batch template in the Template Name box. 5. Select a method from the Method Selection list. The Method Compound Data pane displays the compounds in the method. You cannot edit the compounds list from the Acquisition mode. 6. To continue to the next view, click Next. The Sample Definition view of the Acquisition mode opens. See “Defining the Sample List.” 296 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode Working with Batches To create a screening batch template 1. Click Create or Edit a Template in the navigation pane. Note When user security is activated, this page is available only to users in the LabDirector or Supervisor role. 2. Select the Screening Batch option. 3. Select the project and subproject where you want to create the new batch template. 4. Type a name for the new batch template in the Template Name box. 5. Select a method from the Method Selection list. The Method Compound Data pane displays the compounds in the method. You cannot edit the compounds list from the Acquisition mode. 6. To continue to the next view, click Next. The Sample Definition view of the Acquisition mode opens. See “Defining the Sample List.” Thermo Scientific TraceFinder User Guide 297 5 Using the Acquisition Mode Working with Batches Defining the Sample List Use the Samples page in the Sample Definition view of the Acquisition mode, to create a list of samples for the batch. See “Samples page in the Sample Definition view” on page 306. You can add samples, insert samples, import a sample list, or remove samples from the list. You can use the Reference Sample page to select a reference sample to use as a reference peak in the Data Review. See “Reference Sample page in the Sample Definition view” on page 308. To create the sample list, you can use either of two sets of function buttons (described in the following graphic) or you can use commands on the shortcut menu (see the Shortcut Menu section of the “Samples page parameters” on page 306). As you enter sample values, you can use the Copy Down and Fill Down commands to quickly enter column values. For detailed instructions on using Copy Down and Fill Down to enter column values, see Appendix B, “Using Copy Down and Fill Down.” Use any of the following procedures to create a sample list. When you finish defining the list of samples, click Next. • When you are creating a batch from scratch, creating a batch from a template, or editing a batch template and you click Next, the Report Selection view opens. See “Selecting and Reviewing Reports” on page 309. • When you are editing a prepared batch or reinjecting samples and you click Next, the Finish Selection view opens. See “Submitting the Batch” on page 313. Follow these procedures: • To add samples to the list • To insert samples into the list • To import samples into the list • To remove samples from the list • To reinject a sample from a previously acquired batch • To select channels for the batch • To assign a specific channel to a sample • To select a reference sample To add samples to the list 1. Select the number of sample rows to add and then click the Add icon, or . 2. Type a file name in the Filename column for each sample. Each file name must be unique. 298 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode Working with Batches 3. Select a sample type from the Sample Type list for each sample. Available sample types Specimen QC Solvent Calibrator Unextracted Negative Hydrolysis For a detailed description of each sample type, see “Sample Types” on page 337. 4. For each Calibrator or QC sample, select a level from the Level list. The sample levels are defined in the master method. If there are no levels to select in the Level list, ask a user with Supervisor or LabDirector permissions to edit the method and specify the levels. Then return to the Acquisition mode, and begin the batch again. The application does not save a batch when you leave the Acquisition mode. If you have Supervisor or LabDirector permission, do the following: a. Return to the Method Development mode. b. Open the method. c. Click the Compounds tab. d. Click the Calibration Levels tab. e. Add the levels. f. Save the method. For detailed instructions, see “Calibration Levels” on page 166. 5. For each sample, type a vial position in the Vial Position column. Tip Use the Fill Down command to make entering vial positions easier. 6. For each sample, type a volume in the Injection Volume column. The minimum injection volume value allowed is 0.1 μL; the maximum injection volume value allowed is 5000 μL. 7. (Optional) Type or edit the values for the remaining columns. Note When you use the horizontal scroll bar at the bottom of the sample list, the Status, Filename, Sample Type, and Level columns stay fixed while the other columns scroll right and left. For instructions to automatically copy or fill values in these columns, see Appendix B, “Using Copy Down and Fill Down.” Thermo Scientific TraceFinder User Guide 299 5 Using the Acquisition Mode Working with Batches To insert samples into the list 1. Select the sample above which you want to insert new Specimen samples. You cannot use the Insert command to create the first sample row. 2. Select the number of samples to insert and then click the Insert icon, or . The application inserts the Specimen samples above the selected sample. Inserted samples 3. For each sample, type a file name in the Filename column. Each file name must be unique. 4. For each sample, select a sample type from the Sample Type list. For a detailed description of each sample type, see “Sample Types” on page 337. Available sample types Specimen QC Solvent Calibrator Unextracted Negative Hydrolysis 5. For each Calibrator or QC sample, click the Level cell and select a level from the list. The sample levels are defined in the master method. If there are no levels to select from the Level list, ask a user with Supervisor or LabDirector permissions to edit the method and specify the levels. Then return to the Acquisition mode, and begin the batch again. The application does not save a batch when you leave the Acquisition mode. If you have Supervisor or LabDirector permission, follow the instructions in step 4 of the procedure “To add samples to the list” on page 298. 6. Type a vial position in the Vial Position column for each sample. Tip Use the Fill Down command to make entering vial positions easier. 7. For each sample, type a volume in the Injection Volume column. The minimum injection volume allowed is 0.1 μL; the maximum injection volume allowed is 5000 μL. 300 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode Working with Batches 8. (Optional) Type or edit the values for the remaining columns. Note When you use the horizontal scroll bar at the bottom of the sample list, the Status, Filename, Sample Type, and Level columns stay fixed while the other columns scroll right and left. To import samples into the list 1. Click Import, . The Sample Import Tool dialog box opens. Use this dialog box to import a sample list from a CSV, an XML, or an SLD file. 2. Click Browse and select a CSV, an XML, or an SLD file with the sample definitions that you want to import. Note The .csv, .xml, or .sld file format must match the TraceFinder file format. 3. From the Imported Samples Will Be list, select either Appended to the End of the List or Inserted at the Selected Row. 4. Click Import. The Sample Import Tool dialog box closes, and the application adds the specified samples to the sample list. When you import samples from an Xcalibur sequence file (.sld), the TraceFinder application makes the following column name substitutions. Xcalibur column TraceFinder column Position Vial position Inj Vol Injection volume Dil Factor Conversion Factor When you import samples from an Xcalibur sequence file (.sld), the TraceFinder application makes the following sample type substitutions. Thermo Scientific Xcalibur sample type TraceFinder sample type Blank Negative Std Bracket Calibrator TraceFinder User Guide 301 5 Using the Acquisition Mode Working with Batches 5. For each Calibrator or QC sample, click the Level cell and select a level from the list. The sample levels are defined in the master method. If there are no levels to select from the Level list, ask a user with Supervisor or LabDirector permissions to edit the method and specify the levels. Then return to the Acquisition mode, and begin the batch again. The application does not save a batch when you leave the Acquisition mode. If you have Supervisor or LabDirector permission, follow the instructions in step 4 of the procedure “To add samples to the list” on page 298. For detailed instructions about defining calibration levels, see “Calibration Levels” on page 166. 6. Type a vial position in the Vial Position column for each sample. Tip Use the Fill Down command to make entering vial positions easier. 7. Type a volume in the Injection Volume column for each sample. The minimum injection volume value allowed is 0.1 μL; the maximum injection volume value allowed is 5000 μL. 8. (Optional) Type or edit the values for the remaining columns. Note When you use the horizontal scroll bar at the bottom of the sample list, the Status, Filename, Sample Type, and Level columns stay fixed while the other columns scroll right and left. 9. (Optional) When using multiplexing, select a channel for each imported sample. Imported samples default to Auto. To remove samples from the list 1. Select the samples that you want to remove. Tip Use the CTRL or SHIFT keys to select multiple samples. 2. Right-click and choose Remove Selected Samples from the shortcut menu. To reinject a sample from a previously acquired batch 1. In the sample list, select the sample to reinject. 2. Right-click and choose Reinject Selected Samples from the shortcut menu. The TraceFinder application creates a copy of the selected sample and appends INJ001 to the file name. Additional reinjections of the same sample are numbered INJ002, INJ003, and so forth. The TraceFinder application copies all parameter values from the original sample. 302 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode Working with Batches A green status icon indicates previously acquired samples (acquired and processed) and the sample name is grayed out. A blue status icon indicates samples created for reinjection (not acquired). When you submit this batch, the application acquires only the reinjection samples. To select channels for the batch Note These features are available only when you have activated multiplexing in the Application Configuration mode. See “Multiplexing” on page 66. To disable a configured channel, clear the check box for the channel in the Multiplexing Channels area at the bottom of the page. By default, all configured channels are selected. The configured channels are determined by the multiplexing settings in the Application Configuration mode. See “Multiplexing” on page 66. Clearing a channel in the Multiplexing Channels area does not remove this channel selection from the Channels list for each sample. When you assign a channel to a sample, be careful not to assign a channel that is not available. To assign a specific channel to a sample 1. Scroll to the Channel column. Note The Channel column is available only when you have activated multiplexing in the Application Configuration mode. See “Multiplexing” on page 66. All samples default to Auto. 2. Select a channel from the Channel list. When you submit the batch, samples that are set to Auto run on any of the available channels and samples that are set to a specific channel run only on that channel. Thermo Scientific TraceFinder User Guide 303 5 Using the Acquisition Mode Working with Batches If you select a channel that is not available for this batch, the application flags the sample sequence on the Finish page of the Acquisition mode. See the previous procedure, To select channels for the batch. 3. If you see this error, do the following: a. Click Previous to return to the Sample Definition view. The incorrect sample is marked with an error flag. b. Correct the channel selection. 304 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode Working with Batches To select a reference sample 1. Click the Reference Sample tab. The Reference Sample page in the Sample Definition view opens. See “Reference Sample page in the Sample Definition view” on page 308. You can select one reference sample to use as a reference peak in the Data Review. 2. Right-click the Reference Sample page and choose Add Reference Sample from the shortcut menu. The Open Chromatograph Reference Sample dialog box opens. Note If you are using a new method, you will not see any reference samples here. You must create and save a batch using the current method to see the reference samples in this list. 3. Select a project from the list of projects. 4. Select a subproject from the list of subprojects. 5. Select a batch from the list of batches. The TraceFinder application displays only batches that were created using the current master method. 6. Select a sample from the list of processed samples on the right. The TraceFinder application displays all the processed samples in the selected batch. To use a sample as a reference sample, the sample must have been processed with the current master method. 7. Click Open. 8. The application adds the reference sample to the Reference Sample page. 9. (Optional) Enter values for Sample ID, Sample Name, Comment, and Barcode Actual. 10. (Optional) Change the Vial Position for the sample. The application uses the peak in this sample as a reference peak in the Analysis mode. See “Reference Peak” on page 451. Thermo Scientific TraceFinder User Guide 305 5 Using the Acquisition Mode Working with Batches Figure 74. Samples page in the Sample Definition view Table 54. Samples page parameters (Sheet 1 of 2) Parameter Definition Previous Returns you to the previous Acquisition mode view. Next Takes you to the next Acquisition mode view. Status color codes Sample is not acquired. Sample is acquired but not processed. Sample is acquired and processed. Sample is currently acquiring. Sample Controls Add Adds the specified number of empty rows to the sample grid. Insert Inserts the specified number of empty rows above the selected row. Import Opens the Sample Import Tool where you can import samples defined in a CSV file or an XML file. Multiplexing Channels These features are available only when you have activated multiplexing in the Application Configuration mode. See “Multiplexing” on page 66. All Channels Uses all configured channels to acquire this batch. Channel 1-n Uses only the selected channels to acquire this batch. Shortcut menu commands Add Sample Adds a single empty row to the sample grid. Insert Sample Inserts a single empty row to the sample grid above the selected row. Insert Copy Sample Copies the currently selected row and inserts a copy above the row. Reinject Selected Samples Creates a copy of the selected sample and appends INJ001 to the file name. Additional reinjections of the same sample are numbered INJ002, INJ003, and so forth. 306 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode Working with Batches Table 54. Samples page parameters (Sheet 2 of 2) Parameter Definition Remove Selected Samples Removes selected samples from the sample grid. Copy Down Copies the value in the selected row to all rows below it. For detailed instructions about using the Copy Down command, see Appendix B, “Using Copy Down and Fill Down.” Fill Down Enters sequential values in the column starting with the value in the selected row and ending with the last row in the column. For detailed instructions about using the Fill Down command, see Appendix B, “Using Copy Down and Fill Down.” Modify Columns Opens the Modify Columns dialog box. See “Column Display” on page 345. Enable/Disable Sample Weight Calculation Displays or hides the Sample Volume, Dilution Factor, Sample Weight, Calculation Type, and Final Units columns. Copy Copies the data in the selected rows or columns to the Clipboard. Use this command to copy sample information to another application, such as an Excel spreadsheet. You cannot paste this data back into the Acquisition mode sample list. Copy With Headers Copies the data in the selected rows or columns and the associated column headers to the Clipboard. Use this command to copy sample information to another application, such as a Microsoft Excel spreadsheet. You cannot paste this data back into the Acquisition mode sample list. Paste Pastes a single column of copied data from another application, such as an Excel spreadsheet, into the selected column. Undo Last Paste Removes the last pasted item in the Acquisition mode sample list. Export to CSV File Opens the Save As dialog box where you can save the current sample list to a CSV file. Thermo Scientific TraceFinder User Guide 307 5 Using the Acquisition Mode Working with Batches Figure 75. Reference Sample page in the Sample Definition view Table 55. Reference Sample page parameters Parameter Status Description Sample is not acquired. Sample is acquired but not processed. Sample is acquired and processed. Sample is currently acquiring. Filename Name of the raw data file that contains the sample data. Sample ID A user-defined, alphanumeric string that identifies a sample. Sample Name A user-defined name that identifies a sample. Vial Position The tray vial number used for an autosampler acquisition. Barcode Actual A user-entered barcode for the vial. Shortcut menu commands Add Reference Sample Opens the Open Chromatogram Reference Sample dialog box where you can select a reference sample. Delete Selected Deletes the reference sample. Copy Copies the data in the selected rows or columns to the Clipboard. Use this command to copy sample information to another application, such as an Excel spreadsheet. You cannot paste this data back into the reference sample list. Copy With Headers Copies the data in the selected rows or columns and the associated column headers to the Clipboard. Use this command to copy sample information to another application, such as an Excel spreadsheet. You cannot paste this data back into the reference sample list. Paste Pastes a single column of copied data from another application, such as an Excel spreadsheet, into the selected column. Export to CSV File Opens the Save As dialog box where you can save the current sample list to a CSV file. 308 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode Working with Batches Selecting and Reviewing Reports On the Report Selection view, you can specify the types of reports that you want to create. See “Report Selection view” on page 311. For a complete list of report types and examples of output files, see Appendix A, “Reports.” In addition to the report type, you can specify a report description for each of your reports. • For each standard report that you generate, you can create a hardcopy printout, a PDF file, or an XML file. • For each custom report that you generate, you can create a hardcopy printout or an XLSM file. • For each target screening report that you generate, you can create a hardcopy printout or a PDF file. • For each ToxID report that you generate, you can create a hardcopy printout or a PDF file. Use any of the following procedures to create a reports list. When you finish specifying your report options, click Next to go to the Finish view and submit your batch. See “Submitting the Batch” on page 313. The application writes the resulting output files for your reports to the following folder: …\TraceFinder\3.0\Forensic\Projects\projectname\subprojectname\batchname\Reports Follow these procedures: • To edit a report description • To preview a standard report • To specify a standard report in print format or as a PDF, an XML, or an XLSM file • To specify a custom report in hardcopy or XLSM format • To specify a ToxID or target screening report in hardcopy format or as a PDF file • To export reports to a specific folder To edit a report description Select the Report Title column and edit the default title. The default report title is the same as the report name. Thermo Scientific TraceFinder User Guide 309 5 Using the Acquisition Mode Working with Batches To preview a standard report 1. Click (magnifier icon) to view an example of the report type as a PDF file. The right pane of the view displays an example PDF report with typical PDF viewer buttons. 2. To minimize the PDF viewer, click . Note Only Standard report types have preview documents. To specify a standard report in print format or as a PDF, an XML, or an XLSM file 1. For each type of report that you want to create, select the check box in the Print, Create PDF, or Create XML columns. 2. To duplicate the output type for all reports, right-click the cell and choose Copy Down from the shortcut menu. All check boxes in the column below the selected cell duplicate the selected or cleared state in the selected cell. This action applies only to report types that make this output format available. To specify a custom report in hardcopy or XLSM format 1. For each custom report that you want to create, select the check box in the Print or Create XLSM columns. 2. To duplicate the output type for all reports, right-click the cell and choose Copy Down from the shortcut menu. All check boxes in the column below the selected cell duplicate the selected or cleared state in the selected cell. This action applies only to report types that make this output format available. To specify a ToxID or target screening report in hardcopy format or as a PDF file 1. For each target screening report that you want to create, select the check box in the Print or Create PDF columns. 2. To duplicate the output type for all reports, right-click the cell and choose Copy Down from the shortcut menu. All check boxes in the column below the selected cell duplicate the selected or cleared state in the selected cell. This action applies only to report types that make this output format available. To export reports to a specific folder 1. Select the Export Results check box at the lower left corner of the view. 310 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode Working with Batches The Browse For Folder dialog box opens. 2. Locate and select the folder where you want to save the reports. 3. To create a new reports folder within the selected folder, click Make New Folder and type the new folder name. 4. Click OK. The application writes all reports to the specified folder in addition to the batch Reports folder. Figure 76. Report Selection view Table 56. Report Selection view parameters (Sheet 1 of 2) Parameter Description Example Displays an example PDF for the report type. This example provides a model of the report type only; it does not reflect your specific data. This is available for standard reports only. Report Name The name of a report. Report Title User-editable description to be used on a report. Report Type The type of report: Standard, Custom, ToxID, or Target Screening. Print Reports to be sent to the printer. Create PDF Reports to be saved as PDF files. Available only for standard, ToxID, and target screening reports. Create XML Reports to be exported in XML format. Available only for standard reports. Create XLSM Reports to be exported in Excel Macro-Enabled Workbook (.xlsm) format. Available only for custom reports. Thermo Scientific TraceFinder User Guide 311 5 Using the Acquisition Mode Working with Batches Table 56. Report Selection view parameters (Sheet 2 of 2) Parameter Description Batch Level Rather than creating separate reports for each sample, the application uses a composite of the data from all the samples to create a single report for the entire batch. Batch-level reports are prepended with a B to differentiate them. You cannot select this option from the Report Selection page. You must select the Batch Level option for the report in the report configuration. See “Specifying the Reports Configuration” on page 39. Shortcut menu: Copy Down Copies the selected or cleared state to all subsequent reports in the column. Export Results Writes all reports to the specified folder in addition to the batch Reports folder. 312 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode Working with Batches Submitting the Batch In the Finish view of the Acquisition mode, you can specify a startup method, a shutdown method, or a calibration batch. You can save the batch to be acquired later, or you can acquire and process data and optionally create reports. See “Finish view” on page 320. Note If you are working with a batch template, the only available function is Save. Follow these procedures: • To specify startup or shutdown methods • To automatically update the timed SRM information • To specify a calibration batch • To specify device states • To save a batch for later acquisition • To start an acquisition • To view the output files To specify startup or shutdown methods 1. Select a method from the System Startup Method list. The TraceFinder application runs this method before running the batch. No autosampler injection takes place. This feature is not available for all instruments. 2. Select a method from the System Shutdown Method list. The TraceFinder application runs this method after running the batch. This feature is not available for all instruments. To automatically update the timed SRM information Select the Auto TSRM Update check box. When you submit the batch, the application updates the TSQ method with mass transitions, collision energy, and other appropriate data for TSRM functionality. Thermo Scientific TraceFinder User Guide 313 5 Using the Acquisition Mode Working with Batches To specify a calibration batch 1. In the Calibration area, select a calibration (.calx) file from the list. Note You must acquire at least one batch with the current method to create a .calx calibration file. 2. To add calibration data from the current batch to the selected calibration file, select the Extend Calibration option. To specify device states In the System Status area, select the name of the device, right-click, and then choose a device state from the shortcut menu. Table 57. Instrument states (Sheet 1 of 2) Instrument state Description Turn Device On Keeps the system in the On state when the current run finishes, so you can begin another run without waiting. All power and flows are maintained at operational levels. Default: On Turn Device Standby Keeps the system in the Standby state when the current run finishes, so you can begin another run with only a short delay between runs. Some devices do not have a Standby feature. For devices with this feature, the device enters a power-saving or consumable-saving mode, and you can switch the device back on in approximately 15 minutes. Depending on the instrument, this state turns liquid flows off but maintains heaters and other subsystems in an On state so that there is no warm-up time required when you change from Standby to On. 314 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode Working with Batches Table 57. Instrument states (Sheet 2 of 2) Instrument state Description Turn Device Off Keeps the system in the Off state when the current run finishes. The Off state indicates that all power to the instrument, which the TraceFinder application can control, is turned off. This includes power to all heaters and subassemblies, but in some cases not all subassemblies. Some devices do not have an Off feature. For devices that do have this feature, the device enters a power-saving or consumable-saving mode, and you can switch the device back on. When several runs are queued, the application uses the system power scheme of the last submitted run. Instrument status indicators Green indicates that the device is turned on or is running. Yellow indicates that the device is in standby mode or is waiting for contact closure. Red indicates that the device is turned off or that there is an error with the device. To save a batch for later acquisition From the Finish view, click Save, . The TraceFinder application saves your batch as a prepared file. To start an acquisition 1. Click Submit, . The Submit Options dialog box opens. For detailed descriptions of the parameters, see “Submit Options dialog box” on page 317. 2. (Optional) Select the Create Reports check box. Note By default, the application acquires and processes data when you submit the batch. 3. Select the Use check box for the device that you want to use for this acquisition. 4. (Optional) Select the Start Device check box to indicate the device that will initiate communication with the other instruments. This is usually the autosampler. 5. (Optional) Select the Start When Ready check box, which starts all instruments together when they are all ready. When this is cleared, individual instruments can start at different times and then have to wait for the last instrument to be ready. Thermo Scientific TraceFinder User Guide 315 5 Using the Acquisition Mode Working with Batches 6. (Optional with multiplexing activated) Select the Priority Sequence check box. The application acquires the priority batch on the next available channel or the assigned channel. 7. (Optional without multiplexing activated) Select the Priority Sequence check box and then select one of the following priority options to place the batch in the queue: • Next Available Batch places the batch immediately after the currently acquiring batch. • Next Available Sample places the batch immediately after the currently acquiring sample. Note When you select Full Sequence Submission in the Application Configuration mode, these options are unavailable because the current batch and the current sample are, in effect, the same thing. 8. Do one of the following: To start the selected processes, click OK. The selected processes begin, and the TraceFinder application shows the real-time display at the bottom of the current window. You can begin another batch in the Acquisition mode while you watch the real-time display of the currently acquiring batch. –or– Click Cancel to exit the Acquisition mode without performing any tasks. 316 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode Working with Batches Figure 77. Submit Options dialog box Table 58. Submit Options dialog box parameters (Sheet 1 of 2) Thermo Scientific Parameter Description User Name Name of the current user. Samples Number of samples to be submitted for acquisition, processing, or reporting. Acquire Data (Default) Submits the current batch to acquisition. TraceFinder User Guide 317 5 Using the Acquisition Mode Working with Batches Table 58. Submit Options dialog box parameters (Sheet 2 of 2) Parameter Description Process Data (Default) Processes the data for the current batch. Create Reports Creates reports for the current batch. Priority Sequence With multiplexing activated, places the batch immediately after the currently acquiring batch. Without multiplexing activated, specifies one of the following priority options to place the batch in the queue: Next Available Batch: Places the batch immediately after the currently acquiring batch. Next Available Sample: Places the batch immediately after the currently acquiring sample. Note When you select Full Sequence Submission in the Application Configuration mode, these options are unavailable because the current batch and the current sample are, in effect, the same thing. Acquisition pane Device Name Lists all configured instruments. If the instrument that you want to use is not configured, close the TraceFinder application, configure the instrument, and then reopen the TraceFinder application. You cannot configure an instrument while the TraceFinder application is running. 318 TraceFinder User Guide Use Specifies the instruments used for this acquisition. Start Device Specifies the instrument that initiates the communication with the other instruments. This is usually the autosampler. Start When Ready Starts the specified device when all the instruments are ready to acquire data. When this is cleared, individual instruments can start at different times and then must wait for the last instrument to be ready. Post-run System State Specifies the system state after it acquires the last batch. On (default), Standby, or Off. Hide/Show Details Collapses or expands the acquisition details of the Submit Options dialog box. OK Begins the selected processes. Cancel Closes the Submit Options dialog box without submitting any tasks. Thermo Scientific 5 Using the Acquisition Mode Working with Batches To view the output files Locate the files to view from the following directories: • The TraceFinder application writes saved batches to the subproject folder: …\TraceFinder\3.0\Forensic\Projects\projectname\subprojectname • For each acquired sample, the application writes an RSX file to the batch Data folder: …\projectname\subprojectname\batchname\Data • The application saves method information to the batch Methods folder: …\projectname\subprojectname\batchname\Methods\methodname • The application writes the reports to the batch Reports folder: …\projectname\subprojectname\batchname\Reports Thermo Scientific TraceFinder User Guide 319 5 Using the Acquisition Mode Working with Batches Figure 78. Finish view Table 59. Finish view parameters Parameter Description System Status The System Status pane displays the following: • Devices used for the acquisition • Project, subproject, and name of the batch • Number of samples in the batch • Number of standard and custom reports to be printed and saved as PDF, XML, or XLSM files • Local method and instrument method used for the batch • Number of compounds in the method System Startup Method The instrument method that runs before the batch. No autosampler injection takes place. This feature is not available for all instruments. System Shutdown Method The instrument method that runs after the batch. No autosampler injection takes place. This feature is not available for all instruments. Auto TSRM Update Updates the TSQ method with mass transitions, collision energy, and other appropriate data for TSRM functionality. Calibration • Use calibration: Uses the selected calibration file to process the current data. • Extend calibration: Adds calibration data from the current batch to the selected calibration file. Save Saves the current batch as a prepared batch. Submit Opens the Submit Options dialog box where you can optionally choose to generate reports. 320 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode Using Quick Acquisition Using Quick Acquisition Use the quick acquisition feature to quickly submit a single sample from any view of the Acquisition mode. Note The Quick Acquisition feature is available only when you activate it in the Application Configuration mode. See “Quick Acquisition” on page 64. To run a quick acquisition 1. Choose Go > Quick Acquire Sample from the main menu or click the Quick Acquire Sample icon, . The Quick Acquisition dialog box opens. 2. Select an instrument method. 3. Type a name for the raw data file that you acquire. Do not enter the .raw file extension. 4. For the path, browse to a folder where you want to write the acquired raw data file. 5. Select either the manual injection or the autosampler option: • To perform manual injection, do the following: i. Select the Manual Injection option. ii. Click OK. The application submits the sample to the Acquisition queue. See “Acquisition Page” on page 324. Thermo Scientific TraceFinder User Guide 321 5 Using the Acquisition Mode Using Quick Acquisition • To perform autosampler injection, do the following: i. Select the Use Autosampler option. ii. In the Vial Position box, type a vial position. iii. In the Injection Volume box, type an injection volume. The minimum injection volume allowed is 0.1 μL; the maximum injection volume allowed is 5000 μL. iv. Click OK. The Quick Acquisition dialog box opens. v. Select the Use check box for the device that you want to use for this acquisition. vi. (Optional) Select the Start Device check box to indicate the device that will initiate communication with the other instruments. This is usually the autosampler. vii. (Optional) Select the Start When Ready check box, which starts all instruments together when they are all ready. When this is cleared, individual instruments can start at different times and then must wait for the last instrument to be ready. viii. (Optional) Select the Priority check box to place the sample immediately after any currently acquiring sample. ix. (Optional) Select a value for the Post-run System State: Unknown, On (default), Off, or Standby. The application sets the system to this state after it acquires the last sample. x. Click OK. The application submits the sample to the Acquisition queue. See “Acquisition Page” on page 324. 322 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode Real Time Status Pane Real Time Status Pane You can access the Real Time Status pane from any mode in the TraceFinder application. To access the Real Time Status Pane from any mode Click Real Time Status in the upper right corner of the TraceFinder window. The Real Time Status pane opens at the bottom of the current view. Figure 79. Real Time Status pane The Real Time Status pane has four pages of information and a real-time trace pane: • Acquisition Page • Instrument Page • Devices Page • Queues Page • Real-Time Trace Display Thermo Scientific TraceFinder User Guide 323 5 Using the Acquisition Mode Real Time Status Pane Acquisition Page Use the Acquisition page to monitor the progress as the application acquires the samples. Use the Start, , Stop, , or Pause, , icons to control batches in the Acquisition queue. 324 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode Real Time Status Pane Instrument Page Use the Instrument page to monitor the currently acquiring sample. When you run single sample submission, this displays the sample name. Thermo Scientific TraceFinder User Guide 325 5 Using the Acquisition Mode Real Time Status Pane Devices Page Use the Devices page to monitor the status of the instrument. The feedback you see on the Devices page depends on the instrument you are using. The following examples show an Accela autosampler and an Aria™ multiplexing device. Accela Autosampler Feedback Aria Multiplexing Feedback 326 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode Real Time Status Pane Follow these procedures: • To pause the autosampler • To control the channels • To view the pressure trace • To control the channels To pause the autosampler 1. Click Hold Autosampler. The autosampler finishes the current autosampler step and then pauses. The LC pumps and autosampler continue. 2. To restart the autosampler, click Hold Autosampler again. To control the channels Right-click the channel name and choose a command from the shortcut menu. Table 60. Autosampler shortcut menu commands Command Description On Turns on a stopped pump and continues acquiring the sample list assigned to that channel. Off After the current sample completes, the application stops acquiring and the pump shuts down. Standby After the current sample completes, the application stops acquiring. The pump continues to run. Disable / Enable Disable: Prevents the channel from receiving samples. When you choose Disable during a run, the application finishes the current sample on the channel and then stops. Enable: Allows the channel to receive samples. When you disable a channel that is set to On, the channel is highlighted in green and the status is READY. You can turn the channel to Off or Standby. Thermo Scientific TraceFinder User Guide 327 5 Using the Acquisition Mode Real Time Status Pane To view the pressure trace 1. Click the Pres tab. The Pressure page displays a pump pressure graph for each sample in the batch. A fluctuation or change in the pump pressure could indicate a change in the chromatography conditions. 2. To view the pressure for a specific pump, select the Pres 1 or Pres 2 option. By default, the pressure for all pumps are displayed. 3. To view the pressure for a specific channel, select the corresponding channel number. By default, the pressure for all channels is displayed. 328 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode Real Time Status Pane To access the Aria multiplexing controls Click Direct Control. The Aria MX Direct Control dialog box opens. For detailed descriptions of the features in this dialog box, refer to the Transcend Systems with Xcalibur Software User Guide. Thermo Scientific TraceFinder User Guide 329 Queues Page Use the Queues page to monitor and control the Acquisition, Processing, and Reporting queues. • Use the Queue-Level Commands to pause or remove batches in any of the queues. • Use the Batch-Level Commands to pause or remove entire batches or samples within batches from any of the queues. Queue-Level Commands Use the queue-level commands to pause or remove batches in any of the queues on the Queues page. See “Queue-level shortcut menu” on page 332. Follow these procedures: • To pause all batches in a queue • To remove a single batch from a queue • To remove all batches in a queue • To remove all pending batches To pause all batches in a queue 1. Select a queue (Acquisition, Processing, or Reporting). Note When multiplexing is activated, you can have as many as four samples acquiring at once. Pausing the Acquisition queue does not affect any acquiring samples. 2. Right-click and choose Pause Queue from the shortcut menu. After the current sample completes, the application pauses all batches and samples in the specified queue. Only the selected queue is affected. 3. To restart a paused queue, select the queue, right-click, and choose Resume Queue from the shortcut menu. 5 Using the Acquisition Mode Real Time Status Pane To remove a single batch from a queue 1. Select a queue (Acquisition, Processing, or Reporting). 2. Right-click and choose Stop Active Batch from the shortcut menu. Note This command is available only when there are active batches in the queue. Paused batches and batches that contain only pending samples are not “active.” The application confirms that you want to remove the active batch from the selected queue. After the current sample completes, the application removes the batch and all pending samples from the queue. Only the selected queue is affected. To remove all batches in a queue 1. Select a queue (Acquisition, Processing, or Reporting). 2. Right-click and choose Stop All Batches from the shortcut menu. The application removes all batches with pending samples from the selected queue. The current sample continues to acquire. Only the selected queue is affected. To remove all pending batches 1. Select a queue (Acquisition, Processing, or Reporting). 2. Right-click and choose Remove Pending Batches from the shortcut menu. Note A pending batch is a batch in which all samples are pending. If any sample in the batch is active, the batch is not affected by this command. The application removes all batches that contain only pending samples. Only the selected queue is affected. Thermo Scientific TraceFinder User Guide 331 5 Using the Acquisition Mode Real Time Status Pane Figure 80. Queue-level shortcut menu Table 61. Queue-level shortcut menu commands 332 TraceFinder User Guide Command Description Pause Queue After the current sample completes, the application pauses the specified queue. Only the selected queue is affected. Resume Queue Returns the paused queue to active status. Stop Active Batch Removes all pending samples from the specified queue. The active sample is not affected. Stop All Batches Removes all pending samples and batches from the specified queue. The active sample is not affected. Reactivate All Batches Returns all paused batches to active status. Remove Pending Batches Removes all pending batches from the specified queue. The active batch is not affected. Thermo Scientific 5 Using the Acquisition Mode Real Time Status Pane Batch-Level Commands Use the batch-level commands to pause or remove entire batches or samples within batches from any of the queues on the Queues page. See “Batch-level shortcut menu.” Follow these procedures: • To remove a single pending sample from a batch • To remove all pending samples from a batch • To stop a batch • To remove a pending batch To remove a single pending sample from a batch 1. Select a pending sample. 2. Right-click the sample and choose Remove Sample from the shortcut menu. The application confirms that you want to remove the selected sample from the batch and then removes the sample. To remove all pending samples from a batch 1. Select a batch in any of the queues (Acquisition, Processing, or Reporting). The batch must have at least one pending sample. 2. Right-click and choose Remove Pending Samples from the shortcut menu. The application confirms that you want to remove all pending samples from the batch and then removes the samples. If the batch includes only pending samples, the application removes the batch from the queue. Thermo Scientific TraceFinder User Guide 333 5 Using the Acquisition Mode Real Time Status Pane To stop a batch 1. Select an active batch in any of the queues (Acquisition, Processing, or Reporting). Note The batch must have at least one active sample and one pending sample. 2. Right-click and choose Stop Batch from the shortcut menu. The application confirms that you want to remove the selected batch from the queue. After the current sample completes, the application removes the batch and all pending samples from the queue. To remove a pending batch 1. Select a pending batch in any of the queues (Acquisition, Processing, or Reporting). Note A pending batch is a batch in which all samples are pending. If any sample in the batch is active, this command is not available. 2. Right-click and choose Remove Pending Batch from the shortcut menu. The application confirms that you want to remove the selected batch from the queue and then removes the batch from the queue. Figure 81. Batch-level shortcut menu Table 62. Batch-level shortcut menu commands Command Description Stop Batch After the current sample completes, the application removes all samples in the selected batch. Remove Pending Batch Removes all samples from the selected pending batch. Remove Pending Samples 334 TraceFinder User Guide Removes all pending samples from the selected batch. Thermo Scientific 5 Using the Acquisition Mode Real Time Status Pane Real-Time Trace Display As each sample acquires, the real-time chromatogram pane shows the retention time and intensity of the TIC trace. By default, the Real Time Status pane shows only the TIC trace as each sample acquires. To observe specific traces, such as the internal standard, use the RTV Display Traces function to display multiple traces. When you create your method, you can specify additional traces to display in the real-time viewer and in which order the traces are displayed. The application always displays the TIC trace in the top pane. See “Real Time Viewer” on page 170. Thermo Scientific TraceFinder User Guide 335 5 Using the Acquisition Mode Real Time Status Pane To display multiple traces Right-click the chromatogram pane and choose the number of traces to display. The chromatogram pane displays real-time chromatograms for the selected number of traces. The TIC is always displayed at the top. When there are more traces than can fit in the pane, you can scroll through the traces. For each trace, the application displays the mass or precursor mass. Figure 82. Real-time trace display with multiple traces 336 TraceFinder User Guide Thermo Scientific 5 Using the Acquisition Mode Sample Types Sample Types The TraceFinder application uses the following sample types in all sample definitions and reports. To view example standard reports specific to a sample type, see Appendix A, “Reports.” Table 63. Sample type definitions Thermo Scientific Sample type Definition Negative Contains no target compounds but might contain an ISTD when you use the internal standard quantitative analysis technique. By analyzing a blank sample, you can confirm that there are no residual compounds in the solvent system that can cause erroneous results. Unextracted Similar to a Negative sample, but contains target compounds. By analyzing a sample, you can confirm that there are no residual compounds in the solvent system that can cause erroneous results. Calibrator (Calibration standard) Contains known amounts of all target compounds. The purpose of a standard is to measure the response of the instrument to the target compounds so that the processing software can generate a calibration curve for each compound. QC (Quality Check) Contains a known amount of one or more specific target compounds. The application places check standard samples in the sequence so that it can test quantitative analysis results for quality assurance purposes. After the application analyzes the QC sample, it compares the measured quantity with the expected value and an acceptability range. The quantitative analysis of a QC sample is classified as passed if the difference between the observed and expected quantities is within the user-defined tolerance. A QC sample is classified as failed if the difference between the observed and expected quantities is outside the user-defined tolerance. Solvent Contains only solvent. Specimen Used for quantitative analysis of samples. Hydrolysis Checks the degradation of compounds dissolved in water. TraceFinder User Guide 337 6 Using the Analysis Mode This chapter includes instructions about using the features of the Analysis mode. Contents • Using Quick Acquisition • Working in the Batch View • Creating a Batch Using the Batch Wizard • Working in Data Review for Quantitation Methods • Working in Data Review for Target Screening Methods • Working in the Report View • Working in the Project Administration View • Working in the Local Method View • Working in the Batch Template Editor Use the Analysis mode to do the following: • Submit a single sample for quick acquisition. • Submit batches for acquisition, processing, or reports. • Review batches, batch data, reports, and local methods. Thermo Scientific TraceFinder User Guide 339 6 Using the Analysis Mode To access the Analysis mode Click Analysis in the navigation pane. The Analysis navigation pane opens. 340 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Using Quick Acquisition Using Quick Acquisition Use the quick acquisition feature to quickly submit a single sample from any view of the Acquisition mode. Note The Quick Acquisition feature is available only when you activate it in the Application Configuration mode. See “Quick Acquisition” on page 64. To run a quick acquisition 1. Choose Go > Quick Acquire Sample from the main menu or click the Quick Acquire Sample icon, . The Quick Acquisition dialog box opens. 2. Select an instrument method. 3. Type a name for the raw data file that you acquire. Do not enter the .raw file extension. 4. For the path, browse to a folder where you want to write the acquired raw data file. 5. Select either the manual injection or the autosampler option: • To perform manual injection, do the following: i. Select the Manual Injection option. ii. Click OK. The application submits the sample to the Acquisition queue. See “Acquisition Page” on page 324. Thermo Scientific TraceFinder User Guide 341 6 Using the Analysis Mode Using Quick Acquisition • To perform autosampler injection, do the following: i. Select the Use Autosampler option. ii. In the Vial Position box, type a vial position. iii. In the Injection Volume box, type an injection volume. The minimum injection volume allowed is 0.1 μL; the maximum injection volume allowed is 5000 μL. iv. Click OK. The Quick Acquisition dialog box opens. v. Select the Use check box for the device that you want to use for this acquisition. vi. (Optional) Select the Start Device check box to indicate the device that will initiate communication with the other instruments. This is usually the autosampler. vii. (Optional) Select the Start When Ready check box, which starts all instruments together when they are all ready. When this is cleared, individual instruments can start at different times and then must wait for the last instrument to be ready. viii. (Optional) Select the Priority check box to place the sample immediately after any currently acquiring sample. ix. (Optional) Select a value for the Post-run System State: Unknown, On (default), Off, or Standby. The application sets the system to this state after it acquires the last sample. x. Click OK. The application submits the sample to the Acquisition queue. See “Acquisition Page” on page 324. 342 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Batch View Working in the Batch View In the Batch View, you can manually create and edit a new batch or open and edit a previously saved batch. When you submit a batch, you can acquire and process data and optionally create reports for the submitted samples. This section includes the following topics: • Samples Page • Auto Samples Page • Reference Samples Page To open the Batch View 1. Click Analysis in the navigation pane of the current mode. 2. In the Analysis navigation pane, click Batch View. The Batch View navigation pane opens. Available only when you activate Intelligent Sequencing in the Application Configuration mode. Available only for quantitative batches. The Analysis mode includes a toolbar: Use the toolbar or the equivalent commands on the Batch View shortcut menu to create the sample list and submit samples for acquisition. See “Toolbar” on page 351 or “Batch View Shortcut Menu” on page 355. Thermo Scientific TraceFinder User Guide 343 6 Using the Analysis Mode Working in the Batch View Samples Page To open the Samples page, click Samples in the Batch View navigation pane. This section contains information about the following topics: • Samples Page Features • Creating a New Batch • Editing a Batch • Submitting a Batch Samples Page Features The Samples page is divided into three panes: • Samples pane Use the sample list pane to create a batch. See “Samples Pane” on page 345. • Automated Batch Reports pane Use the Automated Batch Reports pane to select the type of output formats that you want to generate for the reports. See “Automated Batch Reports Pane” on page 357. • Compound Active Status pane Use the Compound Active Status pane to make specific compounds active or inactive. See “Compound Active Status Pane” on page 359. 344 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Batch View Samples pane Automated Batch Reports pane Compound Active Status pane Tip To resize the panes, drag the separators that divide the panes. Samples Pane The samples pane includes the following features: • Column Display • Status Indicators • Blank Subtraction in Target Screening Batches • Sample Weight Calculation • Toolbar • Batch View Sample List • Batch View Shortcut Menu Column Display The sample list contains many columns of information. You can scroll to see all the columns of information, and you can customize which columns to display and their display order. Follow these procedures: • To scroll the sample list • To customize the column display Thermo Scientific TraceFinder User Guide 345 6 Using the Analysis Mode Working in the Batch View To scroll the sample list Use the horizontal scroll bar at the bottom of the sample list to view all the information. When you use the scroll bar at the bottom of the sample list, the Status, Filename, Sample Type, and Level columns stay fixed while the other columns scroll right and left. To customize the column display 1. Right-click the sample list and choose Modify Columns from the shortcut menu. The Modify Columns dialog box opens. See “Modify Columns dialog box.” 2. Use the arrow buttons to move all the columns that you want displayed to the Displayed Columns pane. These columns are displayed after the Status, Filename, Sample Type, and Level columns. 3. To arrange the order of the columns, do the following: a. In the Displayed Columns pane, select a column name. b. Use Up or Down to move the selected column up or down in the list. The first column in the list represents the leftmost column in the Batch View sample list, and the last column in the list represents the rightmost column in the Batch View sample list. Note You cannot move the Status, Filename, Sample Type, or Level column. 4. To change the width of a column, do the following: a. In the Displayed Columns pane, select the column width. b. Type a new value for the width. 5. Repeat step 4 for all columns whose widths you want to change, and click OK. The columns in the sample list immediately reflect your changes. The application uses these settings for all sample lists in the Batch View. 346 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Batch View Figure 83. Modify Columns dialog box Table 64. Modify Columns function buttons Function Description Moves all columns to the Displayed Columns pane. Moves the selected column to the Displayed Columns pane. Moves the selected column to the Available Columns pane. You cannot move the Status, Filename, Sample Type, or Level column. Moves all columns except Status, Filename, Sample Type, and Level to the Available Columns pane. Moves the selected column name in the Displayed Columns pane one row up in the column order. You cannot move the Status, Filename, Sample Type, or Level column. Moves the selected column name in the Displayed Columns pane one row down in the column order. You cannot move the Status, Filename, Sample Type, or Level column. Note In target screening batches only, a Blank Subtraction column is added to the fixed columns. Thermo Scientific TraceFinder User Guide 347 6 Using the Analysis Mode Working in the Batch View Status Indicators Status indicators show the current status of each sample during the acquisition and processing. Sample is not acquired. Sample is acquired but not processed. Sample is acquired and processed. Sample is currently acquiring. Status indicators Blank Subtraction in Target Screening Batches In target screening batches only, use the Blank Subtraction feature to select which negative samples you want to use for peak subtraction. The application subtracts the areas of the peaks in the selected negative samples from the matching areas in the specimen samples. When you process the batch sequence, the application subtracts the peaks in a selected negative sample from all specimen samples that follow it, until it encounters another negative sample. To activate the Blank Subtraction feature, see “To specify peak filter settings” on page 212. 348 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Batch View Sample Weight Calculation Use the sample weight features to calculate the conversion factor for a sample. The application uses different methods to calculate the conversion factor for liquid or solid calculation types. Liquid: SampleVolume DilutionFactor Solid: (SampleVolume × DilutionFactor) SampleWeight Manual: The application does not calculate the Conversion Factor. Instead, you can enter the Conversion Factor value. Follow these procedures: • To display the features for calculating sample weight • To calculate the conversion factor for a liquid sample • To calculate the conversion factor for a solid sample • To manually specify the conversion factor for a sample To display the features for calculating sample weight If the Conversion Factor, Sample Volume, Dilution Factor, Sample Weight, Calculation Type, and Final Units columns are not visible, right-click and choose Enable Sample Weight Calculation from the shortcut menu. To calculate the conversion factor for a liquid sample 1. From the Calculation Type list, select Liquid. For a liquid sample, the Sample Weight value is not editable. 2. In the Sample Volume column, type the volume in ng/mL for your sample. 3. In the Dilution Factor column, type the value for the dilution. For example, if you have 1000 ng/mL of a substance that is too concentrated for the mass spectrometer, you can dilute it by 1000. Then your injection volume is 1, your conversion factor is 1000, and your sample amount is 1000. 4. In the Final Units column, type the units that you want to use for the calculated amount in the Data Review view, on the Active View page in the Report View, or in reports. The application uses the following formula to calculate the Conversion Factor: SampleVolume DilutionFactor Thermo Scientific TraceFinder User Guide 349 6 Using the Analysis Mode Working in the Batch View To calculate the conversion factor for a solid sample 1. From the Calculation Type list, select Solid. 2. In the Sample Weight column, type the weight in ng for your sample. 3. In the Sample Volume column, type the volume in ng/ml for your sample. 4. In the Dilution Factor column, type the value for the dilution. For example, if you have 1000 ng/ml of a substance that is too concentrated for the mass spectrometer, you can dilute it by 1000. Then your injection volume is 1, your conversion factor is 1000, and your sample amount is 1000. 5. In the Final Units column, type the units that you want to use for the calculated amount in the Data Review view, on the Active View page in the Report View, or in reports. The application uses the following formula to calculate the Conversion Factor: (SampleVolume × DilutionFactor) SampleWeight To manually specify the conversion factor for a sample 1. From the Calculation Type list, select Manual. For a manually calculated sample, the only available columns are the Conversion Factor and the Final Units. 2. In the Conversion Factor column, type the conversion factor to use for your sample. 3. In the Final Units column, type the units that you want to use for the calculated amount in the Data Review view, on the Active View page in the Report View, or in reports. The application uses the specified conversion factor when it calculates the amount for the sample. 350 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Batch View Toolbar The Analysis mode includes this toolbar for creating and submitting a batch. Table 65. Toolbar functions Icon Description Adds the specified number of new, empty samples to the end of the sample list. See the instructions “To add samples to the list” on page 363. Inserts a new, empty sample or samples above the selected sample. See the instructions “To insert samples into the list” on page 363. Removes the selected samples from the sample list. See the instructions “To remove samples from the list” on page 364. Adds imported samples from a CSV, an XML, or an SLD file to the sample list. See the instructions “To import samples into the list” on page 363. Submits only the selected samples for acquisition, processing, or report generation. See the instructions “To submit samples in the batch” on page 371. Submits the batch for acquisition, processing, or report generation. See the instructions “To submit samples in the batch” on page 371. Opens the Batch Wizard where you can use a batch template to define a standard sequence composed of various sample types to be assembled into a batch of samples. See “Creating a Batch Using the Batch Wizard” on page 379. Opens the Batch Template Editor where you can create a batch template that contains the basic settings and sample types for your batches. See “Working in the Batch Template Editor” on page 500. Opens the Quick Acquisition dialog box where you can quickly submit a single sample. See “Using Quick Acquisition” on page 341. Thermo Scientific TraceFinder User Guide 351 6 Using the Analysis Mode Working in the Batch View Batch View Sample List The sample list displays all the quantitative data for the samples of a batch. Status indicators for each sample indicate if the sample is currently acquiring, not acquired, acquired, or processed. The sample list includes the following columns of information: Figure 84. Batch View sample list Note • In target screening batches only, the sample list includes a Blank Subtraction column after the Sample Type column. • Cells in the sample list that are not editable, such as Barcode Actual, are shaded and empty. 352 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Batch View Table 66. Batch View sample list columns (Sheet 1 of 2) Column Status Description Sample is not acquired. Sample is acquired but not processed. Sample is acquired and processed. Sample is currently acquiring. Filename Name of the raw data file that contains the sample data. Sample Type Defines how the TraceFinder application processes the sample data. Each sample is classified as one of the following sample types: Specimen, QC, Solvent, Calibrator, Hydrolysis, Unextracted, or Negative Default: Specimen Qual Processing Indicates samples to be processed with the qualitative peak processing criteria specified in the method. The Qualitative View displays processed data for the selected samples. Blank Subtraction Specifies a negative sample to use for blank subtraction. Level The level defined for a calibration sample or quality control sample. Sample ID A user-defined, alphanumeric string that identifies a sample. Sample Name A user-defined name that identifies a sample. Vial Position The tray vial number used for an autosampler acquisition. Injection Volume The injection volume (in microliters) of the injected sample. When you are using an autosampler, you can set the default injection volume in the Autosampler dialog box in the Instrument View. The minimum and maximum injection volumes that you can use depend on the Autosampler you configure. The usable range depends on the injection mode and might be smaller than the displayed range. The Injection Volume value set in the master method overwrites the value in the instrument method. Range: 0.1 through 5000 μL Calculation Type Liquid: The application calculates the Conversion Factor as SampleVolume DilutionFactor Solid: The application calculates the Conversion Factor as (SampleVolume × DilutionFactor) SampleWeight Manual: Sample Volume, Dilution Factor, Sample Weight, and Final Units columns are not available, and the Conversion Factor value is editable. Thermo Scientific TraceFinder User Guide 353 6 Using the Analysis Mode Working in the Batch View Table 66. Batch View sample list columns (Sheet 2 of 2) Column Description Conversion Factor Editable only when Calculation Type is Manual. Default: 1 Sample Volume Default: 1 Dilution Factor Default: 1 Sample Weight Available only when Calculation Type is Solid. Default: 1 Final Units Specifies the calculated amount in the Data Review view, on the Active View page in the Report View, or in reports. Default: 1 Instrument Method Specifies the instrument to use for the acquisition. Channel Specifies the channel on which the sample was run. If the sample is not acquired, the value is Pending. The Channel column is available only when you have activated multiplexing in the Application Configuration mode. See “Multiplexing” on page 66. Barcode Expected A user-entered barcode for the vial. Barcode Actual An actual barcode for the vial. This value is not editable. Comment A user-defined comment for the sample. 354 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Batch View Batch View Shortcut Menu The Batch View includes a shortcut menu for creating a batch. Table 67. Batch View shortcut menu commands (Sheet 1 of 2) Command Description Add Sample Adds a single empty row to the sample grid. Insert Sample Inserts a single empty row to the sample grid above the selected row. Insert Copy Sample Copies the currently selected row and inserts a copy above the row. Reinject Selected Samples Creates a copy of the selected sample and appends INJ001 to the file name. Additional reinjections of the same sample are numbered INJ002, INJ003, and so forth. Remove Selected Samples Removes selected samples from the sample grid. Import Samples Opens the Sample Import Tool. See “To import samples into the list” on page 363. Browse In Raw File Opens a dialog box where you can select a raw data file to use for the selected sample row. Map Raw Files to Samples Opens a dialog box where you can select multiple raw data files to use for the selected sample rows. Copy Down Copies the value in the selected row to all rows below it. This command is available only when you have selected a value that can be copied down. Fill Down Enters sequential values in the column starting with the value in the selected row and ending with the last row in the column. This command is available only when you have selected a value that can be filled down. Modify Columns Opens the Modify Columns dialog box. See “Column Display” on page 345. Copy Copies the data in the selected rows or columns to the Clipboard. Use this command to copy sample information to another application, such as an Excel spreadsheet. You cannot paste this data back into the Batch View sample list. Copy With Headers Copies the data in the selected rows or columns and the associated column headers to the Clipboard. Use this command to copy sample information to another application, such as an Excel spreadsheet. You cannot paste this data back into the sample list. For example Copy With Headers from TraceFinder Thermo Scientific Paste into Excel spreadsheet TraceFinder User Guide 355 6 Using the Analysis Mode Working in the Batch View Table 67. Batch View shortcut menu commands (Sheet 2 of 2) Command Description Paste Pastes a single column of copied data from another application, such as an Excel spreadsheet, into the selected column. Undo Last Paste Removes the last pasted item in the Batch View. Export to CSV File Opens the Save As dialog box where you can save the current sample list to a CSV file. 356 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Batch View Automated Batch Reports Pane In the Automated Batch Reports pane, you can view the reports that are selected for this batch and modify which output formats are generated for each report. To edit the sample-level output formats 1. Click the Sample Level tab. The application displays reports and the output formats as they were specified in the method. For detailed instructions about specifying which reports and output formats are generated, see “Specifying the Reports Configuration” on page 39. 2. Select or clear any of the check boxes for your reports. 3. To duplicate an output format for all reports for this sample, right-click the cell and choose Copy Down from the shortcut menu. All check boxes in the column below the selected cell duplicate the selected or cleared state in the selected cell. You can duplicate the output type only for reports that have this output format available. 4. To duplicate the output format for all samples in the batch, right-click the cell and choose Apply Selection to All Samples from the shortcut menu. Tip In the Batch View, you can change the output formats but you cannot change which reports are available. Thermo Scientific TraceFinder User Guide 357 6 Using the Analysis Mode Working in the Batch View To edit the batch-level output formats 1. Click the Batch Level tab. The application displays the reports and the output formats as they were specified in the method. For detailed instructions about specifying which reports and output formats are generated and which reports are batch-level, see “Specifying the Reports Configuration” on page 39. 2. Select or clear any of the check boxes for your reports. 3. To duplicate the output format for all reports, right-click the cell and choose Copy Down from the shortcut menu. All check boxes in the column below the selected cell duplicate the selected or cleared state in the selected cell. You can duplicate the output type only for reports that have this output format available. Tip In the Batch View, you can change the output formats but you cannot change which reports are available. 358 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Batch View Compound Active Status Pane In the Compound Active Status pane, you can choose specific compounds to be active or inactive. To set a compound as active or inactive 1. In the sample list, select a sample. All compounds in the selected sample are listed in the Compound Active Status pane. The default active/inactive status is determined by the identification settings in the local method. For information about setting the identification parameters, see “Identification” on page 117. • To display compounds alphabetically, right-click and choose Sort by Compound Name from the shortcut menu. • To display compounds from shorter to longer retention time, right-click and choose Sort by Retention Time from the shortcut menu. 2. Select or clear the Active check box for the compound. For instructions about changing the active/inactive status in the Data Review view, see “Inactive and Excluded Compounds” on page 435. Thermo Scientific TraceFinder User Guide 359 6 Using the Analysis Mode Working in the Batch View Compound Active/Inactive Status You can specify which compounds are active or inactive in the Local Method View or the Batch View. Figure 85. Active and inactive compounds in the Local Method View For details about setting the status on the Identification page, see “Identification” on page 117. Figure 86. Active and inactive compounds in the Batch View For details about setting the status in the Batch View, see “Compound Active Status Pane” on page 359. 360 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Batch View Creating a New Batch In the Batch View, you can create a new batch. Follow these procedures: • To create a new batch • To add samples to the list • To insert samples into the list • To import samples into the list • To remove samples from the list • To copy a sample • To reinject a sample • To edit sample values • To browse in raw data files • To customize the column display To create a new batch 1. Click New Batch in the Batch View task pane or choose File > New > Batch. The Create a New Batch dialog box opens. 2. Select to create either a quantitative batch or a screening batch. Thermo Scientific TraceFinder User Guide 361 6 Using the Analysis Mode Working in the Batch View 3. Select a master method from the Method list. The application displays all available methods, either quantitative or screening. 4. Select a drive from the Storage Location list. Tip The application does not display drives that do not have a project and subproject. The project list displays all projects, subprojects, and batches on the selected drive. You cannot use network drives to acquire data. For more information about network drives, see “Working with Drives” on page 493. 5. Select a project and a subproject and type a name for your new batch. Tip To activate the Save button, you must select a subproject and enter a unique batch name. If the Save button is not activated, either you have entered a name that is already used or you have not selected a subproject. 6. Click Save. A new batch opens with one Specimen sample. The batch name in the title bar indicates that you are creating a quantitative or screening batch. 362 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Batch View To add samples to the list 1. To add a single sample row, right-click the sample list and choose Add Sample from the shortcut menu. 2. To add multiple sample rows, select the number of rows and then click the Add Sample icon, . The application adds the specified number of new, empty samples to the end of the sample list. To insert samples into the list Select the sample above which you will insert new, Specimen samples, and then do one of the following: • To insert a single sample row, right-click and choose Insert Sample from the shortcut menu. • To insert multiple sample rows, select the number of rows and then click the Insert Sample icon . The application inserts the Specimen samples above the selected sample. Inserted samples To import samples into the list 1. Choose Batch > Import Samples from the main menu, or click the Import Samples icon, . The Sample Import Tool dialog box opens. From this dialog box, you can import samples from a CSV, an XML, or an SLD file. Thermo Scientific TraceFinder User Guide 363 6 Using the Analysis Mode Working in the Batch View 2. Click Browse and select a CSV, an XML, or an SLD file that contains the samples to import. 3. From the Imported Samples Will Be list, select Appended to the End of the List or Inserted at the Selected Row. 4. Click Import. The Sample Import Tool dialog box closes, and the application adds the specified samples to the sample list. When you import samples from an Xcalibur sequence file (SLD), the TraceFinder application makes the following column name substitutions: Xcalibur column TraceFinder column Position Vial Position Inj Vol Injection Volume Dil Factor Conversion Factor When you import samples from an Xcalibur sequence file (.sld), the TraceFinder application makes the following sample type substitutions: Xcalibur sample type TraceFinder sample type Blank Negative Std Bracket Calibrator 5. (Optional) When using multiplexing, select a channel for each imported sample. Imported samples default to Auto. Note The Channel column is available only when you have activated multiplexing in the Application Configuration mode. See “Multiplexing” on page 66. To remove samples from the list 1. Select the samples that you want to remove. Tip Use the CTRL or SHIFT keys to select multiple samples. 2. Right-click and choose Remove Selected Samples from the shortcut menu. To copy a sample 1. Select the sample that you want to copy. 2. Right-click and choose Insert Copy Sample from the shortcut menu. The TraceFinder application inserts the copy above the selected sample. 364 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Batch View To reinject a sample 1. In the sample list, select the sample that you want to reinject. 2. Right-click and choose Reinject This Sample from the shortcut menu. The TraceFinder application creates a copy of the selected sample and appends INJ001 to the file name. Additional reinjections of the same sample are numbered INJ002, INJ003, and so forth. The TraceFinder application copies all parameter values from the original sample. To edit sample values 1. For each sample, do one of the following: Type a new file name over the current filename. –or– Double-click the Filename column and locate a raw data file to use for the sample. –or– Right-click and choose Browse in Raw File from the shortcut menu, and then locate a raw data file to use for the sample. By default, the application sets the Sample Type to Unknown. 2. For each sample, click the Sample Type column and select a sample type from the list. Available sample types Specimen QC Solvent Calibrator Unextracted Negative Hydrolysis 3. For each Calibrator or QC sample, select a level from the Level list. The sample levels are defined in the master method. If there are no levels to select in the Level list, do the following: a. Return to the Method Development mode. b. Open the method. c. Click the Compounds tab. d. Click the Calibration Levels tab. e. Add the levels. f. Save the method. g. Return to the Analysis mode, and then click Update. The application updates the local method with the new sample levels. For detailed instructions, see Chapter 4, “Using the Method Development Mode.” Thermo Scientific TraceFinder User Guide 365 6 Using the Analysis Mode Working in the Batch View 4. Type a vial position in the Vial Position column for each sample. 5. Type a volume in the Injection Volume column for each sample. The minimum injection volume value allowed is 0.1 μL; the maximum injection volume value allowed is 5000 μL. 6. (Optional) Type or edit the values for the remaining columns. Note When you use the horizontal scroll bar at the bottom of the sample list, the Status, Filename, Sample Type, and Level columns stay fixed while the other columns scroll right and left. For instructions to automatically copy or fill values in these columns, see Appendix B, “Using Copy Down and Fill Down.” To browse in raw data files 1. Do one of the following: Double-click the Filename column. –or– Right-click and choose Browse in Raw File from the shortcut menu. The What Raw File Would You Like to Use dialog box opens. 2. Select a raw data file to use for the sample or use the CTRL key to select multiple files, and then click Open. The application overwrites the selected, unacquired sample in the batch with the first “browsed in” file and adds any additional browsed in files below the selected sample. For all browsed-in raw data files, the application sets the Status to Acquired, the Sample Type to Specimen. , and sets Note You cannot overwrite an acquired sample. When you select a sample that is acquired, the application adds all browsed in files below the selected sample. 366 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Batch View To customize the column display 1. Right-click the Batch View sample list and choose Modify Columns from the shortcut menu. The Modify Columns dialog box opens. Table 68. Modify Columns dialog box function buttons Function Description Moves all columns to the Displayed Columns pane. Moves the selected column to the Displayed Columns pane. Moves the selected column to the Available Columns pane. You cannot move the Status, Filename, Sample Type, or Level columns. Moves all columns except Status, Filename, Sample Type, or Level to the Available Columns pane. Moves the selected column name in the Displayed Columns pane one row up in the column order. You cannot move the Status, Filename, Sample Type, or Level columns. Moves the selected column name in the Displayed Columns pane one row down in the column order. You cannot move the Status, Filename, Sample Type, or Level columns. 2. Use the arrow buttons to move all the columns that you want displayed to the Displayed Columns pane. All the columns you select are displayed after the Status, Filename, Sample Type, or Level columns. Thermo Scientific TraceFinder User Guide 367 6 Using the Analysis Mode Working in the Batch View 3. To arrange the order of the columns, do the following: a. In the Displayed Columns pane, select a column name. b. Use Up or Down to move the selected column up or down in the list. The first column in the list represents the leftmost column in the Batch View sample list, and the last column in the list represents the rightmost column in the Batch View sample list. Note You cannot move the Status, Filename, Sample Type, or Level columns. 4. To change the width of a column, do the following: a. In the Displayed Columns pane, select the column width. b. Type a new value for the width. 5. When you have completed your changes, click OK. The columns in the sample list immediately reflect your changes. The application uses these settings for all sample lists in the Batch View. 368 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Batch View Editing a Batch In the Batch View, you can open a saved batch and edit the sample list. You can add samples, edit samples, or remove samples. If the batch has already been acquired, you can select specific samples for reinjection. If the batch has unacquired samples when you complete your edits, you can save it as a “ready to acquire” batch. Follow these procedures: • To open a saved batch • To open a recent batch • To edit samples in a batch • To reinject a sample from a previously acquired batch • To submit samples in the batch To open a saved batch 1. From the Batch View task pane, click Open Batch. The Open Batch dialog box opens. 2. Select a drive from the Storage Location list. The project list displays all projects, subprojects, and batches on the selected drive. 3. Select a project, subproject, and batch. 4. Click Open. The selected batch opens in the Batch View. Thermo Scientific TraceFinder User Guide 369 6 Using the Analysis Mode Working in the Batch View To open a recent batch Choose File > Recent Files > batchname from the main menu. The selected batch opens in the Batch View. To edit samples in a batch Use the commands described in “Working in the Batch View” on page 343. You can add new samples, edit samples, or delete samples. To reinject a sample from a previously acquired batch 1. In the sample list, select the sample that you want to reinject. 2. Right-click and choose Reinject This Sample from the shortcut menu. The TraceFinder application creates a copy of the selected sample and appends INJ001 to the file name. Additional reinjections of the same sample are numbered INJ002, INJ003, and so forth. The TraceFinder application copies all parameter values from the original sample. A green status icon indicates previously acquired samples (acquired and processed), and the sample name is grayed out. A blue status icon indicates samples created for reinjection (not acquired). When you submit all samples in this batch, the application acquires all samples (including previously acquired samples). 3. To save this batch with the new samples for reinjection, choose File > Save > Batch from the main menu. The batch is saved as a prepared batch that is ready to submit. You can open this batch from the Reinject Samples page in the Acquisition mode and submit the batch. The application acquires only the samples that have not been previously acquired. 370 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Batch View Submitting a Batch In the Batch View, you can submit an entire batch or only selected samples in the batch. When you submit a batch for acquisition and processing, you can choose to create reports for the submitted samples. See “Submit Options dialog box” on page 372. For a description of commands on the shortcut menu, see “Batch View shortcut menu commands” on page 355. To submit samples in the batch 1. Do one of the following: • To submit all samples in the batch, click the Submit Batch icon, . • To submit specific samples, select the samples and click the Submit Selected Samples icon, . The Submit Options dialog box opens. See “Submit Options dialog box” on page 372. 2. Select the tasks that you want to perform: acquire data, process data, or create reports. 3. (Optional) Click Show Details to display additional Acquisition parameters. 4. Select the Use check box for the device that you want to use for this acquisition. 5. (Optional) Select the Start Device check box to indicate the device that will initiate the communication with the other instruments. This is usually the autosampler. 6. (Optional) Select the Start When Ready check box to have all instruments start together when they are all ready. When this is cleared, individual instruments can start at different times and then must wait for the last instrument to be ready. 7. (Optional with multiplexing activated) Select the Priority Sequence check box. The application acquires the priority batch on the next available channel or the assigned channel. 8. (Optional without multiplexing activated) Select the Priority Sequence check box and then select one of the following priority options to place the batch in the queue: • Next Available Batch places the batch immediately after the currently acquiring batch. • Next Available Sample places the batch immediately after the currently acquiring sample. 9. To start the selected processes, click OK. Thermo Scientific TraceFinder User Guide 371 6 Using the Analysis Mode Working in the Batch View Figure 87. Submit Options dialog box Table 69. Submit Options dialog box parameters (Sheet 1 of 2) 372 TraceFinder User Guide Parameter Description User Name Name of the current user. Samples Range of samples to be submitted for acquisition, processing, or reporting. Acquire Data (Default) Submits the current batch to acquisition. Thermo Scientific 6 Using the Analysis Mode Working in the Batch View Table 69. Submit Options dialog box parameters (Sheet 2 of 2) Parameter Description Process Data (Default) Processes the data for the current batch. Create Reports Creates reports for the current batch. Priority Sequence With multiplexing activated, places the batch immediately after the currently acquiring batch. Without multiplexing activated, specifies one of the following priority options to place the batch in the queue: • Next Available Batch places the batch immediately after the currently acquiring batch. • Next Available Sample places the batch immediately after the currently acquiring sample. Acquisition pane Device Name Lists all configured instruments. If the instrument that you want to use is not configured, close the TraceFinder application, configure the instrument, and then reopen the TraceFinder application. You cannot configure an instrument while the TraceFinder application is running. Use Specifies the instruments used for this acquisition. Start Device Specifies the instrument that initiates the communication with the other instruments. This is usually the autosampler. Start When Ready Starts the specified device when all the instruments are ready to acquire data. When this is cleared, individual instruments can start at different times and then must wait for the last instrument to be ready. Post-run System State Specifies the system state after it acquires the last batch. On (default), Standby, or Off. Function buttons Thermo Scientific Hide/Show Details Collapses or expands the acquisition details of the Submit Options dialog box. OK Begins the selected processes. Cancel Closes the Submit Options dialog box without submitting any tasks. TraceFinder User Guide 373 6 Using the Analysis Mode Working in the Batch View Saving a Batch to a New Location You can move the current batch to a different project and subproject, or you can make a copy of the current batch and save the copy to a different project and subproject. Follow these procedures: • To save a batch to another project or subproject • To move a batch to another project or subproject To save a batch to another project or subproject 1. Choose File > Save > Save Batch As from the main menu in the Analysis mode. The Batch Save dialog box opens. 2. Select a storage location. 3. Select a project. 4. Select a subproject. 5. Type a name for the new batch. If you are saving the batch to a different subproject, you must give it a unique name. You cannot overwrite an existing batch in the new subproject. 6. Click Save. When you save the batch to a different subproject, the reports reflect the original project/subproject and the application does not save the calibration history. 374 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Batch View To move a batch to another project or subproject 1. Choose File > Save > Move Batch from the main menu in the Analysis mode. The Batch Save dialog box opens. 2. Select a storage location. 3. Select a project. 4. Select a subproject. 5. Type a name for the new batch. You must give the batch a unique name in the new subproject. You cannot overwrite an existing batch. 6. Click Save. When you move the batch, the reports reflect the original project/subproject and the application does not save the calibration history. Thermo Scientific TraceFinder User Guide 375 6 Using the Analysis Mode Working in the Batch View Auto Samples Page The Auto Samples page identifies the Solvent or Negative samples to use for any Auto Sample or Auto Sample and Reinject failure actions as specified on the Intelligent Sequencing page of the method. See “Editing the Intelligent Sequencing Page” on page 185. Each sample type that you specify for a failure action on the Intelligent Sequencing page must be defined on the samples list on the Auto Samples page. To open the Auto Samples page Click Auto Samples in the Batch View navigation pane. The Auto Samples page opens. See Auto Samples page. To add an auto sample type 1. Right-click and choose Add Auto Sample from the shortcut menu, or click the Add New Auto Sample icon, . The application adds a Solvent sample to the sample list. You can add, insert, or remove samples from this list as you would any sample list. See “Samples Page” on page 344. 2. To change the sample type to a Negative, click the Sample Type column and select Negative from the list. 3. In the Injection Volume column for the sample, type a volume. The minimum injection volume value allowed is 0.1 μL; the maximum injection volume value allowed is 5000 μL. 4. In the Number of Injections column, type the number of injections available in the designated Solvent or Negative vial. After auto sample injections have occurred, you can return to this page to view the number of Injections Used in each vial. 5. In the Vial Position column, type the vial position for the Solvent or Negative sample. 376 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Batch View Figure 88. Auto Samples page Table 70. Auto Samples page parameters Thermo Scientific Column Description Sample Type The sample type for the auto sample injection as specified on the Intelligent Sequencing page—either Solvent or Negative. Default: Solvent Injection Volume The injection volume used for the sample acquisition as specified on the Samples page. Range: 0.1 through 5000 μL Injections Used The number of times a vial has been used. The count is cumulative across all batches. Number of Injections The number of injections available in the designated Solvent or Negative vial. Vial Position Vial position for this sample type as specified on the Samples page. TraceFinder User Guide 377 6 Using the Analysis Mode Working in the Batch View Reference Samples Page The Reference Samples page displays the reference samples that you selected for this batch. To specify a chromatogram reference sample 1. In the Batch View, click Reference Samples. An empty reference sample table opens. 2. Click the Add Reference Sample icon, Reference Sample from the shortcut menu. , or right-click and choose Add The Open Chromatogram Reference Sample dialog box opens. Note If you are using a new method, no reference samples appear here. You must first process a batch using the current method to see the reference samples in this list. 3. Select a project from the list of projects. 4. Select a subproject from the list of subprojects. 5. Select a batch from the list of batches. The application displays only batches that were created using the current master method. 6. Select a sample from the list of processed samples. The application displays all the processed samples in the selected batch. Before using a sample as a reference sample, you must have processed the sample with the current master method. 7. Click Open. 378 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Creating a Batch Using the Batch Wizard Creating a Batch Using the Batch Wizard Using the Batch Wizard, you can define a sequence composed of various sample types to be assembled into a batch of samples. Before you can create a batch with the Batch Wizard, you must have a master method and a batch template. See “Creating a New Master Method” on page 84 and “Working in the Batch Template Editor” on page 500. Note This batch wizard is available only when you select the Batch Template Wizard (EnviroLab/ToxLab/QuanLab forms) style in the Application Configuration mode. See “Batch Wizard Style” on page 65. Follow these procedures in the Batch Wizard to create and submit a batch: • Selecting a Batch Template • Specifying a Batch • Submitting the Batch • (Optional) Selecting Calibration Files and Compounds The Batch Wizard workflow uses the following pages: Batch Template Selection Batch Specification Calibration and Compound Selection Finish To open the Batch Wizard Choose File > New > Batch Using Wizard from the main menu in the Analysis mode, or click the Batch Wizard icon, . Note Creating a batch using the Batch Wizard requires that you have previously created at least one batch template. See “Working in the Batch Template Editor” on page 500. The Batch Template Selection page of the Batch Wizard opens. For descriptions of the parameters on the Batch Template Selection page, see “Batch Template Selection page” on page 381. Thermo Scientific TraceFinder User Guide 379 6 Using the Analysis Mode Creating a Batch Using the Batch Wizard Selecting a Batch Template From the Batch Template Selection page, you can create a list of samples to acquire or process. For descriptions of the parameters on the Batch Template Selection page, see “Batch Template Selection page.” To create a sample list 1. From the Project list, select a project. 2. From the Subproject list, select a subproject. The Available Templates area lists all the templates in the specified subproject. 3. Select a starting vial position. The default is vial position 1, but you can choose to start your acquisition at any vial position. 4. (Optional) To simplify the sample list, select the Quick Mode check box. Quick Mode limits the columns of information on the Batch Specification page to the following: • Sample Type • Sample ID • Injection Volume • Conversion Factor 5. From the Available Templates list, select a template that defines your layout preference. The Template Layout area displays sample information in the selected batch template and a list of methods that use the same assay type as your template. 6. Select an available method. By default, the application selects the method used to create the batch template, but you can choose any method in the Available Methods list. 7. To go to the next wizard page, click Next. From the Batch Specification page of the wizard, you can customize the batch. 380 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Creating a Batch Using the Batch Wizard Figure 89. Batch Template Selection page Table 71. Batch Template Selection page parameters (Sheet 1 of 2) Parameter Description Starting Vial Position The vial position where you want to begin acquiring samples. Default: 1 Total Batch Rows The number of sample rows in the batch template. Assay Type The assay type specified in the master method used to create the batch template. Quick Mode Limits the columns of information on the Batch Specification page to the following: • Sample Type • Sample ID • Injection Volume • Conversion Factor Available Templates All batch templates are saved in the following folder: …\Thermo\TraceFinder\3.0\Forensic\Templates\Batches Thermo Scientific Template Layout Displays sample information in the selected batch template. Available Methods Lists all master methods created with the same assay type as the selected batch template. TraceFinder User Guide 381 6 Using the Analysis Mode Creating a Batch Using the Batch Wizard Table 71. Batch Template Selection page parameters (Sheet 2 of 2) 382 TraceFinder User Guide Parameter Description Help Opens the “Creating a Batch Using the Batch Wizard” topic (this topic) in the application Help tool. Next Returns you to the Batch Specification page where you can enter a sample ID, a sample name, or a comment. You can also add or remove samples from the sample list or edit the column values for the samples. See “Specifying a Batch” on page 383. Cancel Immediately exits the Batch Wizard and does not save the batch. There is no confirming message. Thermo Scientific 6 Using the Analysis Mode Creating a Batch Using the Batch Wizard Specifying a Batch From the Batch Specification page, you must enter either a sample ID, sample name, or comment. You can also add or remove samples from the sample list or edit the column values for the samples. The batch template might contain many samples that you do not want to use for your batch. If you do not enter a sample ID, sample name, or comment for these samples, the application discards them when you save the batch. For descriptions of the parameters on the Batch Specification page, see “Batch Specification page” on page 387. To enter a required sample ID, sample name, or comment 1. In the Sample ID column, type an identifier. The identifier can be any text string. 2. In the Sample Name column, type a name. The name can be any text string. 3. In the Comment column, type a comment. The comment can be any text string. Note The application requires a value in at least one of these fields to acquire a sample. When the batch begins acquisition, it discards any sample that does not have a value in at least one of these fields. To simplify the sample list Select the Quick Mode check box. In Quick Mode, the Batch Specification page displays only the following columns: • Sample Type • Sample ID • Injection Volume • Conversion Factor In Quick Mode, you cannot add or remove samples from the sample list. You can only edit these four column values for the samples specified in the template. When you are not using Quick Mode, follow these procedures: • To change the file names • To remove samples from the batch • To insert samples into the batch • To copy a sample • To move a sample up or down in the sample list • To browse in a raw data file Thermo Scientific TraceFinder User Guide 383 6 Using the Analysis Mode Creating a Batch Using the Batch Wizard To change the file names 1. Select the file name. Not selected for renaming Selected for renaming By default, all samples specified on the Batch Template Selection page are named with a date stamp and the designation “aNNN” as in this example: 9262012_a001. 2. Type a new file name. Note Or, you can right-click and choose Browse in Raw File from the shortcut menu. Follow the instructions “To browse in a raw data file” on page 386. To add samples to the batch 1. Right-click and choose Add Sample from the shortcut menu, or click the add sample icon, . The application adds a new Specimen sample to the end of the sample list. 2. In the Filename column for each sample, do one of the following: • Accept the default file name: UnknownN. • Change the default file name. Follow the instructions “To change the file names.” • Browse in a raw data file name. Follow the instructions “To browse in a raw data file” on page 386. 3. Select a sample type from the Sample Type list for each sample. Available sample types Specimen QC Solvent Calibrator Unextracted Negative Hydrolysis 4. For detailed descriptions of sample types, see “Sample Types” on page 337. 5. For each Calibrator or QC sample, select a level from the Level list. The sample levels are defined in the master method. If there are no levels to select from the Level list, do the following: a. Click Cancel in the Batch Wizard. b. Return to the Method Development mode. c. Open the method. d. Click the Compounds tab. 384 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Creating a Batch Using the Batch Wizard e. Click the Calibration Levels tab. f. Add the levels. g. Save the method. h. Return to the Analysis mode, open the Batch Wizard, and begin your batch again. For detailed instructions about defining sample levels, see Chapter 4, “Using the Method Development Mode.” 6. In the Vial Position column for the new sample, type a vial position. 7. In the Injection Volume column for the new sample, type a volume. The minimum injection volume value allowed is 0.1 μL; the maximum injection volume value allowed is 5000 μL. 8. (Optional) Type or edit the values for the remaining columns. Note The Add Sample function is not available in Quick Mode. To remove samples from the batch 1. Select the samples to remove. 2. Right-click and choose Remove Selected Samples from the shortcut menu, or click the remove samples icon, . The application removes the selected samples from the sample list. Note The Remove Selected Samples function is not available in Quick Mode. To insert samples into the batch 1. Select the sample above where you want to insert a new sample. 2. Right-click and choose Insert Sample from the shortcut menu. The application inserts a new Specimen sample above the selected sample. Note The Insert Sample function is not available in Quick Mode. To copy a sample 1. Select the sample that you want to copy. 2. Right-click and choose Insert Copy Sample from the shortcut menu. The application inserts the copy above the selected sample. Note The Insert Copy Sample function is not available in Quick Mode. Thermo Scientific TraceFinder User Guide 385 6 Using the Analysis Mode Creating a Batch Using the Batch Wizard To move a sample up or down in the sample list 1. Select the sample that you want to move. 2. Right-click and choose Move Sample Up or Move Sample Down from the shortcut menu. The application moves the selected sample up or down one row in the sample list. Note The Move Sample functions are not available in Quick Mode. To browse in a raw data file 1. Double-click the Filename column, or right-click and choose Browse in Raw File from the shortcut menu. A dialog box opens where you can select a raw data file to use for the sample. You can also browse in multiple raw data files to create multiple samples. 2. Locate the raw data file to use for the sample and click Open. Note The Browse in Raw File function is not available in Quick Mode. 386 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Creating a Batch Using the Batch Wizard Figure 90. Batch Specification page Table 72. Batch Specification parameters (Sheet 1 of 2) Parameter Description Batch Template Master Method Batch File Calibration File Displays the path names of the batch template, master method, batch file, and calibration file used to create this batch. Adds a new, Specimen sample to the end of the sample list. This function is not available in Quick Mode. Removes the selected sample. This function is not available in Quick Mode. Quick Mode Limits the columns of information in the Batch Specification page to the following: • Sample Type • Sample ID • Injection Volume • Conversion Factor In Quick Mode, the shortcut menu and add/remove sample icons are unavailable. Thermo Scientific TraceFinder User Guide 387 6 Using the Analysis Mode Creating a Batch Using the Batch Wizard Table 72. Batch Specification parameters (Sheet 2 of 2) Parameter Description Help Opens the “Creating a Batch Using the Batch Wizard” topic (this topic) in the application Help tool. Back Returns you to the Batch Template Selection page where you can choose a different batch template, master method, or starting vial position. Next Takes you to the Finish page where you can submit the batch for acquisition or processing. See “Submitting the Batch.” Cancel Immediately exits the Batch Wizard and does not save the batch. There is no confirming message. Shortcut Menu Add Sample Adds a single empty row to the sample list. Insert Sample Inserts a new, Specimen sample above the selected row. Insert Copy Sample Copies the currently selected row and inserts a copy above the row. Remove Selected Samples Removes selected samples from the sample list. Move Sample Up Moves the selected sample up one row in the sample list. Move Sample Down Moves the selected sample down one row in the sample list. Browse In Raw File Opens a dialog box where you can select a raw data file to use for the sample row. You can also browse in multiple raw data files to create multiple samples. Fill Down Enters sequential values in the column, starting with the value in the selected row and ending with the last row in the column. For detailed instructions about using the Fill Down command, see Appendix B, “Using Copy Down and Fill Down.” Renumber Vial Positions Renumbers vial positions for all samples after the currently selected sample. The selected sample retains its vial position. All subsequent samples are renumbered sequentially. Available only after you add or move samples. 388 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Creating a Batch Using the Batch Wizard Submitting the Batch From the Finish page, you can change the name of the batch, access the Calibration and Compound Selection page to edit the calibration file or edit the list of compounds to identify, or save the batch and open it in Batch View. For descriptions of the parameters on the Finish page, see “Finish page.” Follow these procedures: • To change the name of the batch • To save the batch • To edit the calibration file • To identify specific compounds or groups of compounds To change the name of the batch Edit the name in the Batch Name box. You cannot overwrite an existing batch name. If you enter a name for a batch that already exists, when you click Finish, the Batch Save dialog box asks you to enter another name. To save the batch Click Finish. The application saves the batch and displays it in the Batch View. From the Batch View, you can submit the batch for acquisition, processing, or report generation. See “Submitting a Batch” on page 371. To edit the calibration file 1. Select the Modify Calibrations or Active Compounds by Group check box. The application replaces the Finish button with a Next button. 2. Click Next. The Calibration and Compound Selection page opens. See “Selecting Calibration Files and Compounds” on page 391. To identify specific compounds or groups of compounds 1. Select the Modify Calibrations or Active Compounds by Group check box. The application replaces the Finish button with a Next button. 2. Click Next. The Calibration and Compound Selection page opens. See “Selecting Calibration Files and Compounds” on page 391. Thermo Scientific TraceFinder User Guide 389 6 Using the Analysis Mode Creating a Batch Using the Batch Wizard Figure 91. Finish page Table 73. Finish parameters Parameter Description Modify Calibrations or Active Compounds by Group Activates the Next button that lets you access the Calibration and Compound Selection page. When you have already used the Calibration and Compound Selection page, this option is not available. Batch Name Name of the default batch in this form: MasterMethodName_MMDDYYYY_ Help Opens the Creating a Batch Using the Batch Wizard topic (this topic) in the application Help tool. Back Returns you to the Batch Specification page where you can enter a sample ID, sample name, or comment. You can also add or remove samples from the sample list or edit the column values for the samples. See “Specifying a Batch” on page 383. Finish Saves the batch and displays it in Batch View. From Batch View, you can submit the batch for acquisition, processing, or report generation. See “Submitting a Batch” on page 371. Next Opens the Calibration and Compound Selection page where you can edit the calibration file or edit the list of compounds that you want to identify. Available only when Modify Calibrations or Active Compounds by Group is checked. Cancel 390 TraceFinder User Guide Immediately exits the Batch Wizard and does not save the batch. There is no confirming message. Thermo Scientific 6 Using the Analysis Mode Creating a Batch Using the Batch Wizard Selecting Calibration Files and Compounds From the Calibration and Compound Selection page, you can edit the calibration file or edit the list of compounds that you want to identify. For descriptions of the parameters on the Calibration and Compound Selection page, see “Calibration and Compound Selection Page.” Follow these procedures: • To add calibration data to the calibration file • To identify specific compounds or groups of compounds To add calibration data to the calibration file 1. To add calibration data from another batch to the current calibration file, click Extend Calibrations. The Select a Calibration File to Use dialog box opens. The dialog box lists only calibration batches that use the same master method as the current batch. 2. Select a calibration file to append to the current calibration file and click OK. The application appends the selected calibration file to the current file. 3. To save calibration data from both files into a single file for this batch, click Create New. 4. When you are finished with the Calibration and Compound Selection page, click Next. The Finish page opens. See “Submitting the Batch” on page 389. To identify specific compounds or groups of compounds 1. In the Compound Groups area, select the groups that include the compounds to identify in the samples. 2. In the Included Compounds area, select the Active check box for each compound that you want to identify in the samples. 3. When you are finished with the Calibration and Compound Selection page, click Next. The Finish page opens. See “Submitting the Batch” on page 389. Thermo Scientific TraceFinder User Guide 391 6 Using the Analysis Mode Creating a Batch Using the Batch Wizard Figure 92. Calibration and Compound Selection Page Table 74. Calibration and Compound Selection parameters Parameter Description Calibration File Name of the current batch in this form: MasterMethodName_MMDDYYYY_ Create New Saves calibration data from all calibration files to the current calibration file. Available only after you use Extend Calibrations to append calibration data from another calibration file. Extend Calibrations Adds calibration data from the current batch to the selected calibration file. Compound Groups Displays all available groups defined on the Groups page of the Method View. See “Editing the Groups Page” on page 183. Included Compounds Displays all available compounds that you can identify in the samples. Compounds marked as Active are identified in the batch samples. Help Opens the “Creating a Batch Using the Batch Wizard” topic (this topic) in the application Help tool. Back Returns you to the Batch Specification page where you can enter a sample ID, sample name, or comment. You can also add or remove samples from the sample list or edit the column values for the samples. See “Specifying a Batch” on page 383. Next Opens the Finish page where you can change the name of the batch or save the batch to the Batch View. See “Submitting the Batch” on page 389. Cancel Immediately exits the Batch Wizard and does not save the batch. There is no confirming message. 392 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Working in Data Review for Quantitation Methods In the Data Review view, you can view the data generated by the quantitation master method. Use Data Review to verify the data for a compound before you generate reports. To open the Data Review view 1. Click Analysis in the navigation pane. The Analysis navigation pane opens. 2. Click Data Review. The Data Review navigation pane opens. Choose from a Sample View, Compound View, or Qualitative View in Data Review to analyze the data generated by the master method. This section includes the following topics: • Sample View • Compound View • Qualitative View • Features Common to All Data Review Pages Thermo Scientific TraceFinder User Guide 393 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Sample View The Sample View uses three different panes to display a list of all samples in the current batch, the compound results for all compounds in the method, and peak plots for all compounds found in the currently selected sample. These are the default panes and their locations: Sample Peaks pane Samples pane Compound Results pane When you select a sample in the Samples Pane, the associated Compound Results Pane flags any compound with errors in the selected sample. The associated Sample Peaks Pane displays the chromatogram, retention time, area, height, and signal-to-noise ratio for all compounds in the selected sample. The Sample Peaks pane highlights the compound selected in the Compound Results pane. The Sample View display includes the following features: • Samples Pane • Compound Results Pane • Sample Peaks Pane • Caution Flags • Viewing Sample View Panes 394 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Samples Pane Use the Samples pane to select a specific sample. The associated Compound Results Pane displays all compounds in the method and flags any compound with errors in the selected sample. To hide or display columns in the Samples pane 1. Click the Field Chooser icon, , in the upper left corner of the pane. The Field Chooser displays all available columns of data for the Samples pane. 2. Select the check box for each column that you want to display, or clear the check box for each column that you want to hide. The application immediately displays or hides the column in the Samples pane. 3. When you are finished modifying the column display, click Chooser. Thermo Scientific to close the Field TraceFinder User Guide 395 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Figure 93. Samples pane Compound error in the selected sample Selected sample No compound error in the selected sample Table 75. Samples pane columns Column Description Flags Caution flag displayed when a compound in the sample has an error. See “Caution Flags” on page 400. Status Sample is not acquired. Sample is acquired but not processed. Sample is acquired and processed. Sample is currently acquiring. 396 TraceFinder User Guide Sample Name A user-defined name that identifies a sample. Sample Type Defines how the TraceFinder application processes the sample data. Each sample is classified as one of the following sample types: Specimen, QC, Solvent, Calibrator, Hydrolysis, Unextracted, or Negative Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Compound Results Pane Use the Compound Results pane to select a specific compound in the selected sample. The associated Sample Peaks Pane highlights the selected compound. To hide or display columns in the Compound Results pane 1. Click the Field Chooser icon, , in the upper left corner of the pane. The Field Chooser displays all available columns of data for the Compound Results pane. 2. Select the check box for each column that you want to display, or clear the check box for each column that you want to hide. The application immediately displays or hides the column in the Compound Results pane. 3. When you are finished modifying the column display, click Chooser. Thermo Scientific to close the Field TraceFinder User Guide 397 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Figure 94. Compound Results pane Table 76. Compound Results pane columns Column Description Flags Caution flag displayed when the compound has an error. See “Caution Flags” on page 400. Compound Compound names as identified in the library. Compound Type Specified compound type: Target Compound or Internal Standard. The remainder of the columns in the results list are common to both the Sample View Compound Results and the Compound View Sample Results displays. See “Common Column Parameters” on page 432. 398 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Sample Peaks Pane The Sample Peaks pane displays the chromatogram, retention time, area, height, and signal-to-noise ratio for all compounds in the Compound Results pane. The application highlights the chromatogram for the compound that is currently selected in the Compound Results pane. To display details for a compound Double-click the chromatogram in the Sample Peaks pane. The Compound Details pane opens. The Compound Details pane displays information about the quan peak, calibration curve, confirming ion, internal standard, reference peak, ion overlay, and spectra for the compound. For a detailed description of the available information in the Compound Details pane, see “Compound Details” on page 437. Thermo Scientific TraceFinder User Guide 399 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Caution Flags In the Sample View, the application displays caution flags in both the Samples pane and the Compound Results pane. This section includes the following topics: • Flags in the Samples Pane • Flags in the Compound Results Pane • Error Indicators in the Sample Peaks Pane Flags in the Samples Pane The Flags column in the Samples pane displays a caution flag if any compound in the sample is not in compliance with the method criteria. Click the caution flag icon, , to display the details. Information in the pop-up box shows the compound that is in error and describes the exact error condition. Error condition Compound name 400 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Flags in the Compound Results Pane The Flags column in the Compound Results pane displays a flag if the compound in the selected sample is not in compliance with the method criteria. Selected sample Hold your cursor over the flag icon, sample. Status of the Sulfisomidine compound in the selected sample , to display details for the compound in the selected Flags in the Compound Results pane are displayed in these situations: • A red flag for compounds that have violated (or are activated by) any of the values set in the method. See “Editing the QAQC Page” on page 174. • A red flag for compounds that are outside the specified ion ratio range. See Ion ratio failure flag. • An orange flag for compounds that are below the LOQ, below the LOD, or between the LOD and LOQ values specified in the method. For descriptions of these limits, see “Limits” on page 175. • A green flag for “found” compounds that are over the LOR amount specified in the method. For a description of the LOR limit, see “Limits” on page 175. • A yellow flag for compounds that are equal to or below the LOR amount specified in the method. • A yellow flag for compounds that are not found in Calibrator or QC sample types. The Compound Results pane does not flag compounds that are not found in Specimen sample types. • No flag for compounds that have no errors or where no report options are selected. Note These criteria for flag states do not apply to Negative sample types when the compound is an internal standard. Thermo Scientific TraceFinder User Guide 401 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Error Indicators in the Sample Peaks Pane In the Sample Peaks pane, peak plots are outlined with the color of their associated error flag. In the following example, the FENTHION peak plot is highlighted in blue to indicate that FENTHION is the selected compound, and the Sulfisomidine peak plot is outlined in red to indicate that the Sulfisomidine compound in the selected sample is outside the specified ion ratio range. Figure 95. Ion ratio failure flag Red flag indicating ion ratio failure Selected peak 402 TraceFinder User Guide Peak with ion ratio failure outlined in red Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Viewing Sample View Panes The Sample View display uses multiple panes to display data: Sample Results, Compound Results, Sample Peaks, and Compound Details. You can display, hide, or move any of these panes. To display or hide a Sample View pane From the View menu, choose from the following: • Compounds with Data: Displays or hides the Compound Results pane. • Sample View Peaks: Displays or hides the Sample Peaks pane. • Compound Details: Displays or hides the Compound Details pane. Note The Sample Results pane is required for the Sample View display. You cannot hide the Sample Results pane. Displayed panes are indicated with a check mark. Thermo Scientific TraceFinder User Guide 403 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Data Review Pane Display Features The following procedures are common to all Data Review displays. • To dock a pane • To make a pane floating or dockable • To change a pane from a docked pane to a tabbed pane • To restore the default layout To dock a pane 1. Grab the title bar of the pane and begin dragging the pane. The application displays docking arrows. 2. Drag the pane over one of the arrows. As you hold the cursor over a docking arrow, the application displays a blue region indicating where this arrow will place the pane. 3. Drop the pane onto one of the arrows. To make a pane floating or dockable Do one of the following: • To make a dockable pane floating, right-click the title bar of the pane and choose Floating. While a pane is set as floating, you cannot use the docking arrows to dock it or make it a tabbed pane. • To make a floating pane dockable, right-click the title bar of the pane and choose Dockable. 404 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods To change a pane from a docked pane to a tabbed pane 1. Grab the title bar of the pane and begin dragging the pane. The application displays docking arrows. 2. Hold the cursor over the center of the docking arrows to display a blue region indicating the location of the tabbed pane. 3. Drop the pane over the center of the docking arrows. Note To change a floating pane to a tabbed pane, you must first make the pane a dockable pane, and then you can make it a tabbed pane. To restore the default layout Choose View > Restore Default Layout. The Sample View, Compound View, and Qualitative View each have their own defaults for which panes are displayed and in which location. Thermo Scientific TraceFinder User Guide 405 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Compound View The Compound View uses three different panes to display a list of all compounds available in the method, all samples in the current batch, and the peak plots for all compounds found in each sample. These are the default panes and their locations: Sample Peaks pane Compounds pane Sample Results pane When you select a compound in the Compounds Pane, the Sample Results Pane flags any sample that contains errors with the selected compound. The Sample Peaks Pane highlights the selected compound and displays the name of the sample in which the compound was found and the following information about the compound: chromatogram, retention time, area, height, and signal-to-noise ratio. The Compound View includes the following features: • Compounds Pane • Sample Results Pane • Sample Peaks Pane • Caution Flags 406 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Compounds Pane Use the Compounds pane to select a specific compound. The Sample Results Pane displays all samples in the batch and flags any sample that contains errors with the selected compound. To hide or display columns in the Compounds pane 1. Click the Field Chooser icon, , in the upper left corner of the pane. The Field Chooser displays all available columns of data for the Compounds pane. 2. Select the check box for each column that you want to display, or clear the check box for each column that you want to hide. The application immediately displays or hides the column in the Compounds pane. 3. When you are finished modifying the column display, click Chooser. to close the Field Figure 96. Compounds pane Selected compound Error associated with the selected compound No error associated with the selected compound Table 77. Compounds pane columns Thermo Scientific Column Description Flags Caution flag displayed when a compound has an error in any of the samples. Compound Compound names as identified in the library. If there is no library selected in the method template, the compound name is identified as [email protected] Compound Type Specified compound type: Target Compound or Internal Standard. TraceFinder User Guide 407 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Sample Results Pane Use the Sample Results pane to select a specific compound in a specific sample. The Sample Peaks pane highlights the selected compound and displays the name of the sample in which the compound was found and the following information about the compound: chromatogram, retention time, area, height, and signal-to-noise ratio. See Sample Results pane. To hide or display columns in the Sample Results pane 1. Click the Field Chooser icon, , in the upper left corner of the pane. The Field Chooser displays all available columns of data for the Sample Results pane. 408 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods 2. Select the check box for each column that you want to display, or clear the check box for each column that you want to hide. The application immediately displays or hides the column in the Sample Results pane. 3. When you are finished modifying the column display, click Chooser. to close the Field Figure 97. Sample Results pane Table 78. Sample Results pane columns (Sheet 1 of 2) Column Description Acquisition Order Sequentially numbers the samples. Flags Caution flag displayed when a compound within the sample has an error. State Sample is not acquired. Sample is acquired but not processed. Sample is acquired and processed. Sample is currently acquiring. Sample Name Thermo Scientific A user-defined name that identifies a sample. TraceFinder User Guide 409 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Table 78. Sample Results pane columns (Sheet 2 of 2) Column Description Sample Type Defines how the TraceFinder application processes the sample data. Each sample is classified as one of the following sample types: Specimen, QC, Solvent, Calibrator, Hydrolysis, Unextracted, or Negative The remainder of the columns in the Sample Results pane are common to both the Sample View and the Compound View displays. See “Common Column Parameters” on page 432. 410 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Sample Peaks Pane In the Compound View, the Sample Peaks pane displays the compound chromatogram, retention time, area, height, and signal-to-noise ratio for the selected compound in each of the samples in the batch. The application highlights the compound chromatogram for the sample that is currently selected in the Sample Results pane. To display details for a compound 1. Double-click the chromatogram in the Sample Peaks pane. The Compound Details dialog box opens. The Compound Details dialog box displays information about the quan peak, calibration curve, confirming ion, internal standard, reference peak, ion overlay, and spectra for the compound. For details about the available information in the Compound Details dialog box, see “Compound Details” on page 437. Thermo Scientific TraceFinder User Guide 411 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Caution Flags In the Compound View, the application displays caution flags in both the Compounds pane and in the Sample Results pane. This section includes the following topics: • Flags in the Compounds Pane • Flags in the Sample Results Pane • Error Indicators in the Sample Peaks Pane Flags in the Compounds Pane The Flags column in the Compounds pane displays a caution flag if the compound in any of the samples is not in compliance with the method criteria. Selected Sulfisomidine compound Status of the Sulfisomidine compound in each sample Click the caution flag icon, , to display the details. Information in the pop-up box shows the sample where the compound is in error and describes the exact error condition. Error condition Sample name 412 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Flags in the Sample Results Pane The Flags column in the Sample Results pane displays a flag if the selected compound in the sample is not in compliance with the method criteria. Hold your cursor over the flag icon, the sample. , to display the details for the selected compound in Flags in the Sample Results pane are displayed in these situations: Flag Description A green flag for compounds that are over the LOR amount specified in the method. A red flag for compounds that have violated (or are activated by) any of the values set in the method. See “Editing the QAQC Page” on page 174. A red flag for compounds that are outside the specified ion ratio range. See Ion ratio failure flag. An orange flag for compounds that are not found in Calibrator or QC sample types. “Not found” compounds are below the LOQ, below the LOD, or between the LOD and LOQ values specified in the method. The Sample Results pane does not flag compounds that are not found in Specimen sample types. No flag for compounds that have no errors or where no report options are selected. Note These criteria for flag states do not apply to Negative sample types when the compound is an internal standard. Thermo Scientific TraceFinder User Guide 413 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Error Indicators in the Sample Peaks Pane In the Sample Peaks pane, peak plots are outlined with the color of their associated error flag. In the following example, the peak plot is highlighted in blue to indicate that Benzo_25557 is the selected sample and outlined in red to indicate that the FENTHION compound in the selected sample is outside the specified ion ratio range. Figure 98. Ion ratio failure flag 414 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Viewing Compound View Panes The Compound View display uses multiple panes to display data: Compounds, Sample Results, Sample Peaks, and Compound Details. You can display, hide, or move any of these panes. To display or hide a Compound View pane From the View menu, choose from the following: • Samples with Data: Displays or hides the Sample Results pane. • Compound View Peaks: Displays or hides the Sample Peaks pane. • Compound Details: Displays or hides the Compound Details pane. Note The Compounds pane is required for the Compound View display. You cannot hide the Compounds pane. Displayed panes are indicated with a check mark. For procedures about creating docked, floating, or tabbed panes, see “Data Review Pane Display Features” on page 404. Thermo Scientific TraceFinder User Guide 415 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Qualitative View The Qualitative View uses several different panes to display qualitative information for the selected sample. If it finds no detected peaks for the selected sample, you can manually add peaks. To see processed data for a sample in the Qualitative View, you must select the Qual Processing parameter for that sample in the Batch View before you process the batch. See “Batch View Sample List” on page 352. These are the default panes and their locations: Samples pane Sample Peak Details pane chromatogram pane Peaks pane Spectrum pane Library Hits pane The Qualitative View displays data in the following panes: • Samples Pane • Peaks Pane • Sample Chromatogram Pane • Peak Details Pane 416 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods • Spectrum Pane (Library and Data) • Library Hits Pane • Viewing Qualitative View Panes Samples Pane Use the Samples pane to select a specific sample. The associated Peaks Pane displays all peaks found in the selected sample. To hide or display columns in the Samples pane 1. Click the Field Chooser icon, , in the upper left corner of the pane. The Field Chooser displays all available columns of data for the Samples pane. 2. Select the check box for each column that you want to display, or clear the check box for each column that you want to hide. The application immediately displays or hides the column in the Samples pane. 3. When you are finished modifying the column display, click Chooser. to close the Field Figure 99. Samples pane Table 79. Samples pane columns (Sheet 1 of 2) Thermo Scientific Column Description Acquisition Order Sequentially numbers the samples. Flags Caution flag displayed when a compound in the sample has an error. See “Caution Flags” on page 400. TraceFinder User Guide 417 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Table 79. Samples pane columns (Sheet 2 of 2) Column Status Description Sample is not acquired. Sample is acquired but not processed. Sample is acquired and processed. Sample is currently acquiring. 418 TraceFinder User Guide Sample Name A user-defined name that identifies a sample. Sample Type Defines how the TraceFinder application processes the sample data. Each sample is classified as one of the following sample types: Specimen, QC, Solvent, Calibrator, Hydrolysis, Unextracted, or Negative Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Peaks Pane The Peaks pane works with the Samples pane to display graphical values for a unique sample and peak combination. For detailed descriptions of parameters in the Peaks pane, see “Peaks pane parameters” on page 422. To display peaks for a specific compound 1. From the Samples pane, select a sample. The Peaks pane displays the retention times for peaks identified in the selected sample, the values for the best match methods for each peak, and the library match. The method specifies which technique to use for identifying peaks: peaks within a specific retention time range, as a minimum percentage of the height or area of the largest peak, or as a minimum percentage of the nearest internal standard peak. You can change the method for identifying peaks in the Method Template Editor. See “Creating a Method Template” on page 224. 2. In the Peaks pane, select a peak in the sample. The TraceFinder application displays the selected peak in the Peak Details pane, displays the Qual Data and Qual Library sections in the Spectrum pane, and locates the selected peak in the Sample Chromatogram pane. • The Qual Data section shows spectrum data for the peak in the raw data file. • The Qual Library section shows actual spectrum for the identified library compound. Thermo Scientific TraceFinder User Guide 419 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Figure 100. Peak Details pane Note When you select a data-dependent sample, the peak can be from either a full scan or a QED spectrum of an SRM-filtered chromatogram. Figure 101. Spectrum pane Reference spectrum from the library Actual spectrum data for the compound Figure 102. Selected peak in the Sample Chromatogram pane 420 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods To remove a peak 1. Select a peak in the Sample Chromatogram pane. 2. Right-click the Peak Details pane and choose Remove Qual Peak from the shortcut menu. The TraceFinder application removes the selected peak from all Qualitative View panes. Note There is no undo for this action, but you can manually add a peak to redefine a removed peak. See “Sample Chromatogram Pane” on page 423. To hide or display columns in the Peaks pane 1. Click the Field Chooser icon, , in the upper left corner of the pane. The Field Chooser displays all available columns of data for the Peaks pane. 2. Select the check box for each column that you want to display, or clear the check box for each column that you want to hide. The application immediately displays or hides the column in the Peaks pane. 3. When you are finished modifying the column display, click Chooser. Thermo Scientific to close the Field TraceFinder User Guide 421 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Figure 103. Peaks pane Table 80. Peaks pane parameters Parameter Description Filter Filter used to identify the peaks. Specified in the raw data file or the master method. When your raw data file is data-dependent, the filter indicates this with a “d”. Data-dependent filter 422 TraceFinder User Guide Peak RT Peak retention time. The time after injection when the compound elutes. The total time that the compound is retained on the column. SI Search index method used to search the NIST library. RSI Reverse search index method used to search the NIST library. MP Match probability. Compound Library compound that matches the identified peak. Remove Selected Peak Shortcut menu command that removes the selected peak from the peaks list. Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Sample Chromatogram Pane The Sample Chromatogram pane displays all peaks in the selected sample. The peak selected in the Peaks pane displays a red marker. See “Sample Chromatogram pane” on page 424. For a description of commands on the shortcut menu, see “Sample chromatogram pane shortcut menu commands” on page 424. To zoom in on a peak 1. In the Sample Chromatogram pane, drag the cursor to delineate a rectangle around the peak. The delineated area expands to fill the view. 2. To restore the default view, right-click the Sample Chromatogram pane and choose Reset Scaling from the shortcut menu. To manually add a peak 1. Zoom in to better identify which peak to add to the results set. 2. Right-click the Sample Chromatogram pane, and choose Add Qual Peak from the shortcut menu. 3. Click to indicate the left and right base points for the peak. The TraceFinder application marks the peak in the Sample Chromatogram pane. The TraceFinder application places the peak delimiter tags at the base point locations and automatically updates the peak values in the Peaks pane and Peak Details pane. Thermo Scientific TraceFinder User Guide 423 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Figure 104. Peak Details pane with a manually added peak Manually added base points Figure 105. Sample Chromatogram pane Table 81. Sample chromatogram pane shortcut menu commands 424 TraceFinder User Guide Command Description Add Qual Peak Select the beginning and ending base points for a new qual peak. Available only when no peak is detected. Reset Scaling Resets the original scaling after a zoom operation. Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Peak Details Pane The Peak Details pane displays the selected peak. For detailed descriptions of all parameters on the Peak Details pane, see “Peak Details pane” on page 427. Follow these procedures: • To zoom in on a peak • To manually add a peak • To remove a peak • To switch between method and manual integration modes • To change the displayed information for detected peaks For a description of commands on the shortcut menu, see “Peak Details pane shortcut menu commands” on page 427. To zoom in on a peak 1. In the chromatogram plot, drag the cursor to delineate a rectangle around the peak. The delineated area expands to fill the view. 2. To restore the default view, right-click the chromatogram plot and choose Reset Scaling from the shortcut menu. To manually add a peak 1. Right-click anywhere in the Peak Details pane, and choose Add Qual Peak from the shortcut menu. If a peak is already detected, the Add Qual Peak command is not activated. 2. Click to indicate the left and right base points for the peak. The TraceFinder application places the peak delimiter tags at these locations and automatically updates the peak values (area, height, and so forth) in the result set. Manually added base points Thermo Scientific TraceFinder User Guide 425 6 Using the Analysis Mode Working in Data Review for Quantitation Methods To remove a peak Right-click the Peak Details pane, and choose Remove Qual Peak from the shortcut menu. The TraceFinder application removes the peak displayed in the Peak Details pane. All data for this peak are removed from the Qualitative View panes. To switch between method and manual integration modes Right-click the Peak Details pane and choose Method Integration or Manual Integration from the shortcut menu. Initially, the method and manual integration settings that are stored for a compound and file are identical. When you switch modes, the saved result set does not change. However, when manual data are available, the Peak Details plots and the result set update as you switch between method and manual modes. As you switch between modes, each pane reflects the changes. The generated reports for these data identify the manual modifications. To change the displayed information for detected peaks 1. Right-click the Peak Details pane and hold the cursor over Peak Labels. 2. Choose to display labels for the peak retention time (RT), peak height (AH), peak area (AA), or signal-to-noise (SN). Label not displayed in chromatogram Label displayed in chromatogram 3. To remove a label, select the label type again to clear it. 426 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Figure 106. Peak Details pane Table 82. Peak Details pane shortcut menu commands Thermo Scientific Command Description Reset Scaling Resets the original scaling after a zoom operation. Method Integration Displays method integration settings. Manual Integration Displays manual integration settings. Peak Labels Displays or hides the peak labels (Label Area, Label Retention Time, Label Height, or Label Signal to Noise). Remove Qual Peak Available only for manually added peaks. Removes the peak displayed in the Peak Details pane. TraceFinder User Guide 427 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Spectrum Pane (Library and Data) The Spectrum pane displays the reference spectrum from the library and the spectrum data for the selected sample. The top pane displays the spectrum for the identified compound found in the reference library; the bottom pane displays the actual spectrum data for the selected peak. Figure 107. Spectrum pane Reference spectrum from the library Actual spectrum data for the compound To zoom in on a peak 1. In either spectrum plot, drag the cursor to delineate a rectangle around the peak. The delineated area expands to fill the view. 2. To restore the default view, right-click the spectrum plot and choose Reset Scaling from the shortcut menu. 428 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Library Hits Pane The Library Hits pane displays the best library matches for the selected peak. Use this pane to select a different library entry for the peak. See “Library Hits pane.” When you select a library entry other than the original entry, the TIC Report and TIC Summary Report indicate this with a “P” flag: P flag For detailed descriptions of the Library Hits pane parameters, see “Library Hits pane parameters.” To change the library entry for a selected peak In the Library Hits pane, select the check box for the library entry that you want to use to identify the selected peak. • In the Spectrum pane, the reference spectra change to show the spectra for the selected library entry. • In the Peaks pane, the SI, RSI, MP, and Compound values update to reflect the selected library entry. Selected library entry in the Library Hits pane Reference spectra for Hexanone Peak list for Hexanone Thermo Scientific TraceFinder User Guide 429 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Figure 108. Library Hits pane Table 83. Library Hits pane parameters 430 TraceFinder User Guide Parameter Description <Check box column> Indicates selected library entries for the selected peak. Rank Indicates the order of best matches between the selected peak and library entries. SI Search index method used to search the NIST library. RSI Reverse search index method used to search the NIST library. MP Match probability. Library Entry Library compound that matches the identified peak. Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Viewing Qualitative View Panes The Qualitative View display uses multiple panes to display data: Samples, Peaks, Sample Chromatogram, Peak Details, Spectrum, and Library Hits. You can display, hide, or move any of these panes. To display or hide a Qualitative View pane From the View menu, choose to display or hide the following: • Peaks • Sample Chromatogram • Peak Chromatogram: Displays or hides the Peak Details pane. • Spectrum • Library Hits Note The Samples pane is required for the Qualitative View display. You cannot hide the Samples pane. Displayed panes are indicated with a check mark. For procedures about creating docked, floating, or tabbed panes, see “Data Review Pane Display Features” on page 404. Thermo Scientific TraceFinder User Guide 431 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Features Common to All Data Review Pages The following features are common to all quantitative batch data review pages. • Common Column Parameters • Status Indicators • Inactive and Excluded Compounds • Compound Details Common Column Parameters Table 84. Common parameters for Compound Results and Sample Results tables (Sheet 1 of 2) Column Description Height The distance from the peak maximum to the peak base, measured perpendicular to the ordinate. When the Response Ratio is specified as Height, this column displays an asterisk (*Height). Area The area obtained by integrating peak intensities from the start to the end of the peak. When the Response Ratio is specified as Area, this column displays an asterisk (*Area). Expected RT Expected retention time for the compound. Actual RT Actual retention time for the compound. Retention time is the time after injection when a compound elutes and the total time that the compound is retained on the chromatograph column. Calculated Amt The amount present in the sample, as determined using the calibration curve and the response ratio. Theoretical Amt Theoretical amount of the compound expected in the sample. Sample Amt The injected volume multiplied by the conversion factor. For example, if you have 1000 ng/mL of a substance that is too concentrated for the mass spectrometer, you can dilute it by 1000. Then your injection volume is 1, your conversion factor is 1000, and your sample amount is 1000. Response Ratio The ratio of the Response value to the IS Response value. If the Response is specified as Area in the processing method, the units of both Response and IS Response are counts-sec. If the Response is specified as Height in the processing method, the units of both Response and IS Response are counts. ISTD Amt Amount of internal standard. ISTD Response Response of the internal standard. Integration Mode Integration mode specified in the method. See “Quan Peak” on page 439. 432 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Table 84. Common parameters for Compound Results and Sample Results tables (Sheet 2 of 2) Column Description Active Displays or hides a compound for a particular sample. • When a compound is marked inactive, the application does not remove its data and calculated values from the result set. Instead, the TraceFinder application masks the appearance of that compound for that particular sample and grays the compound in the compounds list. • When a calibration standard is marked inactive, the application no longer uses the data file’s calibration point for the calibration and removes it from the graphical view of the calibration curve displayed in the Compound Details pane. It is no longer part of the result set. In a Sample View, the Active parameter is in the Compound Results pane. In a Compound View, the Active parameter is in the Sample Results pane. Excluded Turns a compound on or off in the calibration curve in the Compound Details pane. %Diff The calculated amount minus the expected amount, divided by the expected amount, and then multiplied by 100. %RSD Standard deviation of the multiple samples of one level, multiplied by 100, and divided by the average of the multiple samples of that level. This calculation is based on the calculated amounts. %CV Coefficient of Variance. Standard deviation of the multiple samples of one level, multiplied by 100, and divided by the average of the multiple samples of that level. This calculation is based on the areas of the peaks. Channel Specifies the channel on which the sample was run. If the sample is not acquired, the value is Pending. The Channel column is available only when you have activated multiplexing in the Application Configuration mode. See “Multiplexing” on page 66. Final Units Specifies the calculated amount. Default: 1 Comment A user-defined comment for the sample. Thermo Scientific TraceFinder User Guide 433 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Status Indicators Status indicators for each sample indicate if the sample is currently acquiring, not acquired, acquired, or processed. Sample is not acquired. Sample is acquired but not processed. Sample is acquired and processed. Sample is currently acquiring. Figure 109. Sample Results Status indicators 434 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Inactive and Excluded Compounds Use the Active and Excluded columns to control which compounds are used for calculating the calibration curve and for reporting. Follow these procedures: • To make a sample active or inactive • To exclude a calibration point To make a sample active or inactive 1. Select the sample in the Samples pane. All compounds in the selected sample are displayed in the Compounds pane. Inactive compounds are grayed out. 2. In the Compounds pane, select the compound whose active/inactive status you want to change. • When a compound it marked inactive, the application does not remove its data and calculated values from the result set. Instead, the TraceFinder application masks the appearance of that compound for that particular sample and grays the compound name in the compounds list. • When a calibration standard is marked inactive, the application no longer uses the data file’s calibration point for the calibration and removes it from the graphical view of the calibration curve displayed in the Qualification pane. The calibration point is no longer part of the result set. 3. In the Samples pane, select or clear the Active check box. Use the horizontal scroll bar at the bottom of the table to scroll to the Active column. Thermo Scientific TraceFinder User Guide 435 6 Using the Analysis Mode Working in Data Review for Quantitation Methods To exclude a calibration point In the sample list, select the Excluded check box for the sample. Note Only calibration samples have the Excluded check box available. Use the horizontal scroll bar at the bottom of the table to scroll to the Excluded column. The application displays a value that is no longer used for calibration as an empty box in the graphical view of the calibration curve. Excluded calibration point 436 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Compound Details Use the Compounds Details pane to display any of the following types of data: • Quan Peak • Confirming Ions • Calibration Curve • Ion Overlay • ISTD • Reference Peak • Spectra To open the Compound Details dialog box 1. Double-click the chromatogram in the Sample Peaks pane. The Compound Details pane opens. By default, the first display pane shows the quantitative peak for the selected compound. In the second pane, select the additional type of data that you want to display. Follow these procedures to change the display of the peak data in either of the panes: • To change the peak panes • To zoom in on a peak Thermo Scientific TraceFinder User Guide 437 6 Using the Analysis Mode Working in Data Review for Quantitation Methods To change the peak panes In any of the peak panes, click to view a list of commands. Command Description Make All Panels the Same Size Evenly divides the area to make all panes the same width. This command does not change the pane height. Move Panel Left Moves the current panel one space to the left. This command is not available when the current pane is the leftmost pane. Move Panel Right Moves the current panel one space to the right. This command is not available when the current pane is the rightmost pane. Add a Panel Adds an empty peak pane to the display. You can display a maximum of four peak panes. To zoom in on a peak 1. In any of the views, drag your cursor to delineate a rectangle around the peak or spectra. The delineated area expands to fill the view. 2. To restore the default view, right-click the chromatogram plot and choose Reset Scaling from the shortcut menu. 438 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Quan Peak A compound can have multiple quantitative peaks. You can switch between quantitative peaks, but you cannot view multiple quantitative peaks at the same time. The indicator in the upper right corner of the Quan Peak pane displays which of the multiple quantitative peaks you are viewing. The Quan Peak pane uses a unique shortcut menu. See “Quan Peak pane shortcut menu commands” on page 443. Figure 110. Quantitative peak pane with multiple quantitative peaks Peak 1 of 2 Peak 2 of 2 Follow these procedures to modify the quantitative or confirming ion peak data: • To manually add a peak • To remove a manually created peak • To switch between method and manual integration modes • To change the displayed information for detected peaks • To modify the peak detection settings Thermo Scientific TraceFinder User Guide 439 6 Using the Analysis Mode Working in Data Review for Quantitation Methods To manually add a peak 1. Right-click anywhere in the quantitative peak pane, and choose Add Quan Peak from the shortcut menu. 2. Click the left base of the peak you want to identify. 3. Drag to the right base and release the mouse. The application places the peak delimiter tags at these locations and automatically updates the peak values (area, height, and so forth) in the result set. Manually added right and left base points To remove a manually created peak Right-click the pane, and choose Cancel Add Peak from the shortcut menu. The application cancels the Add Peak operation. If you have already completed adding the peak, select the peak and then choose Remove Quan Peak from the shortcut menu. To manually integrate a quantitative peak 1. Hold your cursor over one of the two peak delimiter tags in the peak pane. When the tag can be selected, the cursor changes to a crosshair-style cursor. You can zoom in on the baseline to make it easier to select the tag. Crosshair cursor 2. Drag the peak delimiter tag to another location and automatically update the peak values (area, height, and so forth) into the result set. The generated reports for these data identify the manual modifications. You can store two peak value sets (method and manual integration settings) with each compound in each file. These settings can result in a different set of stored values. The application originally calculates the method values based on the processing method parameters. The manual values are a result of what you have edited. 440 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods To switch between method and manual integration modes Right-click the chromatogram view and choose Method Integration Settings or Manual Integration Settings from the shortcut menu. Initially, the method and manual integration settings that are stored for a compound and file are identical. When you switch modes, the saved result set does not change. However, when manual data are available, the chromatogram plots and the result set update as you switch between method and manual modes. As you switch between modes, each pane reflects the changes. The generated reports for these data identify the manual modifications. To change the displayed information for detected peaks 1. Right-click the peak pane and hold the cursor over Peak Labels. 2. Choose to display labels for the peak retention time, peak height, peak area, or signal to noise. The label types in the list are selected for displayed labels and are cleared for labels that are not displayed. 3. To remove a label, select the label type again and clear it. Label settings are globally applied to quantitative peaks, confirming ion peaks, and internal standard peaks. Tip The labels do not always update on all peak displays. To update all labels, select a different compound, and then reselect the compound whose labels you changed. To modify the peak detection settings 1. Right-click the chromatogram view and choose one of the following from the shortcut menu: • Peak Detection Settings > Edit Local Method Peak Detection Settings: Makes changes to the selected compound for all samples in this batch. • Peak Detection Settings > Edit User Defined Peak Detection Settings: Makes changes to the selected compound for only the selected sample. The TraceFinder application saves these changes with the batch and stops applying the local method detection settings to the compound for this sample only. The Peak Detection Settings dialog box opens where you can adjust detection settings that were specified in the method. The title bar of the dialog box lists the selected compound and indicates whether you are making changes to only the selected sample or to the local method. Thermo Scientific TraceFinder User Guide 441 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Figure 111. Peak Detection Settings dialog box Editing all samples in the batch Editing only the selected sample 2. Edit any of the detection settings. For detailed descriptions of all detection settings, see “Detection” on page 119. 3. To save your changes to this compound, click Apply. • When you are editing a single sample, the application makes changes to the selected compound for this sample. If the sample is a calibration sample type, this update changes the calibration curve which, in turn, affects all calculated amounts. • When you are editing the local method, the application makes changes to the selected compound for all samples in this batch. Note The Peak Detection Settings commands are also available on the Confirming Ions pane. 442 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Table 85. Quan Peak pane shortcut menu commands (Sheet 1 of 2) Command Description Method Integration Settings Use Local Method Peak Detection Settings: Applies the local method integration settings to the selected compound. To edit these peak detection settings, use the Peak Detection Settings > Edit Local Method Peak Detection Settings command. Use User Peak Detection Settings: Applies the user-customized method integration settings to the selected compound. To edit these user-customized settings, use the Peak Detection Settings > Edit User Defined Peak Detection Settings command. Thermo Scientific Manual Integration Settings Displays manual integration settings. Add Quan Peak –or– Remove Quan Peak –or– Cancel Add Peak Adds a peak, removes a peak, or cancels an add peak operation in progress. Confirming Ion List Select the confirming ions to be viewed. Not available for analog compounds. Send RT to Method Sets the current retention time as the expected retention time for the compound in the local method. Peak Labels Displays or hides the peak labels (Label Area, Label Retention Time, Label Height, or Label Signal to Noise). TraceFinder User Guide 443 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Table 85. Quan Peak pane shortcut menu commands (Sheet 2 of 2) Command Description Show Peak Info Displays peak information for the selected compound. For example Reset Scaling Resets the original scaling after a zoom operation. Peak Detection Settings Edit User Defined Peak Detection Settings: Opens the Peak Detection Settings dialog box where you can make changes to the selected compound for this sample. Edit Local Method Peak Detection Settings: Opens the Peak Detection Settings dialog box where you can make changes to the selected compound for all samples in this batch. After you apply either of these updates, the application does not retain manual integration settings. 444 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Confirming Ions The Confirming Ions pane displays a graphical view of all qualifying/confirming ions for the selected compound and displays calculated ion ratios and ion ratio acceptance windows. A red border indicates that an ion ratio is outside of its window. The Confirming Ions pane uses a unique shortcut menu. See Confirming Ions pane shortcut menu commands. Note For compounds with an analog detection type, the application displays “No Confirming Ions are Enabled” in the Confirming Ions pane. Figure 112. Quantitative peak with multiple confirming ions Figure 113. Confirming ion with coelution failure Thermo Scientific TraceFinder User Guide 445 6 Using the Analysis Mode Working in Data Review for Quantitation Methods To manually integrate a confirming ion peak 1. Hold your cursor over one of the two peak delimiter tags in the peak pane. When the tag can be selected, the cursor changes to a crosshair-style cursor. You can zoom in on the baseline to make it easier to select the tag. 2. Drag the peak delimiter tag to another location and automatically update the peak values (area, height, and so forth) into the result set. The generated reports for these data identify the manual modifications. You can store two peak value sets (method and manual integration settings) with each compound in each file. These settings can result in a different set of stored values. The application originally calculates the method values based on the processing method parameters. The manual values are a result of what you have edited. Note Because a Blank Report displays only the quantitation mass, when you manually integrate a confirming ion, the manual integration flag in the report is displayed on the quantitation mass. Table 86. Confirming Ions pane shortcut menu commands (Sheet 1 of 2) Command Description Method Integration Settings Displays the method integration settings. Manual Integration Settings Displays the manual integration settings. Add Quan Peak Adds a quantitation peak, removes a peak, or cancels an add peak –or– operation in progress. Remove Quan Peak –or– Cancel Add Quan Peak 446 TraceFinder User Guide Range Calc Method: Manual Selects the method used to calculate the ion ratio range windows: Manual, Average, Weighted Average, or Level. Range Calc Level Displays the range based on the calibration level. Target Ratio Specifies the theoretical ratio of the confirming ion's response to the quantification ion's response. Window Type Specifies the Absolute or Relative calculation approach for determining the acceptable ion ratio range. Window Specifies the acceptable ion ratio range as a percentage. Peak Labels Displays or hides the peak labels (Label Area, Label Retention Time, Label Height, or Label Signal to Noise). Show Peak Info Displays peak information for the selected compound. Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Table 86. Confirming Ions pane shortcut menu commands (Sheet 2 of 2) Thermo Scientific Command Description Reset Scaling Resets the original scaling after a zoom operation. Peak Detection Settings Opens the Peak Detection Settings dialog box for the selected compound. TraceFinder User Guide 447 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Calibration Curve The Calibration Curve pane displays a graphical view of the calibration curve for the selected compound and key statistical values for evaluating the quality of the calibration. The Calibration Curve pane uses a unique shortcut menu. See Calibration Curve pane shortcut menu commands. Figure 114. Quantitative peak with a calibration curve plot To manually exclude a calibration point In the sample list, select the Excluded check box for the sample. Use the horizontal scroll bar at the bottom of the table to scroll to the Excluded column. When a value is no longer used for calibration, it is displayed as an empty box in the graphical view of the calibration curve. Excluded calibration point 448 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Table 87. Calibration Curve pane shortcut menu commands Thermo Scientific Command Description Standard Type Sets the standard type to External or Internal. Calibration Curve Type Sets the calibration curve type to one of the following: • Linear: Allows all settings with this exception: When Origin is set to Include, all Weighting values are grayed out and Weighting is set to Equal. • Quadratic: Allows all settings with this exception: When Origin is set to Include, all Weighting values are grayed out and Weighting is set to Equal. • Average RF: Allows no Weighting or Origin selections. All Weighting and Origin values are grayed out. Weighting is set to Equal, and Origin is set to Ignore. Response Via Sets the response to Area or to Height. Weighting Sets the weighting to equal, 1/X, 1/X^2, 1/Y, or 1/Y^2. Origin Sets the origin to Ignore, Force, or Include. Units Sets the units. Done with Settings Saves the calibration curve settings. Reset Scaling Resets the original scale in the calibration curve pane. TraceFinder User Guide 449 6 Using the Analysis Mode Working in Data Review for Quantitation Methods Ion Overlay The Ion Overlay pane represents an overlay of the entire ion set—quantification and qualifying/confirming—for the selected compound. Use this pane to graphically review the peak apex alignment and coeluting peak profiles. Note For compounds with an analog detection type, the application displays “No Data” in the Ion Overlay pane. Figure 115. Quantitative peak with confirming ion overlay 450 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods ISTD The ISTD pane displays the internal standard specified for the compound in the method. See “To specify an internal standard for a compound” on page 164. Figure 116. Quantitative peak with an internal standard Reference Peak The Reference Peak pane displays the reference peak as specified in the method. Figure 117. Quantitative peak with a reference peak Thermo Scientific TraceFinder User Guide 451 6 Using the Analysis Mode Working in Data Review for Quantitation Methods To specify a chromatogram reference peak 1. In the Batch View task pane, click Reference Sample. An empty reference sample table opens. 2. Click the Add Reference Sample icon, Reference Sample from the shortcut menu. , or right-click and choose Add The Open Chromatograph Reference Sample dialog box opens. Note If you are creating a new method, you will not see any reference samples here. You must create and save a batch using the current method to see the reference samples in this list. 3. Select a project from the list of projects. 4. Select a subproject from the list of subprojects. 5. Select a batch from the list of batches. The TraceFinder application displays only batches that were created using the current master method. 6. Select a sample from the list of processed samples. The TraceFinder application displays all the processed samples in the selected batch. To use a sample as a reference sample, the sample must have been processed with the current master method. 452 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Quantitation Methods 7. Click Open. The selected sample is displayed as the chromatogram reference sample in the Method View in the Method Development mode. Tip To clear the reference sample from the master method, select None in the Set Chromatogram Reference Samples pane. Spectra The Spectra pane displays a comparison of the spectra found in the data and the method reference. Note For compounds with an analog detection type, the application displays “Not Available” in the Spectra pane. Figure 118. Quantitative peak with data and reference spectra Thermo Scientific TraceFinder User Guide 453 6 Using the Analysis Mode Working in Data Review for Target Screening Methods Working in Data Review for Target Screening Methods The Data Review view displays the data generated by the target screening master method. Use Data Review to verify the data for a compound before you generate reports. To open the Data Review view 1. Click Analysis in the navigation pane. The Analysis navigation pane opens. 2. Click Data Review. The Data Review navigation pane opens. In the target screening display, the panes show a list of all samples in the current batch, the compound results for all compounds in the method, and chromatogram and spectrum plots for all compounds found in the currently selected sample. 454 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Target Screening Methods Figure 119. Target Screening panes Chromatogram pane Samples pane Compounds pane Spectrum pane When you select a sample in the Samples pane, the associated Compounds pane flags any compound with errors in the selected sample. The associated Chromatogram pane displays the chromatogram, retention time, area, height, and signal-to-noise ratio for all compounds in the selected sample. The Spectrum pane highlights the compound selected in the Compounds pane. You can display, hide, or move any of these panes. To display or hide a Target Screening pane From the View menu, choose to display or hide the following: • Samples • Target Screening Results: Displays or hides the Compounds pane. • Chromatogram • Spectrum Note The Samples pane is required for the Target Screening display. You cannot hide the Samples pane. Thermo Scientific TraceFinder User Guide 455 6 Using the Analysis Mode Working in Data Review for Target Screening Methods Displayed panes are indicated with a check mark. For procedures about creating docked, floating, or tabbed panes, see “Data Review Pane Display Features” on page 404. The target screening display includes the following features: • Samples Pane • Compounds Pane • Chromatogram Pane • Spectrum Pane 456 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Target Screening Methods Samples Pane Use the Samples pane to select a specific sample in the batch. The associated Compounds Pane displays all compounds in the method and flags any compound with errors in the selected sample. Flags in the Samples pane indicate one of the following: A green circle when the sample/compound/peak combination is identified and fully confirmed. A yellow triangle when the sample/compound/peak combination is identified but not fully confirmed. A red square when the sample/compound/peak combination is not identified. Figure 120. Samples pane Table 88. Samples pane shortcut menu commands Thermo Scientific Command Description Sort by Alphabetical Sorts the samples alphabetically by sample name. Sort by Import Order Sorts the samples in the order they were processed. TraceFinder User Guide 457 6 Using the Analysis Mode Working in Data Review for Target Screening Methods Compounds Pane The Compounds pane displays all found peaks in the selected sample and flags any compound with errors. The Target Screening Results grid reflects the identified compounds found in the compound database and the results of the method processing criteria. Color Coding for Measured or Calculated Values The Compounds pane uses color-coded text to indicate the following: • Green—Indicates that the measured value of scoring and confirmations pass the criteria specified in the method. • Red—Indicates that the measured or calculated value does not pass the criteria specified in the method. Displaying Multiple Adducts When the TraceFinder application finds multiple adducts at the same retention time in a sample, the Compounds pane displays the adducts on a single row in the table. The table shows information for the most intense adducts for each retention time for a compound. 458 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Target Screening Methods Exporting Compounds To export compounds to an Excel spreadsheet 1. Choose File > Export Data To > Excel from the main menu. The Export Data to Excel dialog box opens. 2. Locate the folder where you want to save the file. 3. Type a file name for the XLSX file and click Save. The application saves the specified compound data to an Excel spreadsheet. You specify the format for the Excel spreadsheet and the types of peaks that are exported in the Target Screening Report Settings in the master method. See “To specify options for exporting compounds to an Excel worksheet” on page 209. To export compounds to a CSV file 1. Choose File > Export Data To > CSV from the main menu. The Export Data to CSV dialog box opens. 2. Locate the folder where you want to save the file. 3. Type a file name for the CSV file and click Save. The application saves the specified compound data to a comma-separated value (.csv) file. You specify the format for the CSV file and the types of peaks that are exported in the Target Screening Report Settings in the master method. See “To specify options for exporting compounds to an Excel worksheet” on page 209. Figure 121. Compounds pane Thermo Scientific TraceFinder User Guide 459 6 Using the Analysis Mode Working in Data Review for Target Screening Methods Table 89. Compounds pane parameters Column Description Displays the current compound database. When you have multiple screening databases, the application lists the results for each database separately. Expand the list of found compounds in the screening database. Flag Indicates the status of the identification and confirmation criteria. • A green circle when the sample/compound/peak combination is identified and fully confirmed. • A yellow triangle when the sample/compound/peak combination is identified but not fully confirmed. • A red square when the sample/compound/peak combination is not identified. Compound Name The compound name match in the compound database. Match Result Name The compound name match in the compound database and the retention time. Formula The formula for the peak as specified in the compound database. Confirmed The number of confirmation tests that passed out of the total number specified in the method. m/z (Expected) Mass-to-charge ratio from the compound database. Charge is presumed to be 1. m/z (Measured) Mass-to-charge ratio found in the spectra for the peak. Charge is presumed to be 1. m/z (Delta (ppm)) Difference between the expected and measured mass-to-charge ratio. Charge is presumed to be 1. RT (Expected) The retention time for the peak as specified in the compound database. RT (Measured) The found retention time for the peak apex. RT (Delta) Difference between the expected and measured retention time for the peak. Measured Area The AA value from the chromatogram pane. Isotopic Pattern Score (%) The percentage of the number of total isotopes to the number of matched isotopes. Num Isotopes Matched The number of isotopes matched in the theoretical calculated isotope spectra. Lib Match Name The name of the compound match in the library search. Library Score (%) The score from the library fit. S/N The signal-to-noise ratio calculated for the found peak. Left RT The time point of the left leading edge of the integrated peak. Right RT The time point of the right leading edge of the integrated peak. 460 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Target Screening Methods Chromatogram Pane Use the Chromatogram pane to display all extracted chromatograms of all adducts of the selected compound. The first tab displays the most intense target adduct for the peak result. Additional (optional) tabs display extracted ion chromatograms for other adducts for the target compound at the same retention time in order of intensity. If no signal exists for an adduct, it displays the XIC of the expected m/z within the specified retention and chromatogram windows. When you do not specify a retention time or window, the application displays the full time range. Figure 122. Chromatogram pane Table 90. Chromatogram pane shortcut menu commands Thermo Scientific Command Description Reset Scaling Resets the original scaling after a zoom operation. Copy to Clipboard Copies the graphic display to the Clipboard. TraceFinder User Guide 461 6 Using the Analysis Mode Working in Data Review for Target Screening Methods Spectrum Pane Use the Spectrum pane to display the spectrum, isotopes, fragments, and library search information for the selected adduct in the Chromatogram pane. The Spectrum pane displays only the identification and confirmation criteria specified in the method. The confirmations are based only on the most intense adduct. See “To specify identification and confirmation settings” on page 216. The Spectrum pane includes the following pages of information (when available) for each selected sample/compound/peak combination: • Spectrum • Isotopes • Fragments • Library Spectrum The application displays the neutral loss (NL) and compound/peak name information on the right side of the Spectrum page. When data is available, the plot width is the full mass range in the raw data file. Otherwise, the application scales the width to the scan range. Figure 123. Spectrum page Table 91. Spectrum page shortcut menu commands 462 TraceFinder User Guide Command Description Reset Scaling Resets the original scaling after a zoom operation. Copy to Clipboard Copies the graphic display to the Clipboard. Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Target Screening Methods Isotopes The isotopes page displays isotopic pattern results according to the threshold and deviation parameters defined in the screening method. To identify or confirm the presence of a compound, the resulting score percentage from isotopic pattern matching must be higher than the specified fit threshold percentage. An isotope peak is not found if its intensity, relative to the monoisotopic ion’s intensity, is more than the specified intensity deviation percentage away from the theoretical relative intensity of the isotope ion. An isotope peak is found if its measured m/z is less than the specified mass deviation amount away from its expected m/z. To specify threshold and deviation parameters, see “To specify identification and confirmation settings” on page 216. Figure 124. Isotopes page with stacked spectra Theoretical isotope spectrum Experimental spectrum Thermo Scientific TraceFinder User Guide 463 6 Using the Analysis Mode Working in Data Review for Target Screening Methods Figure 125. Isotopes page with overlaid spectra Theoretical isotope spectrum displayed in blue. Experimental spectrum displayed in black. Table 92. Isotopes page shortcut menu commands 464 TraceFinder User Guide Command Description Reset Scaling Resets the original scaling after a zoom operation. Copy to Clipboard Copies the graphic display to the Clipboard. Display Overlay Spectra Display Stack Spectra Overlays the two spectrum displays, or stacks the simulated spectrum and the peak apex spectrum. Show/Hide Noise Label Adds a noise label to each peak. Theoretical isotope peaks (displayed in blue) do not display a noise label. Show/Hide Resolution Label Adds a resolution label to each peak. Theoretical isotope peaks (displayed in blue) do not display a resolution label. Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Target Screening Methods Fragments The Fragments page displays the maximum number of fragments as specified in the screening method. See “To specify identification and confirmation settings” on page 216. You must define fragments in the screening library. See “To add a fragment to a target peak” on page 257. Figure 126. Fragments page Table 93. Fragments page shortcut menu commands Thermo Scientific Command Description Reset Scaling Resets the original scaling after a zoom operation. Copy to Clipboard Copies the graphic display to the Clipboard. Display Overlay Spectra Display Stack Spectra Overlays the two spectrum displays, or stacks the simulated spectrum and the peak apex spectrum. TraceFinder User Guide 465 6 Using the Analysis Mode Working in Data Review for Target Screening Methods Library The Library page displays the matching library spectrum (in blue) and the experimental spectrum (in black). The resulting score percentage from a library search match must be higher than your specified threshold value to identify or confirm the presence of a compound. See “To specify identification and confirmation settings” on page 216. The application scales both the matched library spectrum and the highest peak in the experimental spectra at 100 percent intensity and displays the resulting neutral loss (NL) value for the matched library entry name on the right of the plot. Figure 127. Library page with stacked spectra Figure 128. Library page with overlaid spectra 466 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in Data Review for Target Screening Methods Table 94. Library page shortcut menu commands Thermo Scientific Command Description Reset Scaling Resets the original scaling after a zoom operation. Copy to Clipboard Copies the graphic display to the Clipboard. Display Overlay Spectra Display Stack Spectra Overlays the two spectrum displays, or stacks the simulated spectrum and the peak apex spectrum. TraceFinder User Guide 467 6 Using the Analysis Mode Working in the Report View Working in the Report View Use the Report View to display or generate reports for the currently selected batch in the Analysis mode. See Report View in Analysis mode. You must process each sample in the batch before you can view or generate a sample-level report for that sample. To open the Report View 1. Click Analysis in the navigation pane from any mode. 2. In the Analysis navigation pane, click Report View. The Report View for the currently selected batch opens. To refresh the Report View If you make changes to your reports, click New Data Available - Refresh. Figure 129. Report View in Analysis mode • View Only: Displays a PDF or Excel spreadsheet preview of the selected report type for the batch, sample, or compound. See “Viewing Reports.” – For quantitative batches, preview reports for all Standard report types are always available. – For target screening batches, preview reports for all Standard and Target Screening report types are always available. – You must generate Custom and ToxID report types before they are available. The Report View page displays one of the following report outputs: – Standard reports as PDF files – Custom reports in XLSM format – ToxID reports as PDF files – Target Screening reports as PDF files (available only for target screening batches) • Generate Only: Creates all specified report output formats for the selected sample-level or batch-level report. See “Generating Reports” on page 473. 468 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Report View This section includes the following topics: • Viewing Reports • Generating Reports • Working with Reports • Working with the Active View Viewing Reports Use the View Only features to view all configured standard or target screening reports and any custom or ToxID reports that you have generated. After you generate a report, the application displays the report in the View Only report list. Follow these procedures: • To select a report • To select a sample • To select a compound • To select a sample and a compound To select a report 1. Select the View Only option. 2. Open the Select a Report list to display all configured report types. These reports reflect the Displayed Reports selections in the Application Configuration mode. To change the configured reports that are available in this view, see “Specifying the Reports Configuration” on page 39. To sort the reports, click the column headers. The application maintains this sort order each time you open the Report View for this batch. To help organize your reports, you can filter the list. 3. To limit the types of reports to display in the report list, select any combination of report filter options in the Filter Reports area. Thermo Scientific TraceFinder User Guide 469 6 Using the Analysis Mode Working in the Report View Table 95. Filter Reports options Option Behavior Only Show Automated Batch Reports Displays only report types that have an output format specified in the Automated Batch Reports area in the Batch View. See “Automated Batch Reports Pane” on page 357. Standard Reports Displays Standard report types. Custom Reports Displays generated Custom report types. Custom reports are not available for viewing until you have generated the report. ToxID Reports Displays generated ToxID report types. ToxID reports are not available for viewing until you have generated the report. Target Screening Reports Displays Target Screening report types. Note When you make changes to the method in the Local Method view, to the peaks in the Data Review view, or to the samples in the Batch View, you must regenerate the custom or ToxID reports before these changes take effect. 4. Double-click the name of the report. The report list closes. • When the selected report is a batch-level report, the application displays the report on the Report View page. • When the selected report includes separate reports for each sample, you must select a sample file. Follow the procedure “To select a sample” on page 471. • When the selected report includes separate reports for each compound, you must select a compound. Follow the procedure “To select a compound” on page 471. • When the selected report includes separate reports for each sample and each compound in the sample, you must select both a sample and a compound. Follow the procedure “To select a sample and a compound” on page 471. 470 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Report View To select a sample 1. Open the Sample File list to display all processed samples in the batch. Note Unprocessed samples are not listed. A message in the sample list reports the number of unprocessed samples in the batch. 2. To show only samples that would be included in the selected report, select the Only Show Samples Relevant… check box. For example, if you selected the Quality Control Report, the sample list displays only QC samples. Note Click the column headers to sort the samples. The application maintains this sort order each time you open the Report View for this batch. 3. Double-click the name of the sample. The Sample File list closes. The Report View page displays the sample-level report. To select a compound 1. Open the Compound list to display the names and retention times of all compounds in the sample. 2. Double-click a single compound or All Compounds. The compound list closes. The Report View page displays the compound-level report. To select a sample and a compound 1. Open the Sample File list to display all samples in the batch. 2. To show only samples that would be included in the selected report, select the Only Show Samples Relevant… check box. Thermo Scientific TraceFinder User Guide 471 6 Using the Analysis Mode Working in the Report View For example, if you selected the Quality Control Report, the sample list displays only QC samples. Tip Click the column headers to sort the samples. The application saves this sort order in the Report View for this batch. 3. Double-click the name of the sample. The Sample File list closes. 4. Open the Compound list to display the names and retention times of all compounds in the sample. 5. Double-click a single compound or All Compounds. The Compound list closes. The Report View page displays the compound-level report for the selected sample and compound. 472 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Report View Generating Reports Use the Generate Only features to create sample-level reports. You cannot use the View Only features to view custom, ToxID, or target screening reports until you generate the report. When you make changes to either the method in the Local Method view or the peaks in the Data Review view, you must regenerate the custom, ToxID, or target screening reports to see the effects of those changes. Follow these procedures: • To select a report • To select a sample To select a report 1. Select the Generate Only option. 2. Open the Select a Report list to display the available reports. The application displays only configured sample-level report types in the list. You cannot generate batch-level or compound-level reports from this view. To change the configured reports that are available in this view, see “Specifying the Reports Configuration” on page 39. If you have many reports, you can filter the list. Thermo Scientific TraceFinder User Guide 473 6 Using the Analysis Mode Working in the Report View 3. To limit the types of reports to display in the report list, select any combination of report filter check boxes in the Filter Reports area. Option Behavior Only Show Automated Batch Reports Displays only sample-level reports that have an output format specified in the Automated Batch Reports area in the Batch View. See “Automated Batch Reports Pane” on page 357. If you have only batch-level reports specified in the Batch View, selecting this option excludes all reports in the Report Name list. Standard Reports Displays sample-level Standard report types. Custom Reports Displays sample-level Custom report types. ToxID Reports Displays sample-level ToxID report types. Target Screening Reports Displays sample-level Target Screening report types. Note Click the column headers to sort the samples. The application saves this sort order in the Report View for this batch. 4. Double-click the name of the report. The report list closes. You must select a sample file for the selected report. 474 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Report View To select a sample 1. Open the Sample File list to display all samples in the batch. 2. To show only samples that would be included in the selected report, select the Only Show Samples Relevant… check box. For example, if you selected the Quality Control Report, the sample list displays only QC samples. Note Click the column headers to sort the samples. The application saves this sort order in the Report View for this batch. 3. Select the check box for each sample that you want to include in the report. 4. Click Generate. The Report Selection Confirmation dialog box opens. 5. In the What Action Would You Like to Perform area, select the types of reports that you want to create. Note The application automatically selects required output formats. These options are not editable. Thermo Scientific TraceFinder User Guide 475 6 Using the Analysis Mode Working in the Report View 6. Click Continue. The application submits the selected samples to the report queue. When you have already generated this report in the Batch View or Acquisition mode, the application time-stamps the new report to differentiate it from the original report. 7. To view the report you generated, follow the instructions in “Viewing Reports” on page 469. Note When you make changes to the method in the Local Method view, the peaks in the Data Review view, or the samples in the Batch View, you must regenerate the custom or target screening reports before those changes take effect. 476 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Report View Working with Reports Use the icons on the Report View page to view, print, or export a report. • For each standard report, you can create a hardcopy printout, a PDF file, or an XML file. • For each custom report, you can create a hardcopy printout or an Excel Macro-Enabled Workbook (.xlsm) file. • For each ToxID report, you can create a hardcopy printout or a PDF file. • For each target screening report, you can create a hardcopy printout, a PDF file, or an XML file. Follow these procedures: • To print a report • To export a standard report • To search for text • To enlarge the report text To print a report 1. Select the report to print from the Select a Report list. 2. (Optional) Select a sample from the Sample File list. The application displays the report on the Report View page. Thermo Scientific TraceFinder User Guide 477 6 Using the Analysis Mode Working in the Report View 3. Click the Print Report icon, . The Print dialog box for your default printer opens. 4. Follow the typical procedure to print from your printer. Landscape reports automatically rotate to fit the paper. To export a standard report 1. Select the report that you want to print from the Select a Report list. 2. (Optional) Select a sample from the Sample File list. The application displays the report on the Report View page. 3. Click the Export Report icon, . The Export Report dialog box opens. 4. Locate the folder where you want to write the report file. 5. Type a file name for the exported report file. 6. Select a file type from the Save as Type list: 7. Click Save. The TraceFinder application saves the file as the specified file type and writes the report file to the specified folder. 478 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Report View To search for text 1. Select a report from the Select a Report list. 2. (Optional) Select a sample from the Sample File list. The application displays the report on the Report View page. 3. Click the Find Text icon, . The Find Text dialog box opens. 4. Enter your text and click Find Next. When the TraceFinder application locates the text, it encloses the text in a red box. To enlarge the report text 1. Select a report from the Select a Report list. 2. (Optional) Select a sample from the Sample File list. The application displays the report on the Report View page. 3. Click the Zoom icon, Thermo Scientific , and select a zoom scale. TraceFinder User Guide 479 6 Using the Analysis Mode Working in the Report View Working with the Active View Use the Active View page to view quantitative data for each sample in a report. Data in the Active View are labeled with flag information. These flags are based on a comparison of the batch data to criteria defined in the master method. To display the Active View page Click the Active View tab. The Active View page displays quantitative data and QAQC error flags for each sample. For detailed descriptions of all active view parameters, see “Active View page.” To display a report 1. Select a report type from the Select a Report list. Only the report types created for the current batch are displayed in the list. 2. (Optional) When the report type includes separate reports for each sample, select a sample file. Each standard report that uses the Active View displays values that are both common to all reports and specific to that report. See “Active View Report Contents” on page 485. To filter which compounds to display Click the Showing button to switch the display to either all compounds or only compounds that are flagged for failing a QAQC test. 480 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Report View Figure 130. Active View page Table 96. Active View page parameters (Sheet 1 of 4) Parameter Description View Only Makes the Active View pane available for reports that support the active view. Generate Only Switches the pane to Report View and makes the Active View pane not available. Select a Report Displays the report types created for the current batch. Sample File Used when the report type includes separate reports for each sample. Total Rows The number of compound rows currently displayed in the pane. Showing Displays all compounds or only the flagged compounds. Thermo Scientific TraceFinder User Guide 481 6 Using the Analysis Mode Working in the Report View Table 96. Active View page parameters (Sheet 2 of 4) Parameter Description Column headings Many column headings are specific to individual reports. See “Active View Report Contents” on page 485. Status Indicates the status of the reported compound. • A yellow check mark indicates one of the following conditions: – The compound was manually integrated. – Any of the confirming peaks was manually integrated. – The compound has quantitation flags. • A red check mark indicates that the QAQC checks failed. • A green check mark indicates that none of these conditions exist. When the compound is an internal standard, warnings are displayed only on the internal standard report. The Status column is blank for Manual Integration reports. Compound Name Alphanumeric name assigned to the compound. Compound Type Target Compound or Internal Standard. QAQC Flags Indicates that the QAQC check for the sample failed. Manual Integration reports do not use the QAQC column. Quan Flags • • • • • • Limit of Detection (LOD) Limit of Quantitation (LOQ) Limit of Reporting (LOR) Values between the limit of detection and the limit of quantitation, known as the J flag Upper Limit of Linearity (ULOL) Est indicating the estimated compound type for semi-quantitative compounds Quan flags do not apply to these sample types: Calibrator, QC, or Solvent. Manual Integration reports do not use the Quan Flag column. Manual Flags Indicates manually integrated peaks. M: Indicates a manually integrated quantitative peak. m: Indicates a manually integrated confirming peak. Depending on the selected report, the Active View page contains any or all of the following parameters: Quan Peak m/z Mass-to-charge ratio for the selected quantitative peak. Total Response The sum of all Quan Peak Response values for the compound. Quan Peak Response Response of the quantitative peak. Quan Peak RT Retention time for the quantitative peak. Theoretical Amount Theoretical amount of the compound. Reports N/A when not applicable. Concentration The injected concentration. 482 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Report View Table 96. Active View page parameters (Sheet 3 of 4) Parameter Description Confirming n Mass Mass of the confirming peak. Confirming n Response Response of the confirming peak. Confirming n Manual Indicates a manually integrated confirming peak. Flag Confirming n Ion Ratio Flag Indicates that the ion ratio is out of range. Not available for analog compounds. Confirming n Ion Ratio Actual ratio of the confirming ion response to the quantitation ion response. Confirming n Range Acceptable range for the confirming ion. Retention Time The time after injection when the compound elutes. The total time that the compound is retained on the column. Quan Mass The mass-to-charge ratio used to determine the peak area and peak height of the compound. Response Sum of all Quan Peak Response values for the compound. Injection Concentration Calculated amount as the sample was injected, with no conversion applied. Injection Units Injection units specified on the Calibration page in Method Development mode. See “Calibration” on page 164. Sample Concentration The injected concentration multiplied by the conversion factor. Sample Units Sample units specified on the Calibration page in Method Development mode. See “Calibration” on page 164. QIon Mass range for the quantitative peak. When you select the analog detector in the signal parameters for the master method, the application displays this value as Analog and reports with spectra displays show the spectra as Not Available. See “Signal” on page 135. RT Retention time. The time after injection when the compound elutes. The total time that the compound is retained on the column. Manual Integration reports m/z Mass-to-charge ratio for the quantitative peak. Method RT Apex retention time for the method-integrated peak. Method Peak Height Height of the method-integrated peak. Method Peak Area Area of the method-integrated peak. Manual RT Apex retention time for the manually integrated peak. Manual Peak Height Height of the manually integrated peak. Manual Peak Area Area of the manually integrated peak. Thermo Scientific TraceFinder User Guide 483 6 Using the Analysis Mode Working in the Report View Table 96. Active View page parameters (Sheet 4 of 4) Parameter Description Internal Standard reports Std Response Average of the internal standard’s response as found in the calibration file. Minimum Response Minimum response time as specified on the ISTD page in Method Development mode. See “ISTD” on page 179. Maximum Response Maximum response time as specified on the ISTD page in Method Development mode. See “ISTD” on page 179. Sample Response Area found in the sample. Std RT Average retention time as found in the calibration file. Min RT Minimum retention time as specified on the ISTD page in Method Development mode. See “ISTD” on page 179. Max RT Maximum retention time as specified on the ISTD page in Method Development mode. See “ISTD” on page 179. Sample RT Retention time found in the sample. Graphical data Quan Peak 1 Displays a graphical view of the quan peak for the selected sample and compound. Calibration Curve Displays a graphical view of the calibration curve for the selected compound and key statistical values for evaluating the quality of the calibration. For semi-quantitative compounds, the displayed curve is a linked calibration curve and is indicated with a blue-green background. Spectra Displays a comparison of the spectra found in the data and the method reference. QED Spectra Displays the averaged QED spectra from the raw data file and the database match. If the sample contains no QED data, the page is blank. Confirming Ions Displays a graphical view of all qualifying/confirming ions for the selected sample and compound, and displays calculated ion ratios and ion ratio acceptance windows. 484 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Report View Active View Report Contents Each standard report that uses the Active View displays values that are common to all reports. See “Common Active View report columns” on page 486. In addition to the common values, the following reports display additional active view features: • Blank Report Active View columns • Calibration Report Active View columns • High Density Sample reports (Report 1 and Report 1 Long) Active View columns • High Density Sample reports (Report 2 and Report 2 Long) Active View columns • High Density Sample reports (Report 3 and Report 3 Long) Active View columns • Internal Standard Summary Report Active View columns • Ion Ratio Failure Report Active View columns • Manual Integration Report Active View columns • Quality Control Report Active View columns • Quantitation Report Active View columns • Solvent Blank Report Active View columns Thermo Scientific TraceFinder User Guide 485 6 Using the Analysis Mode Working in the Report View Table 97. Common Active View report columns Column Description Status Indicates the status of the reported compound. • A yellow caution sign indicates one of the following conditions: – The compound was manually integrated. – Any of the confirming peaks was manually integrated. – The compound has quantitation flags. – The compound has a QAQC failure. • A green check mark indicates that none of these conditions exists. When the compound is an internal standard, warning flags are displayed only on the internal standard report. Compound Name Alphanumeric name assigned to the compound. Compound Type Target Compound or Internal Standard. QAQC Flags Indicates that the QAQC check for the sample failed. The Method Validation and MDL reports do not use the QAQC column. Quan Flags • • • • • • Limit of Detection (LOD) Limit of Quantitation (LOQ) Limit of Reporting (LOR) Values between the limit of detection and the limit of quantitation, known as the J flag Upper Limit of Linearity (ULOL) Est indicating the estimated compound type for semi-quantitative compounds (Blank, Quantitation, and High Density reports only) Quan flags do not apply to these sample types: Calibrator, QC, or Solvent. The Calibration report does not use the Quan Flags column. The Calibration Curve report does not use the Quan Flags column. Manual Flags Indicates manually integrated peaks. • M indicates a manually integrated quantitative peak. • m indicates a manually integrated confirming peak. Table 98. Blank Report Active View columns (Sheet 1 of 2) Column Description Retention Time Retention time for the quantitation mass. The time after injection when the compound elutes. The total time that the compound is retained on the column. Quan Mass Mass range for the quantitative peak. Response Sum of all Quan Peak Response values for the compound. 486 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Report View Table 98. Blank Report Active View columns (Sheet 2 of 2) Column Description Inj Conc Calculated amount as the sample was injected, with no conversion applied. Inj Units Injection units specified on the Calibration page in Method Development mode. See “Calibration” on page 164. Sample Conc Calculated amount multiplied by the conversion factor. Sample Units Sample units specified on the Calibration page in Method Development mode. See “Calibration” on page 164. Table 99. Calibration Report Active View columns Column Description Curve Type The type of curve used when calibrating the compound (linear, quadratic, or average response factor). Average RF The average response factor. Applicable if curve type is Average RF. Average Response The average response for the internal standard across all calibration points. Applies only to Internal Standard sample types. A0 The value with no X. Applies only to linear and quadratic curves. A1 The X value. Applies only to linear and quadratic curves. A2 The X^2 value. Applies only to quadratic curves. R^2 The minimum correlation coefficient (r2) for an acceptable calibration (when in linear or quadratic mode). RSD Relative standard deviation. Applies only to internal standards and targets calibrated with an average RF curve. Level The column specifies the level name; the field value specifies the data point used in calibration. This field can be Response Factor for external calibration, Response Ratio for internal linear or quadratic, or Relative Response Factor for Internal Average RF. There is one column for each level in the curve. If the batch uses an extended calibration, there might be more columns than calibration standards in the current batch. Note The Calibration Report does not report semi-quantitative compounds. Table 100. High Density Sample reports (Report 1 and Report 1 Long) Active View columns (Sheet 1 of 2) Column Description m/z Mass-to-charge ratio for the quantitative peak. Total Response The sum of all Quan Peak Response values for the compound. Quan Peak Response Response of the quantitative peak. Quan Peak RT Retention time for the quantitative peak. Thermo Scientific TraceFinder User Guide 487 6 Using the Analysis Mode Working in the Report View Table 100. High Density Sample reports (Report 1 and Report 1 Long) Active View columns (Sheet 2 of 2) Column Description T Amount Theoretical amount of the compound. Reports N/A when not applicable. Conc Calculated (injected) amount. Table 101. High Density Sample reports (Report 2 and Report 2 Long) Active View columns Column Description m/z Mass-to-charge ratio for the quantitative peak. Total Response Sum of all Quan Peak Response values for the compound. Quan Peak Response Response of the quantitative peak. Quan Peak RT Retention time for the quantitative peak. T Amount Theoretical amount of the compound. Reports N/A when not applicable. Conc Calculated (injected) amount. Confirming 1 Mass Mass of the confirming peak. Confirming 1 Response Response of the confirming peak. Confirming 1 Manual Flag Indicates a manually integrated confirming peak. Confirming 1 Ion Ratio Flag Indicates that the ion ratio is out of range. Not available for analog compounds. Confirming 1 Ion Ratio Actual ratio of the confirming ion response to the quantitation ion response. Confirming 1 Range Acceptable range for the confirming ion. Table 102. High Density Sample reports (Report 3 and Report 3 Long) Active View columns (Sheet 1 of 2) Column Description m/z Mass-to-charge ratio for the quantitative peak. Total Response Sum of all Quan Peak Response values for the compound. Quan Peak Response Response of the quantitative peak. Quan Peak RT Retention time for the quantitative peak. T Amount Theoretical amount of the compound. Reports N/A when not applicable. Conc Calculated (injected) amount. Confirming 1 Mass Mass of the confirming peak. Confirming 1 Response Response of the confirming peak. Confirming 1 Manual Flag Indicates a manually integrated confirming peak. Confirming 1 Ion Ratio Flag Indicates that the ion ratio is out of range. Not available for analog compounds. Confirming 1 Ion Ratio Actual ratio of the confirming ion response to the quantitation ion response. 488 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Report View Table 102. High Density Sample reports (Report 3 and Report 3 Long) Active View columns (Sheet 2 of 2) Column Description Confirming 1 Range Acceptable range for the confirming ion. Confirming 2 Mass Mass of the confirming peak. Confirming 2 Response Response of the confirming peak. Confirming 2 Manual Flag Indicates a manually integrated confirming peak. Confirming 2 Ion Ratio Flag Indicates that the ion ratio is out of range. Not available for analog compounds. Confirming 2 Ion Ratio Actual ratio of the confirming ion response to the quantitation ion response. Confirming 2 Range Acceptable range for the confirming ion. Table 103. Internal Standard Summary Report Active View columns Column Description Std Response Average of the internal standard’s response as found in the calibration file. Minimum Response Minimum response time as specified on the ISTD page in Method Development mode. See “ISTD” on page 179. Maximum Response Maximum response time as specified on the ISTD page in Method Development mode. See “ISTD” on page 179. Sample Response Area found in the sample. Std RT Average retention time as found in the calibration file. Min RT Minimum retention time as specified on the ISTD page in Method Development mode. See “ISTD” on page 179. Max RT Maximum retention time as specified on the ISTD page in Method Development mode. See “ISTD” on page 179. Sample RT Retention time found in the sample. Table 104. Ion Ratio Failure Report Active View columns Column Description Quan Ion The ion for quantitative peak. Qual Ion The ion for the confirming peak. Quan Ion Response Response of the quantitation ion. Qual Ion Response Response of the qualitative ion. Ratio The ratio of the confirming ion response to the quantitation ion response. Range The acceptable range. Thermo Scientific TraceFinder User Guide 489 6 Using the Analysis Mode Working in the Report View Table 105. Manual Integration Report Active View columns Column Description m/z Mass-to-charge ratio for the quantitative peak. Method RT Apex retention time for the method-integrated peak. Method Peak Height Height for the method-integrated peak. Method Peak Area Area for the method-integrated peak. Manual RT Apex retention time for the manually integrated peak. Manual Peak Height Height of the manually integrated peak. Manual Peak Area Area of the manually integrated peak. Table 106. Quality Control Report Active View columns Column Description Curve Type L - Linear A - Average RF Q - Quadratic Daily RF The response factor value for Average RF curve types. For all other curve types, this column is blank. Mean RF The average response factor as found in the calibration file. Displayed for Average RF curve types. For all other curve types, this column is blank. Min RF Minimum QC response factor as found on the QC Check page in the method. RF % D Percent difference between daily and average response factor. Max RF Diff (%) Maximum QC response factor as found on the QC Check page in the method. QC Amount The amount defined by the level for the compound. Calculated Amount Reportable amount of concentration. Amount % Difference Percentage difference between the calculated amount and the QC amount. Use the injected concentration to calculate this value. Max Amount % Difference Maximum allowed percentage difference between the calculated amount and the QC amount. 490 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Report View Table 107. Quantitation Report Active View columns Column Description RT Retention time for the peak. The time after injection when the compound elutes. The total time that the compound is retained on the column. QIon Mass range for the quantitative peak. When you select the analog detector in the signal parameters for the master method, the application displays this value as Analog and reports with spectra displays show the spectra as Not Available. See “Signal” on page 135. Response Sum of all quantitative peak response values for the compound. Injected Concentration Calculated amount as the sample was injected, with no conversion applied. As each additional sample is processed, calibration data change; therefore, except for the final sample in a batch, a report in active view or report view shows different values from a physical (PDF, XML, or printed) report created at the end of processing. To avoid this discrepancy, do one of the following: • For the standard Quantitation Report or Quantitation Report - 2, observe the active or report view for only the last sample in the batch. • For the custom Quantitation Report, make the report a batch-level report. Injected Units Injection units specified on the Calibration page in Method Development mode. See “Calibration” on page 164. Sample Conc Calculated injection amount multiplied by the conversion factor. See the Injected Concentration description. Sample Units Sample units specified on the Calibration page in Method Development mode. See “Calibration” on page 164. Table 108. Solvent Blank Report Active View columns Column Description RT Retention time for the quantitative peak. The time after injection when the compound elutes. The total time that the compound is retained on the column. QIon Mass range for the quantitative peak. When you select the analog detector in the signal parameters for the master method, the application displays this value as Analog and reports that display spectra report the spectra as Not Available. See “Signal” on page 135. Response Sum of all Quan Peak Response values for the compound. Method Method of evaluation defined in the method. Upper Limit Defined in the method. Thermo Scientific TraceFinder User Guide 491 6 Using the Analysis Mode Working in the Project Administration View Working in the Project Administration View When user security is activated, in either the LabDirector or ITAdmin role, you can create and manage projects and subprojects on fixed or network drives in the Project Administration view of the Analysis mode. This section includes the following topics: • Working with Drives • Working with Projects To open the Project Administration view 1. Click Analysis in the navigation pane of the current mode. 2. In the Analysis navigation pane, click Project Administration. The Project Administration view opens. By default, all projects are created under a main Projects folder on drive C: C:\Thermo\TraceFinder\3.0\Forensic\Projects 492 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Project Administration View Working with Drives Drives can be any of the following: • Fixed: Directly connected to your computer. • Network: Either a remote box or a mapped drive. A shared folder that is mapped to a drive letter might physically exist on your computer, but because it is mapped, it is considered to be a Network drive. • Removable: Temporary drives such as a 3.5 in. disk or a USB drive. Follow these procedures: • To choose a drive • To change the default drive • To hide a drive from the display • To refresh the display To choose a drive 1. In the Available Drives area, click any drive other than the default drive C. If you have not created a Projects directory on this drive, you see this message: 2. Click Create Project Directory. The TraceFinder application adds a new Projects directory to the selected drive. To create projects and subprojects on this drive, see “To create projects or subprojects” on page 495. Thermo Scientific TraceFinder User Guide 493 6 Using the Analysis Mode Working in the Project Administration View To change the default drive Select the check box in the Default column. You can set only fixed drives as the default drive. The default drive is the only drive that you can use to acquire data. To hide a drive from the display Clear the check box in the Show column. The application does not list the hidden drive in the drive lists. You cannot hide the default drive. To refresh the display Choose File > Refresh Available Drives from the main menu. The Available Drives table refreshes to show any drives that have changed (for example, if you inserted a USB drive). You can now configure any new drives. 494 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Project Administration View Working with Projects When you create a batch, the application stores the data files, local method, and reports in a project and subproject that you create in the C:\Thermo\TraceFinder\3.0\Forensic\Projects folder. If you installed the TraceFinder example data, the main Projects folder includes an Example project folder that contains subprojects with example batches that you can use to experiment. To install the example data from the InstallShield Wizard, see the instructions “To reinstall the TraceFinder application” on page 10. Follow these procedures: • To create projects or subprojects • To delete projects or subprojects • To remove all empty folders • To copy the folder hierarchy from another drive To create projects or subprojects 1. Select the top-level project. You can select the main Projects folder and create a new project under it, or you can select one of the existing projects and create a subproject under it. When you select a project folder, the application activates the plus sign icon, indicating that you can create a folder within the selected folder. , 2. Click the plus sign. The TraceFinder application creates a new, unnamed project folder under the selected project. 3. While the new project is still highlighted, type a new name. Project names are limited to 30 characters and can contain spaces and special characters, except for the following special characters: \ / : * ? " < > | Note After you add a subproject to a project, you cannot rename the project. 4. To save the new name, press ENTER or click anywhere in the view. Thermo Scientific TraceFinder User Guide 495 6 Using the Analysis Mode Working in the Project Administration View To delete projects or subprojects 1. Select the project or subproject that you want to delete. You can delete projects that do not have subprojects. You can delete subprojects that do not have batches. When the selected project or subproject is available for deletion, the application activates the minus sign icon, . 2. Click the minus sign, or right-click and choose Remove Project from the shortcut menu. 3. At the prompt, click Yes to remove the selected project or subproject. To remove all empty folders 1. Select the project or subproject that contains empty folders. 2. Right-click and choose Remove All Empty Child Folders from the shortcut menu. There is no undo for this command. 3. At the prompt to remove all empty folders, click OK. The application removes all folders that have no folders or files. To copy the folder hierarchy from another drive 1. Select the top-level Projects directory in the Project Administration area. When you copy the hierarchy from the drive to your Projects folder, the application will add new folders to the current hierarchy, but it will not remove folders. 2. Right-click and choose Copy Folder Hierarchy from Drive from the shortcut menu. 3. Choose a drive from the list of available drives. At the prompt, you must confirm that you want to create a folder hierarchy that matches that of the specified drive. 496 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Project Administration View 4. Click OK. To replicate the hierarchy from the specified drive, the application will add new folders to the current hierarchy, but it will not remove folders. Note The Copy Folder Hierarchy from Drive command copies only the project and subproject folders; it does not copy batches within the folders. Thermo Scientific TraceFinder User Guide 497 6 Using the Analysis Mode Working in the Local Method View Working in the Local Method View A local method is a copy of a master method associated with a batch. You can edit only the local copy of the method, or you can edit the master method and overwrite the local copy with the edited master method. In the Local Method view, you can edit the local method parameters. A local method is a copy of a master method associated with a batch. Local methods are named BatchName_MasterMethodName. To open the Local Method View 1. Click Analysis in the navigation pane. 2. In the Analysis navigation pane, click Local Method. The Local Method view for the currently selected batch opens. You can edit many of the method parameters in a local method. Editing the local method does not affect parameters in the master method. For detailed descriptions of method parameters, see “Working with Master Methods” on page 83. 3. Enter any local changes to the method. 4. When you have finished editing the local method, choose File > Save. 5. To process the batch or create new reports with the edited local method, return to the Batch View and submit the batch. To overwrite the local method with the master method in the Batch View In the Batch View, click Update. The application overwrites the local method with the master method of the same name. You can use this feature to overwrite an edited local method with the original master method or to overwrite the local method with an updated master method. 498 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Local Method View Figure 131. Local Method View of a quantitation method Figure 132. Local Method View of a screening method Thermo Scientific TraceFinder User Guide 499 6 Using the Analysis Mode Working in the Batch Template Editor Working in the Batch Template Editor In the Batch Template Editor, you can create a batch template that contains the basic settings for your batches. See “Batch Template Editor” on page 506. Batches are created as a routine operation and, because the nature and types of batches are often similar (in some cases specified by laboratory operating procedure), you can define a batch template that supplies the basic structure of a batch. To create a batch using a batch template, choose File > New > Batch Using Wizard from the application menu. See “Creating a Batch Using the Batch Wizard” on page 379. Follow these procedures: • To create a new batch template • To specify active compounds • To specify template method information • To specify active compounds • To insert a sample into the list • To copy a sample • To remove samples from the list • To edit sample values • To add multiple samples of the same type • To specify report options • To specify active compounds To create a new batch template 1. Choose File > New > Batch Template from the application menu. The Open Method dialog box opens where you can select a master method to use for your template. 500 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Batch Template Editor 2. Select a master method and click Open. The Batch Template Editor opens. For detailed descriptions of all parameters, see “Batch Template Editor” on page 506. The editor uses the selected master method for the template. To open a batch template 1. Choose File > Open > Batch Template from the application menu. The Open Batch Template dialog box opens. 2. Select a batch template and click Open. The Batch Template Editor opens with the settings from the selected template. To view the editor and for detailed descriptions of the parameters, see “Batch Template Editor” on page 506. To specify template method information 1. From the Project list, select a project name. 2. From the Subproject list, select a subproject name. Tip If there are no projects or subprojects to select, go to the Project Administration view and create a new subproject. See “Working in the Project Administration View” on page 492. 3. To change the current method, click Select Method and select a new method. Thermo Scientific TraceFinder User Guide 501 6 Using the Analysis Mode Working in the Batch Template Editor To add a sample to the batch Right-click and choose Add Sample from the shortcut menu, or click the add sample icon, . The application adds a new, Specimen sample to the end of the sample list. To insert a sample into the list 1. Select the sample above which you will insert a new, Specimen sample. 2. Right-click and choose Insert Sample from the shortcut menu. The application inserts a new, Specimen sample above the selected sample. Inserted sample To copy a sample 1. Select the sample that you want to copy. 2. Right-click and choose Insert Copy Sample from the shortcut menu. The application inserts the copy above the selected sample. To remove samples from the list 1. Select the sample that you want to remove. Use the SHIFT or CTRL keys to select multiple samples. 2. Right-click and choose Remove Selected Samples from the shortcut menu, or click the Remove Sample icon, . The application removes the selected samples from the list. To edit sample values 1. For each sample, click the Sample Type column and select a sample type from the list. Available sample types 502 TraceFinder User Guide Specimen QC Solvent Calibrator Unextracted Negative Hydrolysis Thermo Scientific 6 Using the Analysis Mode Working in the Batch Template Editor 2. For each QC or Calibrator sample, click the Level cell and select a level from the list. The calibration and QC levels were defined in the master method. If there is nothing to select in the Level list, do the following: a. Close the Batch Template Editor. b. Return to the Method Development mode. c. Open the master method. d. Click the Compounds tab. e. Click the Calibration Levels tab. f. Add the levels. g. Save the method. h. Return to the Analysis mode, and begin this batch template again. You must close your original batch template without saving it and start a new template. For detailed instructions, see “Editing a Quantitation Master Method” on page 106. 3. (Optional) Type a sample ID, sample name, or comment. These values can be any text string. To add multiple samples of the same type In the Repeat Sample Count column, type the number of samples that you want to create for each sample type. When you use this template to create a batch, the batch will contain this number of individual samples of the specified type. In the batch, you can change any of the column values for the individual samples. To specify report options 1. To specify the type of report output to create for each report type, select the check box in the appropriate column. By default, all report output types are cleared. 2. To duplicate the output type for all reports below the selected report, click the cell to select it, and then right-click and choose Copy Down from the shortcut menu. All check boxes in the column below the selected cell duplicate the selected or cleared state of the selected cell. You can duplicate the output type only for reports that have this output format available. Thermo Scientific TraceFinder User Guide 503 6 Using the Analysis Mode Working in the Batch Template Editor 3. To duplicate the selected report output formats for all samples in the batch, right-click the cell and choose Apply Selection to All Samples from the shortcut menu. Here is an example: Copying selected report output formats from the first sample Duplicates the selected report output formats to all samples in the batch 504 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Batch Template Editor To specify active compounds 1. In the sample table, click anywhere in the sample row to select the sample for which you want to specify active compounds. Compound selections are specific to a sample. You can select different compounds for each of the samples even if they are the same sample type. 2. In the Compound Active Status area, select the Active check box for each compound that you want identified in the selected sample. If you created compound groups, you can make the entire group active or inactive. Right-click and choose the group from the list. Inactive groups Thermo Scientific Active groups TraceFinder User Guide 505 6 Using the Analysis Mode Working in the Batch Template Editor Figure 133. Batch Template Editor Table 109. Batch Template Editor parameters (Sheet 1 of 2) Parameter Description Template Method Information Project The top-level project for the batch. Subproject The lower-level project for the batch. Method The master method to use for the batch. The Select Method button opens the Open Method dialog box where you can select a different master method for the batch template. Assay Type The name for the analysis type to be targeted by the method. The assay type associates the method with the analysis of a compound or specific class of compounds (for example, an assay type of PAH might be used for the analysis of Polynuclear Aromatic Hydrocarbons). The application uses this assay type in the batch template. You can also select an appropriate combination of method and batch template. 506 TraceFinder User Guide Thermo Scientific 6 Using the Analysis Mode Working in the Batch Template Editor Table 109. Batch Template Editor parameters (Sheet 2 of 2) Parameter Description Column values Sample Type Defines how the application processes the sample data. Each sample is classified as one of the following sample types: Specimen, QC, Solvent, Calibrator, Hydrolysis, Unextracted, or Negative Level The level defined for a calibration sample or quality control sample. Sample ID A user-defined, alphanumeric string that identifies a sample. Sample Name A user-defined name that identifies a sample. Comment A user-defined comment for the sample. Repeat Sample Count Number of samples to create for this sample type. Sample Level / Batch Level Report Name The name of a report. Type Standard, Custom, or Target Screening Print Sends reports to the printer. Create PDF Saves reports as PDF files. Available only for standard and target screening reports. Create XML Saves reports as XML files. Available only for standard reports. Create XLSM Saves reports in Excel Macro-Enabled Workbook (.xlsm) format. Available only for custom reports. Compound Active Status Compound Name List of all compounds for the method. Active Compounds to identify in the selected sample. Thermo Scientific TraceFinder User Guide 507 A Reports This appendix contains information about standard, custom, ToxID, and target screening reports. Contents • Specifying Reports • Report Flags • Sample Standard Reports The report engine can generate several different types of reports designed to meet the needs of the laboratory, the laboratory's customers, and key regulatory agencies that might review the results. The reports listed in this appendix meet the requirements of various methods and worldwide regulatory agencies and are designed to help track the performance of the system and method. The TraceFinder application can produce standard reports, custom reports, and reports specific to target screening and ToxID features. Specifying Reports As a user in the ITAdmin or LabDirector role, you can configure a list of reports that are available for the Method Development or Acquisition mode. For detailed information about configuring reports in the Application Configuration mode, see “Specifying the Reports Configuration” on page 39. For detailed information about specifying reports when you create a method in the Method Development mode, see “Editing the Reports Page” on page 189. For detailed information about viewing reports in the Acquisition mode, see “Selecting and Reviewing Reports” on page 309. This section lists all available reports for the following report types: • “Standard Reports” on page 510 • “Custom Reports” on page 511 • “Target Screening Reports” on page 511 • “ToxID Reports” on page 511 Thermo Scientific TraceFinder User Guide 509 A Reports Specifying Reports Standard Reports For each standard report you generate, you can create a version in hardcopy print, as a PDF (.pdf ) file, or in an XML (.xml) or XLSM (.xlsm) output format. In addition to the report type, you can specify a report title that appears at the top of each of your reports. The default report title is the report name. The TraceFinder application can generate the following types of standard reports: • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • Batch Report Batch Summary Report Batch Report Rev 1 Calibration Report Calibration Curve Report Chromatogram Report Compound Calibration Report Compound Calibration Report - Alternate Confirmation Report High Density Calibration Report High Density Internal Standard Report High Density Internal Standard Report Long High Density Sample Report 1 High Density Sample Report 1 Long High Density Sample Report 2 High Density Sample Report 2 Long High Density Sample Report 3 High Density Sample Report 3 Long Intelligent Sequencing Report Internal Standard Summary Report Ion Ratio Failure Report Manual Integration Report Method Report Negative Report Qualitative Peak Report Qualitative Summary Report Quality Control Report Quantitation Report Quantitation Report - 2 Sample Report Sample Report Long Solvent Blank Report To view an example of each type of standard report, see “Sample Standard Reports” on page 513. 510 TraceFinder User Guide Thermo Scientific A Reports Specifying Reports Custom Reports For each custom report you generate, you can create a hardcopy printout or an Excel Macro-Enabled Workbook (.xlsm) output file. The default report description is the report name. A user in the ITAdmin or LabDirector role can configure custom reports to generate a single report for an entire batch or create a separate report for each sample. The TraceFinder application can generate the following types of custom reports: • • • • • • • • • • • • • • • • • • • • • • AltCalibrationReport Alternate BatchReport Alternate CalibrationReport Alternate ConfirmationReport Alternate MatrixSpikeReport Alternate SampleReport Alternate SummaryReport BatchReport BlankReport CalibrationDensityReport CalibrationReport CheckStandardReport CompoundCalibrationReport ConfirmationReport ConfirmationReport2 HighDensitySampleReport1Long HighDensitySampleReport2Long HighDensitySampleReport3Long HighDensitySampleReport4 HighDensitySampleReport5 QuantitationReport SteroidAnalysisReport Target Screening Reports The TraceFinder application can generate the following types of target screening reports: • Target Screening High Density Sample Report • Target Screening Summary Report ToxID Reports ToxID reports are available only when you install the ToxID™ software and activate the ToxID features. For a detailed procedure for enabling ToxID features, see “ToxID” on page 64. The TraceFinder application can generate the following types of ToxID reports: • Target Screening Long Report • Target Screening Summary Report Thermo Scientific TraceFinder User Guide 511 A Reports Report Flags Report Flags When generating or viewing a report, you might see one of the following quantification or calibration flags listed on the page. Table 110. Quantification flags Flag Definition b Compound was observed at a concentration in a Matrix Blank sample above the specified limit. s Compound was observed at a response in a solvent blank sample above the specified limit. J Compound was observed at a concentration above the limit of detection, but below the limit of quantitation. I or * Confirming/qualifying ion ratio for a compound was observed outside the target ratio range or the coelution between quantification and confirming/qualifying ion was larger than acceptable limit. C Compound was observed at a concentration above the specified carryover limit. ? Compound was observed at a concentration above the specified linearity limit. D Compound was observed at a concentration below the specified limit of detection. Q Compound was observed at a concentration below the specified limit of quantitation. POS Compound was observed at a concentration above the specified cutoff. Table 111. Calibration flags Flag Definition D Calibration for this compound exceeded the specified maximum percent relative standard deviation (%RSD). F Response factor for this compound was below the specified minimum response factor (Min RF). R Calibration for this compound was below the specified minimum correlation coefficient (r2). A Back calculation of the calibration points for this compound exceeded the specified maximum percent difference (Max %D). X Calibration point for this compound was excluded from the overall calibration by manual selection. X(ISNF) Calibration point for this compound was excluded from the overall calibration because its associated internal standard was not found. A flags failure is identified by an asterisk (*), a shaded row, or the word Fail. Values on a report that are the result of a manual integration use an uppercase M to signify a manually integrated quantification ion and a lowercase m to signify a manually integrated qualifying/confirming ion. On alternate reports, manual integration uses a black box around the value. 512 TraceFinder User Guide Thermo Scientific A Reports Sample Standard Reports Sample Standard Reports This section shows samples of the following standard report types: • Batch Report • Batch Report Rev 1 • Calibration Report • Chromatogram Report • Compound Calibration Report • Compound Calibration Report - Alternate • • • • • • • • • • • Confirmation Report High Density Calibration Report High Density Internal Standard Report High Density Internal Standard Report Long High Density Sample Report 1 High Density Sample Report 1 Long High Density Sample Report 2 High Density Sample Report 2 Long High Density Sample Report 3 High Density Sample Report 3 Long Internal Standard Summary Report • Ion Ratio Failure Report • Manual Integration Report • Method Report • Quality Control Report • Quantitation Report • Quantitation Report - 2 • Solvent Blank Report Tip To easily view reports in landscape format, choose View > Rotate View > Clockwise from the Adobe Acrobat™ viewer menu. Thermo Scientific TraceFinder User Guide 513 514 1&* 1& 4& TraceFinder User Guide 2 2 $ 2 2 $ 2 2 +,$ 2 2:$ 85)# 85)# 85)# 85)# 2 29,,9$ 2 29$ 2 29+,, $ 2 2,,$ 2 2,+9$ 2 2+,+$ 2 2,,$ 2 2,9$ 2 2+,+$ 2:2,+7$ 2:2, 7$ 2:2+, 7$ 2:2, 7$ 2:2,,7$ 2:2+,97$ 2:2,7$ 2:2,97$ 2:2+, 7$ 2:2,7$ 2:2, 7$ 2:2+,,7$ 2:2+,97$ 2:2+,7$ 2:2++,97$ 2:2,,,7$ 2:2,,,7$ 2:2,+,7$ 2:2,7$ )+$ ) "$1 85)# ) ) ) ) )+ ), ) ) ): )9 ) ) 85)# ) ) ) )+ ), ) ) ): )9 ) ) 85)# ) ) ) 2 2:$ 2 2+$ +85)# 2 2:+,, $ 2 29$ 85)# )+ 2 2$ 85)# $5#) 2 2,+$ 5*)# : , + 9 : , + 9 : , + 9 : , + ) ) 85)# ) ) )9 ): ) ) ), )+ ) ) 85)# ) ) )9 ): ) ) ), )+ ) ) ) 85)# ) "$1 )+$ )+ $5# 85)# 85)# 85)# 85)# +85)# 85)# 85)# 5*)# 27 27 85 27 27 27 27 27 27 27 27 27 27 85 27 27 27 27 27 27 27 27 27 27 27 85 27 27 27 27 85 85 85 85 +85 85 85 27 6 ; 6 ; "61% 6 ; 6 ; 6 ; 6 ; 6 ; 6 ; 6 ; 6 ; 6 ; 6 ; "61% 6 ; 6 ; 6 ; 6 ; 6 ; 6 ; 6 ; 6 ; 6 ; 6 ; 6 ; "61% 6 ; 6 ; 6 ; 6 ; "&1% "&1% "&1% "&1% "&1% "&1% "&1% $'.&6 1&3 , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , 0'& #-&. *2' ('& *)+, # "&'('& !" #)*)+, $ % ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - /0 & " 4( " A Reports Sample Standard Reports Batch Report Thermo Scientific Thermo Scientific 2:2, 7$ 2:2,,7$ 2:2+,97$ 2:2,7$ 2:2,97$ 2:2+, 7$ 2:2,7$ 2:2, 7$ 2:2+,,7$ 2:2+,97$ 2:2+,7$ 2:2++,97$ ) ) 85)# ) ) ) )+ ), ) ) ): )9 ) 2:2,7$ 2:2+, 7$ )9 2:2,+,7$ 2:2, 7$ ): ) 2:2,+7$ ) ) 2 2+,+$ ) 2:2,,,7$ 2 2,9$ ), 85)# ) 2 2,,$ )+ 2:2,,,7$ 2 2+,+$ ) ) 2 2,+9$ 2 2:+,, $ )+ ) 2 2:$ $5#) 2 2,,$ 2 2:$ 85)# 2 29+,, $ 2 2 +,$ 85)# ) 2 2 $ 85)# 85)# ) 2 2 $ 85)# 2 29,,9$ 2 2+$ +85)# 2 29$ 2 29$ 85)# ) "$1 2 2$ 85)# )+$ *2' 2 2,+$ ('& 1&* : , + 9 : , + 9 : , + 9 : , + 1& ) ) 85)# ) ) )9 ): ) ) ), )+ ) ) 85)# ) ) )9 ): ) ) ), )+ ) ) ) 85)# ) "$1 )+$ )+ $5# 85)# 85)# 85)# 85)# +85)# 85)# 85)# 5*)# 4& 27 27 85 27 27 27 27 27 27 27 27 27 27 85 27 27 27 27 27 27 27 27 27 27 27 85 27 27 27 27 85 85 85 85 +85 85 85 27 1&3 6 ; 6 ; "61% 6 ; 6 ; 6 ; 6 ; 6 ; 6 ; 6 ; 6 ; 6 ; 6 ; "61% 6 ; 6 ; 6 ; 6 ; 6 ; 6 ; 6 ; 6 ; 6 ; 6 ; 6 ; "61% 6 ; 6 ; 6 ; 6 ; "&1% "&1% "&1% "&1% "&1% "&1% "&1% $'.&6 , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , 0'& #-&. 5*)# *)+, # "&'('& !" #)*)+, $ % /0 & " 4( ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - ,- - " A Reports Sample Standard Reports Batch Report Rev 1 TraceFinder User Guide 515 A Reports Sample Standard Reports Calibration Report ) )*!!+, )*!!+,- !" !" &%&!'!( %&!'!( !" #$ 3/ / .)/ 0! 0 /4 3 01 21 21 53% 6$/&6$ * !! #!1( 47#1! !#7777 6 * !! ,#''7( 41#',1 !#7777 * !! #!,( 48#1! !#7777 % * !! 8#78' 4,#78 !#777( 0&36 * !! 8#'''' 4#7+8 !#777 * !! 1#7(,( #!7'1 !#777! /9 * !! #'(8( 4#+1(1 !#7777 0&361 * !! #,!'( 41#',, !#7777 6$/ * !! +#,',' 47#,+(! !#7777 / * !! 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AB ' AB, A4B A"B)>A B1 "> 534 TraceFinder User Guide Thermo Scientific A Reports Sample Standard Reports High Density Sample Report 3 Long () * + ) ) , &) !" - .) ##"$ #"$ /) %&' 1 * /( 0 ( / $ 5 234# 234 234# 6 62 4'#4' +67)9% +67)2% 8)5"9 8) )%2": >8) $2"99" $2"99" 5))- )%:;2%2$: )"%2<"% = 8+ ) 25%9, 8+ ) 25%, 4 +67) 2$% +67) 5%" 8)$" 59 8)"92 )"%2: >8)"92 )$%"9:;9%"9: )"%"<"%"= 8+ ) $5% 9, 8+ ) $5%, / +67) 2% +67) $% 8)$$9$9 8)" 5 92 29 )5%2: >8)" 5 92 29 )%:;25%9: )"%<"%$= 8+ )"2%", 8+ )"2%, /.)[email protected]?4A*B* !+AB0ACB AB & AB+ A4B AB,>AB0 > Thermo Scientific TraceFinder User Guide 535 A Reports Sample Standard Reports Internal Standard Summary Report 3DJHRI 7KHUPR)LVKHU/DERUDWRU\ 7KHUPR6FLHQWLILF,QVWUXPHQW $0(5?MDPLHKXPSKULHV 'UXJB$ 536 FDO QJP/ FDOB 'UXJB$B'UXJB$ 'UXJB$ 'UXJB$FDO[ OHYHO 30 ,QWB6WG ,QWB6WG TraceFinder User Guide Thermo Scientific Thermo Scientific & 6' 9 #: 123 / 9 123(% ."-6'( !' . ) % #$" 4 ! 0 + " , 4,1 74 *1* %,$ - )(*+ %()(*+ 123(% . ! &"' 1, 11,+ 5514& ) 414 177 ! *1,44 *,1+ 7,78*7,7 *,78*,7 A Reports Sample Standard Reports Ion Ratio Failure Report TraceFinder User Guide 537 A Reports Sample Standard Reports Manual Integration Report $% !!&! !"# ' !!&!)*)+,!! *)+,!! ( !!&!-%. 1 /* ( 0 / (* , 4 #23)&!!! #23 #23)&!!! 5!5#!!4 63&)" 59!-4 ' 7. & 7 -+ + !+4#!#! 7. 538 TraceFinder User Guide -+ & #8,, 7 8+88!# Thermo Scientific A Reports Sample Standard Reports Method Report Thermo Scientific TraceFinder User Guide 539 A Reports Sample Standard Reports 540 TraceFinder User Guide Thermo Scientific A Reports Sample Standard Reports Thermo Scientific TraceFinder User Guide 541 A Reports Sample Standard Reports Method Validation Report Method Validation Report Lab name: Instrument: User: Batch: Thermo Fisher Laboratory Thermo Scientific Instrument AMER\jamie.humphries Preview2 Page 1 of 3 Preview2_EPA536-Triazines EPA536-Triazines Cali File: Preview2.calx Method: Method Validation Summary Compound DIA D-5 DIA DEA D-7 Theo Conc % Diff Min Conc Max Conc 0.358 0.500 -28.34 0.250 0.750 1778658 0.602 DEA Cyanazine D-5 Cyanazine Simazine D-10 Simazine Atrazine D-5 Atrazine Propazine Propazine D-14 Manually integrated 542 Avg Conc 295652 TraceFinder User Guide 0.500 20.45 0.250 0.750 20.00 0.00 IS 20.00 0.00 0.500 12.90 0.250 0.750 505462 0.607 0.00 0.00 2224244 0.565 % RSD Max % RSD 0.00 IS 0.00 IS 20.00 0.00 IS 0.500 21.49 0.250 0.750 0.00 0.512 0.500 2.46 0.250 0.750 0.00 20.00 0.757 0.500 51.41 0.250 0.750 0.00 20.00 <<< 2334865 272050 20.00 0.00 IS 0.00 IS <<< = Failure Thermo Scientific A Reports Sample Standard Reports Method Validation Report Lab name: Instrument: User: Batch: Thermo Fisher Laboratory Thermo Scientific Instrument AMER\jamie.humphries Preview2 Method Validation Report Data Compound DIA D-5 DIA Page 2 of 3 Preview2_EPA536-Triazines EPA536-Triazines Cali File: Preview2.calx Method: 1 295652 0.358 DEA D-7 DEA 1778658 0.602 Cyanazine D-5 Cyanazine Simazine D-10 Simazine Atrazine D-5 2224244 0.565 505462 0.607 2334865 Atrazine 0.512 Propazine 0.757 Propazine D-14 Manually integrated Thermo Scientific 272050 <<< = Failure TraceFinder User Guide 543 A Reports Sample Standard Reports Method Validation Report Lab name: Instrument: User: Batch: Pos Tray1:10 Thermo Fisher Laboratory Thermo Scientific Instrument AMER\jamie.humphries Preview2 Sample ID SampleID003 Manually integrated 544 TraceFinder User Guide Filename 500ppt-003 Page 3 of 3 Preview2_EPA536-Triazines EPA536-Triazines Cali File: Preview2.calx Method: Level N/A Sample Name D003 File Date 6/26/2007 10:18:49 PM Comment New Dilutions 6/26/2007 H <<< = Failure Thermo Scientific A Reports Sample Standard Reports MSMSD Report ! 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raceFinder User Guide Thermo Scientific B Using Copy Down and Fill Down This appendix describes the Copy Down and Fill Down commands that you can use to make entering column values easier. • Use the Fill Down command for the Filename, Sample Name, Sample ID, and Vial Position columns. • Use the Copy Down command for the Sample Type, Vial Position, Injection Volume, Conv Factor, Level, Comment, and other columns. Follow these procedures: • To automatically copy column values • To automatically enter sequential column values • To use Copy Down or Fill Down for a range of samples To automatically copy column values 1. Select the cell whose value you want to copy to all cells below it. Observe the difference between a selected and nonselected cell. Selected Not selected 2. Right-click and choose Copy Down from the shortcut menu. The value is copied to all rows below the selected row. To automatically enter sequential column values 1. Enter a value for the first row of the fill down sequence. This does not have to be the first sample row. You can begin the fill down procedure from any row in the sequence. Thermo Scientific TraceFinder User Guide 551 B Using Copy Down and Fill Down 2. Select the cell whose value is the first in the fill down sequence. Observe the difference between a selected and nonselected cell. Selected Not selected 3. Right-click and choose Fill Down from the shortcut menu. The application enters sequential column values starting with the value in the selected row and ending with the last row in the column. You can repeatedly use the Fill Down command to create multiple sequences. When you use the Fill Down command for the Vial Position column with an autosampler configured, the TraceFinder application knows the number of vial positions configured in your autosampler and numbers the positions accordingly. 552 TraceFinder User Guide Thermo Scientific B Using Copy Down and Fill Down To use Copy Down or Fill Down for a range of samples 1. To select a range of sample values, do one of the following: Drag your cursor to select a contiguous group of sample values. –or– Hold down the SHIFT key to select a contiguous group of sample values. 2. Right-click and choose the appropriate command from the shortcut menu. The column values are copied or entered sequentially starting with the value in the first selected row and ending with the last selected row. Thermo Scientific TraceFinder User Guide 553 I Index Symbols .cdb, defined 2 .csv, defined 2 .meth, defined 2 .pmd, defined 2 .raw, defined 2 .xml, defined 2 # Background Scans parameter application configuration 52 method development 147 % Test parameter 169 %CV parameter 433 %Diff parameter 433 %RSD parameter 433 A Account Number parameter 74 Acquire a New Raw Data File parameter 94 Acquisition command 33 Active parameter Data Review sample list 433 Identification page 118 Active View page 480 Actual RT parameter 432 Add Compound command 251 Add Compound from Compound Database command 115 Add Group command 184 Add Sample command Acquisition mode 306 Batch View sample list 355 Batch Wizard 388 Add This Mass as New Confirming Ion command 161 Add This Mass to Existing Quan Mass Ranges command 161 Add User parameter 74 Adduct 1–n parameter 201 Adduct parameter, Compound Database 248 Amount parameter 165 Thermo Scientific Analysis command 33 Application Configuration command 36 Area Noise Factor parameter application configuration 54 Detect page 150 Area parameter 432 Area Scan Window parameter application configuration 55 Detect page 151 Area Tail Extension parameter application configuration 55 Detect page 151 Area Threshold, event type 58 Assay Type parameter Batch Wizard 381 Method View 111, 206 Associate a Raw Data File dialog box 97 Auto TSRM Update parameter 320 Autocalc Initial Events parameter, Avalon 153 automated background subtraction options 109 Automatically Create the Master Method parameter 93 Available Methods parameter 381 Available Templates parameter 381 Avalon detection algorithm 46 Avalon Event List dialog box 57 B background subtraction options 109 Background Subtraction Range Option parameter 112 Barcode Actual parameter 308, 354 Barcode Expected parameter 354 Baseline Window parameter application configuration 54 Detect page 150 Batch Level parameter method development 190 report configuration 39 Batch Selection view 290 TraceFinder User Guide 555 Index: C Batch view 343 batches Acquisition mode 286 Analysis mode 343 calibration 314 development batch 275 Best Match Method parameter 232 Browse In Raw File command 355 Bunch Factor, event type 58 C cal1-caln parameter 167 Calculate Concentration As parameter 195 Calculated Amt parameter 432 Calculation Based On parameter 201 Calculation Type parameter 353 Calibration Curve Type command 449 Calibration Levels page, Method View 166 Calibration Method parameter 232 Calibration page Compounds page 164 QAQC page 176 Calibration parameter 320 Calibrator sample type, defined 337 Cancel Changes parameter 74 Carryover Limit parameter 175 CAS No parameter, Identification page 118 CAS parameter, Compound Database 246 Category parameter, Compound Database 246 caution flags 400, 412 Channel parameter Batch View 354 Data Review 433 Charge State parameter, Compound Database 248 Collision Energy parameter, Compound Database confirming peak 250 target peak 249 color codes, Sample Definition view 306 commands Acquisition 33 Add Compound 251 Add Compound from Compound Database 115 Add Group 184 Add Sample Acquisition mode 306 Batch View sample list 355 Batch Wizard 388 Add This Mass as New Confirming Ion 161 Add This Mass to Existing Quan Mass Ranges 161 Analysis 33 Application Configuration 36 556 TraceFinder User Guide Apply to All Peaks in Compound Avalon 153 Genesis 148 ICIS 151 Apply to All Peaks in Method Avalon 153 Genesis 147 ICIS 151 Apply to All Peaks with Like Sensitivity Settings Avalon 153 Genesis 148 ICIS 151 Browse In Raw File 355 Calibration Curve Type 449 Confirming Ion List 443 Copy Down 551 Copy With Headers Acquisition mode 307 Batch View sample list 308, 355 Create New 392 Delete Compound from Method 181 Display Retention Time Column 181 Export SRM Data 236 Export to CSV File Acquisition mode 307 Batch View sample list 308, 356 Extend Calibrations 392 Fill Down 551 Import Compounds 262 Import Published Method 235 Import Samples 355 Insert Copy Sample Acquisition mode 306 Batch View sample list 355 Batch Wizard 388 Insert Sample Acquisition mode 306 Batch View sample list 355 Batch Wizard 388 Log Off 36 Manual Integration Settings 443 Map Raw Files to Samples 355 Method Integration Settings 443 Methods 33 Modify Columns, Batch View sample list 346 Move Sample Down 388 Move Sample Up 388 New Compound Database converting legacy data 264 creating new database 241 Open Compound Database 241 Pause Queue 332 Peak Detection Settings 444 Peak Labels 443 Thermo Scientific Index: D Reactivate All 332 Real Time Status 36 Reinject Selected Samples Acquisition mode 306 Batch view sample list 355 Remove Pending Batch 334 Remove Pending Batches 332 Remove Pending Samples 334 Remove Selected Samples Acquisition mode 307 Batch view sample list 355 Batch Wizard 388 Save Compound Database As 242 Send RT to Method 443 Set This Mass as a New Quan Peak 161 Set This Mass as Quan Mass 161 Show Peak Info 444 Stop Active Batch 332 Stop All Batches 332 Stop Batch 334 Turn Device Off 315 Turn Device On 314 Turn Device Standby 314 Update Confirming Ion Ratios with This Spectrum 161 comma-separated values, defined 2 Comment parameter Batch View 354 Data Review 433 Company Logo parameter 200 Company Name parameter 200 Compound Database views 243 Compound parameter Calibration page 176 Compound Database 246 QC levels page 169 Compound Type parameter Calibration 165 Identification page 117 compound types internal standards Detection page 120 Identification page 117 quan Detection page 120 Identification page 117 target Detection page 120 Identification page 117 Compounds page, Method View 114 compounds, importing to compound database 262 Confirming Ion List command 443 Confirming n Ion Ratio Flag parameter 483 Thermo Scientific Confirming n Ion Ratio parameter 483 Confirming n Manual Flag parameter 483 Confirming n Mass parameter 483 Confirming n Range parameter 483 Confirming n Response parameter 483 Constrain Peak Width parameter Genesis application configuration 51 Detect page 146 ICIS application configuration 54 Detect page 150 Conversion Factor parameter 354 Copy Down command 551 Copy With Headers command Acquisition mode 307 Batch View sample list 308, 355 Create Blank Quantitation Method parameter 97 Create New command 392 Create PDF parameter Batch Template Editor 507 Method view 190, 210 Create XLSM parameter Batch Template Editor 507 Method View 190 Create XML parameter Batch Template Editor 507 Method View 190, 210 Curve Type parameter Calibration page 165 Method Template Editor 232 custom reports, listed 6 Cutoff parameter 175 CV Test (%) parameter 176–177, 179 D Data Review view 393, 454 Decimal Places to be Reported parameter 194 Delete Compound from Method command 181 Detection Method parameter Avalon application configuration 56 Detect page 152 Genesis application configuration 50 Detect page 146 ICIS application configuration 53 Detect page 150 Detection page, Method View 119 Detection Type parameter, Times page 133 TraceFinder User Guide 557 Index: E Detector parameter, Signal page 142 Development Batch view 275 Device Name parameter Acquisition mode 318 Batch View 373 dialog boxes Add Library 17 Associate a Raw Data File 97 Avalon Event List 57 Import an Xcalibur Method 95 Open Chromatograph Reference Sample 305, 378, 452 Open Compound Database 241 Save Compound Database As 242 Save New Compound Database 241, 264 Select Compounds from Database 115 Select Compounds to Add 102 Thermo Library Manager 17 Thermo Xcalibur Instrument Setup 108, 204 Thermo Xcalibur Roadmap 16 Dilution Factor parameter 354 Disable Cluster Off, event type 59 Disable Cluster On, event type 59 Display Compounds Above Set Limit parameter 194 Display Quan Flags and Legend parameter 194 Display Retention Time Column command 181 Displayed Reports parameter 43 E Edit User parameter 74 Email Address parameter 74 Enable parameter, Ratios page 163 Enable Peak Threshold parameter 232 Enable Tune Time Tracking parameter 195 Enable Valley Detection parameter application configuration 51 method development 146 Enabled parameter 74 End RT parameter, Times page 134 End Threshold, event type 58 Energy Ramp parameter, Compound Database 249 Estimation Method parameter 165 Event parameter 57 Event types 58 Exact Mass Window parameter 201 Example parameter, Reports page 190 Exclude Matching Quan Peaks parameter 233 Excluded parameter 433 Exclusion Window parameter 233 Expected RT parameter 432 Expected RT parameter, Times page 133 Expected Width parameter 558 TraceFinder User Guide application configuration 51 method development 146 Experiment parameter, Compound Database 246 Export SRM Data command 236 Export to CSV File command Acquisition mode 307 Batch View sample list 308, 356 Extend Calibrations command 392 Extracted Ion Chromatogram 260 Extracted Mass parameter, Compound Database fragment 250 target peak 248 F feature summary 3 file types, supported 2 Filename parameter, Batch View 308, 353 Fill Down command 551 Filter parameter, Detection 142 Filter parameter, Signal page 141 Final Units parameter Batch View 354 Data Review 433 Finish view 313 Flag Values Above Carryover parameter 195 Flag Values Above LOR parameter 195 Flag Values Above ULOL parameter 195 Flag Values Below LOD parameter 195 Flag Values Below LOQ parameter 195 Flag Values Between LOD and LOQ parameter 195 Flags parameter 396, 398, 407, 409, 417 Force Cluster Off, event type 59 Force Cluster On, event type 59 Formula parameter, Compound Database 246 Full Name parameter 74 G General page Background Subtraction Range Option 112 editing 107 Include Data Dependent Filters parameter 113 Injection Volume parameter Batch View 353 method development 112, 206 Instrument Method parameter 112, 206 Ion Range Calc Method parameter 112 Library Search Type parameter 207 Mass Precision parameter 112, 206 Mass Tolerance parameter 113, 207 Method View 107 Number of Scans to Subtract parameter 112 Thermo Scientific Index: H Qualitative Peak Processing Template parameter 112 Show All Compounds parameter 207 Stepoff Value parameter 112 Generate Only parameter 481 Genesis detection algorithm 46 Groups page, Method View 183 H Height parameter 432 Hydrolysis page, Master Method View 181 Hydrolysis sample type, defined 337 I ICIS detection algorithm 46 Identification page, Method View 117 Import an Xcalibur Method dialog box 95 Import Compounds command 262 Import parameter 43 Import Published Method command 235 Import Samples command 355 Include Compound Peak Spectrum as Reference Spectrum parameter 232 Include Confirming Ions parameter 232 Include Data Dependent Filters parameter 113 Injection Amount parameter 94 Injection Concentration parameter 483 Injection Units parameter 483 Injection Volume parameter Batch View 353 method development 112, 206 Insert Copy Sample command Acquisition mode 306 Batch View sample list 355 Batch Wizard 388 Insert Sample command Acquisition mode 306 Batch View sample list 355 Batch Wizard 388 Installed Reports parameter 43 installing NIST and QED libraries 16 Instrument Method parameter Batch View 354 General page 112, 206 Method Forge 94 instrument status indicators 315 Instrument view 269 instruments, supported viii Integration Mode parameter 432 Ion Coelution parameter Thermo Scientific application configuration 49 Ratios page 163 Ion Range Calc Method parameter 112 Ion Ratio Window parameter 201 Ionization parameter, Compound Database 246 ISTD Amt parameter 432 ISTD Matching parameter 233 ISTD page, Method View 179 ISTD parameter 165 ISTD Resp parameter 432 IT Administrator role 75 L Lab Name parameter 111, 206 Laboratory Name parameter 200 Lens parameter, Compound Database 249 Level parameter Batch View 353 QC Levels page 169 Library Search Type parameter 207 licenses, types of ix Limit Library Hits parameter 232 Limit the Retention Time Range parameter 232 Limits page, Method View 175 Linked Compound parameter 165 Local Method view 498 LOD (Detection Limit) parameter 175 Log Off command 36 Login parameter 14 LOQ (Quantitation Limit) parameter 175 M m/z Window parameter 200 Manual Flags parameter 482 Manual Injection parameter 94 Manual Integration Settings command 443 Map Raw Files to Samples command 355 Mass parameter Compound Database target peak 247 Mass parameter, Compound Database confirming peak 249 Mass parameter, Compound Database, confirming peak 250 Mass Precision parameter 112, 206 Mass Tolerance parameter 113, 207 Master Method View Hydrolysis page 181 Negative page 178 Max Amt Diff (%) parameter 176 TraceFinder User Guide 559 Index: N Max Conc parameter 178 Max Recovery (%) parameter, ISTD page 179 Max RF Diff (%) parameter 177 Max RSD (%) parameter, Calibration page 176 Max RT (+min) parameter, ISTD page 179 Measurement Unit parameter 201 Method Integration Settings command 443 Method parameter Matrix Blank page 178 Solvent Blank page 180 Method Template Editor 231 Method View Calibration Levels page 166 Calibration page Compounds page 164 QAQC page 176 Compounds page 114 Detection page 119 General page 107 Groups page 183 Identification page 117 ISTD page 179 Limits page 175 QC Levels page 167 Ratios page 162 Real Time Viewer page 170 Reports page 189 Solvent Blank page 180 Spectrum page 157 Suitability page 154 Method view 84 Method View, QAQC page 174 methods importing Xcalibur 95 instrument 269 local 498 master 83 Method Template Editor 231 update TSQ method 313 Methods command 33 Min Peak Height (S/N) parameter Genesis application configuration 51 Detect page 147 ICIS application configuration 54 Detect page 150 Min Peak Width parameter application configuration 55 Detect page 151 Min recovery (%) parameter, ISTD page 179 Min RF parameter 177 560 TraceFinder User Guide Min RT (–min) parameter 179 modes, choosing 33 Modify Calibrations or Active Compounds by Group parameter 390 Modify Columns command, Batch View sample list 346 Move Sample Down command 388 Move Sample Up command 388 MS Order parameter, Compound Database confirming peak 250 target peak 248 MS2 Search Library parameter 200 MS3 Search Library parameter 200 Multiplet Resolution parameter application configuration 55 Detect page 151 Multiplexing Channels parameter 306 N Name the Master Method parameter 93 Negative page, Master Method View 178 Negative Peaks, event type 58 Negative sample type, defined 337 Neutral Mass parameter, Compound Database 246 New Compound Database command converting legacy data 264 creating new database 241 NIST library, installing 16 No Specified Retention Time parameter 201 Noise Method parameter application configuration 55 Detect page 151 Number of Confirming Ions parameter 232 Number of Scans to Subtract parameter 112 O Only Select Top Peaks parameter 232 Open Chromatograph Reference Sample dialog box 305, 378, 452 Open Compound Database command 241 Open Compound Database dialog box 241 Origin parameter Calibration 165 Method Template Editor 233 P parameters # Background Scans 147 application configuration 52 % Test 169 Thermo Scientific Index: P %CV 433 %Diff 433 %RSD 433 Account Number 74 Acquire a New Raw Data File 94 Active Data Review sample list 433 Identification page 118 Actual RT 432 Add User 74 Adduct 1–n 201 Adduct, Compound Database 248 Amount 165 Area 432 Area Noise Factor application configuration 54 Detect page 150 Area Scan Window application configuration 55 Detect page 151 Area Tail Extension application configuration 55 Detect page 151 Assay Type Batch Wizard 381 Method View 111, 206 Auto TSRM Update 320 Autocalc Initial Events, Avalon 153 Automatically Create the Master Method 93 Available Methods 381 Available Templates 381 Background Subtraction Range Option 112 Barcode Actual 308, 354 Barcode Expected 354 Baseline Window application configuration 54 Detect page 150 Batch Level method development 190 report configuration 39 Best Match Method 232 cal1-caln 167 Calculate Concentration As 195 Calculated Amt 432 Calculation Based On 201 Calculation Type 353 Calibration 320 Calibration Method 232 Cancel Changes 74 Carryover Limit 175 CAS No, Identification page 118 CAS, Compound Database 246 Category, Compound Database 246 Channel Thermo Scientific Batch View 354 Data Review 433 Charge State, Compound Database 248 Collision Energy, Compound Database confirming peak 250 target peak 249 Comment Batch View 354 Data Review 433 Company Logo 200 Company Name 200 Compound Calibration page 176 Compound Database 246 QC levels page 169 Compound Type Calibration 165 Identification page 117 Confirming n Ion Ratio 483 Confirming n Ion Ratio Flag 483 Confirming n Manual Flag 483 Confirming n Mass 483 Confirming n Range 483 Confirming n Response 483 Constrain Peak Width Genesis application configuration 51 Detect page 146 ICIS application configuration 54 Detect page 150 Conversion Factor 354 Create Blank Quantitation Method 97 Create PDF Batch Template Editor 507 Method view 190, 210 Create XLSM Batch Template Editor 507 Method View 190 Create XML Batch Template Editor 507 Method View 190, 210 Curve Type Calibration page 165 Method Template Editor 232 Cutoff 175 CV Test (%) 176–177, 179 Decimal Places to be Reported 194 Detection Method Avalon application configuration 56 Detect page 152 Genesis application configuration 50 TraceFinder User Guide 561 Index: P Detect page 146 ICIS application configuration 53 Detect page 150 Detection Type, Times page 133 Detector 142 Device Name Acquisition mode 318 Batch View 373 Dilution Factor 354 Display Compounds Above Set Limit 194 Display Quan Flags and Legend 194 Displayed Reports 43 Edit User 74 Email Address 74 Enable Peak Threshold 232 Enable Tune Time Tracking 195 Enable Valley Detection application configuration 51 method development 146 Enable, Ratios page 163 Enabled 74 End RT, Times page 134 Energy Ramp, Compound Database 249 Estimation Method 165 Event 57 Exact Mass Window 201 Example, Reports page 190 Exclude Matching Quan Peaks 233 Excluded 433 Exclusion Window 233 Expected RT 432 Expected RT, Times page 133 Expected Width application configuration 51 method development 146 Experiment, Compound Database 246 Extracted Mass, Compound Database fragment 250 target peak 248 Filename, Batch View 308, 353 Filter 141 Filter, Detection 142 Final Units Batch View 354 Data Review 433 Flag Values Above Carryover 195 Flag Values Above LOR 195 Flag Values Above ULOL 195 Flag Values Below LOD 195 Flag Values Below LOQ 195 Flag Values Between LOD and LOQ 195 Flags 396, 398, 407, 409, 417 Formula, Compound Database 246 Full Name 74 562 TraceFinder User Guide Generate Only 481 Height 432 Import 43 Include Compound Peak Spectrum as Reference Spectrum 232 Include Confirming Ions 232 Include Data Dependent Filters 113 Injection Amount 94 Injection Concentration 483 Injection Units 483 Injection Volume Batch View 353 method development 112, 206 Installed Reports 43 Instrument Method Batch View 354 General page 112, 206 Method Forge 94 Integration Mode 432 Ion Coelution application configuration 49 Ratios page 163 Ion Range Calc Method 112 Ion Ratio Window 201 Ionization, Compound Database 246 ISTD 165 ISTD Amt 432 ISTD Matching 233 ISTD Resp 432 Lab Name 111, 206 Laboratory Name 200 Lens, Compound Database 249 Level Batch View 353 QC levels page 169 Library Search Type 207 Limit Library Hits 232 Limit the Retention Time Range 232 Linked Compound 165 LOD (Detection Limit) 175 Login 14 LOQ (Quantitation Limit) 175 m/z Window 200 Manual Flags 482 Manual Injection 94 Mass Compound Database confirming peak 249 target peak 247 Mass Precision 112, 206 Mass Tolerance 113, 207 Mass, Compound Database, confirming peak 250 Max Amt Diff (%) 176 Max Conc 178 Max Recovery (%), ISTD page 179 Thermo Scientific Index: P Max RF Diff (%) 177 Max RSD (%), Calibration page 176 Max RT (+min), ISTD page 179 Measurement Unit 201 Method Matrix Blank page 178 Solvent Blank page 180 Min Peak Height (S/N) Genesis application configuration 51 Detect page 147 ICIS application configuration 54 Detect page 150 Min Peak Width application configuration 55 Detect page 151 Min recovery (%) ISTD page 179 Min RF 177 Min RT (–min) 179 Modify Calibrations or Active Compounds by Group 390 MS Order, Compound Database confirming peak 250 target peak 248 MS2 Search Library 200 MS3 Search Library 200 Multiplet Resolution application configuration 55 Detect page 151 Multiplexing Channels 306 Name the Master Method 93 Neutral Mass, Compound Database 246 No Specified Retention Time 201 Noise Method application configuration 55 Detect page 151 Number of Confirming Ions 232 Number of Scans to Subtract 112 Only Select Top Peaks 232 Origin Calibration 165 Method Template Editor 233 Password login screen 14 user administration 74 Path 94 Peak Height (%) Genesis application configuration 51 Detect page 146 ICIS Thermo Scientific application configuration 54 method development 150 Peak Noise Factor application configuration 54 method development 150 Peak S/N Cutoff application configuration 52 Detect page 147 Percentage 178 Phone Number 74 Polarity, Compound Database 248 Post-run System State 318, 373 Precursor Mass, Compound Database, target peak 247 Precursor, Compound Database, confirming peak 249 Priority Sequence 318, 373 Processing Configuration File 200 Product Mass, Compound Database confirming peak 249 target peak 247 QAQC Flags 482 QC1-QCn 169 QIon 483 Qualitative Peak Processing Template 112 Quan Flags 482 Quan Mass 483 Quan Peak m/z 482 Quan Peak Response 482 Quan Peak RT 482 Quick Mode 381 R^2 Threshold 176 Ranges, compound detection 142 Raw Filename 94 Reference Compound, Identification page 118 Remove User 74 Report All Compounds Listed in Configuration File 201 Report Concentration 194 Report Name 190, 210 Report Noise As application configuration 52 Detect page 147 Report Semi-Quantitative Result 201 Report Title 190, 210 Report Type 190, 210 Reset Password 74 Response 483 Response Ratio 432 Response Threshold, Compound Database 246 Response Via Calibration 165 Method Template Editor 233 Retention Time 483 RMS TraceFinder User Guide 563 Index: P application configuration 55 Detect page 151 Role 74 RT Calibration 165 Calibration levels 167 Calibration page 176 Chk Std page 177 Compound Database 249 Hydrolysis page 181 Identification page 117 ISTD page 179 Limits page 175 Matrix Blank page 178 QC levels page 169 Solvent Blank page 180 RT Window 200 S/N Threshold application configuration 51 method development 146 Sample Amt 432 Sample Comment 94 Sample Concentration 483 Sample File 481 Sample ID, Batch View 308, 353 Sample Name Batch View 308, 353 Data Review 409 Sample Type Batch View 353 Data Review 396, 410, 418 Sample Units 483 Sample Volume 354 Sample Weight 354 Save Changes 74 Screening Method 200 Select a Report 481 Sensitivity Avalon application configuration 56 Detect page 152 Genesis application configuration 50 Detect page 146 ICIS application configuration 53 Detect page 150 Method Template Editor 232 Separate Ion Overlay Display 194 Set Ion Ratio to All Confirming Peaks in Compound 163 Set Ion Ratio to All Confirming Peaks in Method 163 564 TraceFinder User Guide Set Peak Windows Settings to All Peaks in Compound 134 Set Peak Windows Settings to All Peaks in Method 134 Shade Row when Sample is Outside of Evaluation Criteria 194 Show All Compounds 207 Show Chromatogram on Quantitation Report 194 Show Quan Peaks Only 170 Showing, Active View 481 Smoothing Avalon application configuration 56 Detect page 153 Genesis application configuration 50 Detect page 146 ICIS application configuration 54 Detect page 150 Specify Default Ion Ratio Ranges 232 Standard type 165 Start Device 318, 373 Start RT, Times page 134 Start When Ready 318, 373 Starting vial number 381 Status Active View 482 Batch View 308, 353 Data Review 409 Stepoff Value 112 System Shutdown Method 320 System Startup Method 320 System Status 320 Tailing Factor Genesis application configuration 51 method development 146 ICIS application configuration 54 method development 150 Target Ratio 163 Template Layout 381 Theoretical Amount 482 Theoretical Amt 432 Threshold/Lower Limit 181 Time 57 Time Range Peak, Compound Database 248 Time/Event/Value 56 Total Batch Rows 381 Total Response 482 Total Rows 481 Trace, Detection 142 Thermo Scientific Index: P Tune File Lifetime 195 ULOL (Linearity Limit) 175 Units 165 Upper Limit Hydrolysis page 181 Solvent Blank page 180 Use Alternate Calibration Report Format 194 Use an Existing Raw Data File 93 Use as RT Reference, Identification page 118 Use Autosampler 94 Use Average Scan 201 Use Data Dependent Scans 234 Use Full MS Scan to Confirm 201 Use Genesis Algorithm for Qual Processing 233 Use Method Forge 85, 89, 95 Use Scan at Peak Apex 201 Use These Libraries 232 User Security 64 Username 74 Valley Rise (%) application configuration 52 Detect page 147 Valley S/N application configuration 52 method development 147 Value 57 Vial Position Batch View 308, 353 Method Forge 94 View Only 481 View Width application configuration 49 Times page 134 Weighting Calibration 165 Method Template Editor 233 Window application configuration ion ratio 49 retention time 49 Compound Database 249 Ratios page 163 Times page 133 Window Type application configuration 49 Ratios page 163 XIC 141 Password parameter login screen 14 user administration 74 password, administrator 12 Path parameter 94 Pause Queue command 332 Thermo Scientific Peak Detection Settings command 444 Peak Height (%) parameter Genesis application configuration 51 Detect page 146 ICIS application configuration 54 method development 150 Peak Labels command 443 Peak Noise Factor parameter application configuration 54 method development 150 Peak S/N Cutoff parameter application configuration 52 Detect page 147 Percentage parameter 178 Phone Number parameter 74 Polarity parameter, Compound Database 248 Post-run System State parameter 318, 373 P-P Threshold, event type 58 Precursor Mass parameter, Compound Databasem, target peak 247 Precursor parameter, Compound Database, confirming peak 249 Priority Sequence parameter 318, 373 procedures acquisition mode access real-time display 323 add samples to the sample list 298 assign a specific channel to a sample 303, 305 create a batch template 296–297 export reports to a folder 310 import samples into the sample list 301 insert samples into the sample list 300 pause all batches in a queue 330 preview a standard report 310 re-inject a sample from 302 remove a batch from a queue 334 remove a pending batch from a queue 334 remove a pending sample from a queued batch 333 remove a single batch from a queue 331 remove all batches in a queue 331 remove all pending batches in a queue 331 remove pending samples from a queued batch 333 remove samples from the sample list 302 save a to-be-run batch 315 select a previously acquired batch 295 select a ready-to-acquire batch 294 specify a calibration batch 314 specify device states 314 specify startup or shutdown methods 313 start a new batch 290, 292 start an acquisition 315 TraceFinder User Guide 565 Index: P update TSRM data 313 view output files 319 analysis mode access the Analysis mode 340 add samples to the samples list 363 change the displayed information for detected peaks qualitative peak 426 quantitative peak Data Review 441 method development 120 change the library entry for a selected peak 429 change the peak panes display 438 copy a sample in the samples list 364 create a new batch 361 customize the column display, Batch View 367 display peaks for a specific compound, qualitative view 419 edit samples in a batch 370 edit the batch-level output formats 358 edit the sample-level output formats 357 enlarge the report text 479 exclude a calibration point 436 export a report 478 insert samples in the samples list 363 make a compound active or inactive 435 manually add a peak chromatogram pane 423 qual peak pane 425 quantitation peak 440 manually exclude a calibration point 448 manually integrate a confirming ion peak 446 manually integrate a quantitative peak 440 modify the peak detection settings 441 open a recent batch 370 open a saved batch 369 open the Batch View 343 open the Data Review view 393, 454 open the Local Method View 498 open the Report View 468 print a report 477 reinject a sample 365 reinject a sample from a previously acquired batch 370 remove a manually created peak 440 remove a peak from the peak list 421 remove a peak from the qual peak pane 426 remove samples from the samples list 364 scroll the samples list 346 search for text 479 select a compound 471 select a report generating reports 473 viewing reports 469 select a sample 566 TraceFinder User Guide generating reports 475 viewing reports 471 submit all samples in the batch 371 switch between method and manual integration qual mode 426 quan mode 441 zoom in on a peak chromatogram navigation 423 qual peak 425 quantitation peak 438 spectra pane 428 application configuration mode access the Application Configuration mode 37 activate user security 64 add a quantitation peak to a compound 253 change the default drive 494 choose a drive 493 copy the folder hierarchy from another drive 496 create projects or subprojects 495 delete projects or subprojects 496 edit user information 71 hide a drive from display 494 import compounds 262 import new report types 40 open the Defaults page 44 open the Project Administration view 492 open the User Administration view 69 refresh the drives display 494 remove a compound 252 remove a user 73 remove all empty folders 496 specify common detection parameters 46 specify default laboratory and instrument names 44 specify default mass precision and intensity scale 45 configuration mode add a user 70 getting started choose a node 33 display a log of instrument errors 34 install the NIST library 16 install the QED library 16 log in to the TraceFinder application 12 monitor the instrument status 34 start the TraceFinder application 11 method development mode 166 access the Method Development mode 79 acquire selected samples 280 acquire the batch 280 add a compound to the database 251 add a mass as a new compound 127 add a mass as a new confirming ion peak 130 add a mass to the existing quan mass ranges 125 add a quan peak 126 add a quan peak to an existing compound 159 Thermo Scientific Index: Q add compounds to the method 121 add confirming ions to an existing compound 160 add ions to get an accumulated signal 159 add sample to the development batch 276 automatically select compounds to create a new method 85 calculate and report semi-quantitative results 197 calibrate the compounds 227 change the compound reference spectrum 124 change the quantitation mass used for a quan peak specify mass tolerance 110 specify peak criteria 225 specify QC levels and concentrations 167 specify qualitative peak processing 229 specify quantitation flag options 192 specify quantitation limits 191 specify ranges of ions for detection and integration 135 specify standard report types and output formats 190, 208 specify the default parameters 196 specify the exact mass window 198 specify the Exactive parameters 198 specify the ion ratio calculation method 198 specify the maximum concentration as a percentage 157 copy a sample 277 create a blank method 97 create a group 183 create a new instrument method 270 create a new multiplexing instrument method 272 create a target screening method 104 enter a note for the method 110, 230 enter column values 277 export SRM data to an XML file 236 filter the displayed compounds 117, 120 identify the peaks 226 import a master method 235 import an instrument method 274 import an Xcalibur method 95 insert samples into the development batch 276 manually select compounds to create a new method 89 open a compound database 241 open a saved master method 106, 202 open an instrument method 273 open the Compound Database editor 240 open the Development Batch view 275 open the Instrument View 269 open the Qual Browser 281 remove all samples from the samples list 279 remove selected samples from the samples list 278 replace a confirming ion peak 130 replace a quantitation mass 125 replace a quantitative peak with a confirming ion peak 128 resize or reorganize the columns 278 save the database to a new name 241–242 save the method template 230 save the new method 130 select compounds from the compound database 102 set a confirming ion peak as an additional quantitative peak 128 set automated background subtraction options 109 specify a chromatogram reference sample 378 specify a location for development batch data 276 specify an internal standard for a compound 164 specify general information for a master method 107 specify ion ratio criteria 162 Thermo Scientific 178 specify user interface options 192 track the use of the tune file 193 update confirming ion ratios 157 zoom in the chromatogram or spectrum displays 160 Processing Configuration File parameter 200 Product Mass parameter, Compound Database confirming peak 249 target peak 247 Project Administration view 492 projects and subprojects, creating 492 Q QAQC Flags parameter 482 QAQC page, Method View 174 QAQC role 77 QC Levels page, Method View 167 QC1-QCn parameter 169 QED library, installing 16 QIon parameter 483 Qualitative Peak Processing Template parameter 112 quality check (QC) sample type, defined 337 Quan Flags parameter 482 Quan Mass parameter 483 Quan Peak m/z parameter 482 Quan Peak Response parameter 482 Quan Peak RT parameter 482 quan report settings, specifying 191 Quick Mode parameter 381 R R^2 Threshold parameter 176 Ranges parameter, compound detection 142 Ratios page, Method View 162 Raw Filename parameter 94 TraceFinder User Guide 567 Index: S Reactivate All command 332 Real Time Status command 36 Real Time Viewer page, Method View 170 Reference Compound parameter, Identification page 118 reference spectra 428 Reinject Selected Samples command Acquisition mode 306 Batch view sample list 355 Remove Pending Batch command 334 Remove Pending Batches command 332 Remove Pending Samples command 334 Remove Selected Samples command Acquisition mode 307 Batch view sample list 355 Batch Wizard 388 Remove User parameter 74 Report All Compounds Listed in Configuration File parameter 201 Report Concentration parameter 194 report formats, specifying 189 Report Name parameter 190, 210 Report Noise As parameter application configuration 52 Detect page 147 Report selection view 309 Report Semi-Quantitative Result parameter 201 Report Title parameter 190, 210 Report Type parameter 190, 210 Report View 468 reports Acquisition mode 309 Analysis mode 468 configuring 39 flags defined 512 listed 5 sample PDFs 513 viewing landscape in PDF 513 Reports page, Method View 189 Reset Password parameter 74 Response parameter 483 Response Ratio parameter 432 Response Threshold parameter, Compound Database 246 Response Via parameter Calibration 165 Method Template Editor 233 Retention Time parameter 483 RMS parameter application configuration 55 Detect page 151 Role parameter 74 568 TraceFinder User Guide RT parameter Calibration 165 Calibration levels 167 Calibration page 176 Chk Std page 177 Compound Database 249 Hydrolysis page 181 Identification page 117 ISTD page 179 Limits page 175 Matrix Blank page 178 QC levels page 169 Solvent Blank page 180 RT Window parameter 200 S S/N Threshold parameter application configuration 51 method development 146 Sample Amt parameter 432 Sample Comment parameter 94 Sample Concentration parameter 483 Sample definition view 298 Sample File parameter 481 Sample ID parameter, Batch View 308, 353 Sample Name parameter Batch View 308, 353 Data Review 409 Sample Type parameter Batch View 353 Data Review 396, 410, 418 sample types, defined 337 Sample Units parameter 483 Sample Volume parameter 354 Sample Weight parameter 354 Save Changes parameter 74 Save Compound Database As command 242 Save Compound Database As dialog box 242 Save New Compound Database dialog box 241, 264 Screening Method parameter 200 Select a Report parameter 481 Select Compounds from Database dialog box 115 Select Compounds to Add dialog box 102 Selected Reaction Monitoring 258 Send RT to Method command 443 Sensitivity parameter Avalon application configuration 56 Detect page 152 Genesis Thermo Scientific Index: T application configuration 50 Detect page 146 ICIS application configuration 53 Detect page 150 Method Template Editor 232 Separate Ion Overlay Display parameter 194 Set Ion Ratio to All Confirming Peaks in Compound parameter 163 Set Ion Ratio to All Confirming Peaks in Method parameter 163 Set Peak Windows Settings to All Peaks in Compound parameter 134 Set Peak Windows Settings to All Peaks in Method parameter 134 Set This Mass as a New Quan Peak command 161 Set This Mass as Quan Mass command 161 Shade Row when Sample is Outside of Evaluation Criteria parameter 194 Shoulders On, event type 59 Show All Compounds parameter 207 Show Chromatogram on Quantitation Report parameter 194 Show Peak Info command 444 Show Quan Peaks Only parameter 170 Showing parameter, Active View 481 SIM experiment type 259 Single Ion Monitoring 259 Smoothing parameter Avalon application configuration 56 Detect page 153 Genesis application configuration 50 Detect page 146 ICIS application configuration 54 Detect page 150 Solvent Blank page, Method View 180 Solvent sample type, defined 337 Specify Default Ion Ratio Ranges parameter 232 Specimen sample type, defined 337 Spectrum page, Method View 157 SRM data, exporting 236 SRM experiment type 258 standard reports, listed 5 Standard type parameter 165 Start Device parameter 318, 373 Start RT parameter, Times page 134 Start Threshold, event type 58–59 Start When Ready parameter 318, 373 Thermo Scientific Starting vial number parameter 381 status color codes, Sample Definition view 306 Status parameter Active View 482 Batch View 308, 353 Data Review 409 Stepoff Value parameter 112 Stop Active Batch command 332 Stop All Batches command 332 Stop Batch command 334 Suitability page, Method View 154 Supervisor role 76 supported file types, defined 2 supported software and hardware viii system requirements viii System Shutdown Method parameter 320 System Startup Method parameter 320 System Status parameter 320 T Tailing Factor parameter Genesis application configuration 51 method development 146 ICIS application configuration 54 method development 150 Tangent Skim, event type 59 Target Ratio parameter 163 target screening export settings, specifying 196 target screening reports, listed 7 Technician role 76 Template Layout parameter 381 templates batch 296–297 method 224 Tension, event type 59 Theoretical Amount parameter 482 Theoretical Amt parameter 432 Thermo Xcalibur Instrument Setup dialog box 108, 204 Threshold/Lower Limit parameter 181 Time parameter 57 Time Range Peak parameter, Compound Database 248 Time/Event/Value parameter 56 Total Batch Rows parameter 381 Total Response parameter 482 Total Rows parameter 481 Trace parameter, Detection 142 Tune File Lifetime parameter 195 Turn Device Off command 315 TraceFinder User Guide 569 Index: U Turn Device On command 314 Turn Device Standby command 314 Batch Selection 290 Compound Database 243 Data Review 393, 454 Development Batch 275 Finish 313 Instrument 269 Local Method 498 Method 84 Project Administration 492 Report selection 309 Report View 468 Sample definition 298 User Administration 69 U ULOL (Linearity Limit) parameter 175 Unextracted sample type, defined 337 Units parameter 165 Update Confirming Ion Ratios with This Spectrum command 161 Upper Limit parameter Hydrolysis page 181 Solvent Blank page 180 Use Alternate Calibration Report Format parameter 194 Use an Existing Raw Data File parameter 93 Use as RT Reference parameter, Identification page 118 Use Autosampler parameter 94 Use Average Scan parameter 201 Use Data Dependent Scans parameter 234 Use Full MS Scan to Confirm parameter 201 Use Genesis Algorithm for Qual Processing parameter 233 Use Method Forge parameter 85, 89, 95 Use Scan at Peak Apex parameter 201 Use These Libraries parameter 232 user accounts, creating 69 User Administration view 69 user roles and permissions 75 user roles, defined 75 User Security parameter 64 user security, activating 64 Username parameter 74 Weighting parameter Calibration 165 Method Template Editor 233 Window parameter application configuration ion ratio 49 retention time 49 Compound Database 249 Ratios page 163 Times page 133 Window Type parameter application configuration 49 Ratios page 163 workflow acquisition mode 288 general 4 X V Valley Rise (%) parameter application configuration 52 Detect page 147 Valley S/N parameter application configuration 52 method development 147 Value parameter 57 Vial Position parameter Batch View 308, 353 Method Forge 94 View Only parameter 481 View Width parameter application configuration 49 Times page 134 views Batch 343 570 W TraceFinder User Guide XIC experiment type 259 XIC parameter, Signal page 141 Thermo Scientific
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