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Freestyle 1.0 User Guide Version A FreeStyle User Guide Software Version 1.0 XCALI-97660 Revision A November 2013 © 2013 Thermo Fisher Scientific Inc. All rights reserved. Foundation and FreeStyle are trademarks, and Thermo Scientific and Xcalibur are registered trademarks of Thermo Fisher Scientific Inc. in the United States. The following are registered trademarks in the United States and other countries: Adobe, Flash, and Reader are registered trademarks of Adobe Systems, Inc. Microsoft and Windows are registered trademarks of Microsoft Corporation. All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries. Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the product operation. This document is copyright protected and any reproduction of the whole or any part of this document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc. The contents of this document are subject to change without notice. All technical information in this document is for reference purposes only. System configurations and specifications in this document supersede all previous information received by the purchaser. Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error- free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might result from any use of this document, even if the information in the document is followed properly. This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of Sale shall govern all conflicting information between the two documents. Release history: Revision A, November 2013 Software version: (Thermo) Foundation 3.0 and later; FreeStyle 1.0 and later. For Research Use Only. Not for use in diagnostic procedures. C Contents Preface . .v Related Documentation . .vi System Requirements . .vi License Activation and Deactivation . vii Cautions and Special Notices . vii Contacting Us . .viii Chapter 1 Introduction . .1 Chapter 2 Using the FreeStyle Window . .3 FreeStyle Workspaces and Templates . 4 Workspace Options Toolbar . 6 FreeStyle Toolbars. 8 FreeStyle Views . 8 FreeStyle Info Bar Pages . 11 Chapter 3 Working with Chromatograms . .13 Chromatogram-Specific Toolbars . 14 Workspace Processing Toolbar – Chromatograms. 14 Chromatogram Display Options Toolbar . 16 Sequence Toolbar . 19 Zoom Options Toolbar. 20 Chromatogram-Specific Views . 21 Active Traces View . 22 Chromatogram View. 26 Peak List View. 40 Chromatogram-Specific Pages in the Info Bar . 47 Sequence Page . 48 ICIS Peak Detection Settings Page . 48 Avalon Peak Detection Settings Page. 52 Genesis Peak Detection Settings Page . 56 Detector Type Page . 61 Trace Type Page . 62 Filter Page . 63 Thermo Scientific FreeStyle User Guide iii Contents Chapter 4 Working with Spectra . .65 Spectra-Specific Toolbars . 66 Workspace Processing Toolbar – Spectrum . 66 Spectrum Display Options Toolbar. 67 Spectrum List Display Options Toolbar . 70 Spectra-Specific Views. 70 Spectrum View . 71 Spectrum List View . 79 Search Results View. 80 Chemical Structure View. 81 Elemental Composition Results View . 81 Spectra-Specific Info Bar Pages . 83 Elemental Composition Page. 83 Isotope Simulation Page . 90 Library Search Page . 93 Chapter 5 Viewing Experiment and Instrument Information. .101 Workspace Options Toolbar . 101 Scan Header View . 102 Status Log View. 104 Instrument Method View . 106 Tune Method View. 110 Sample Information View . 111 Appendix A FreeStyle Default Parameters. .113 Default Mass Precision Page . 113 Default Peak Detection Algorithm Page . 115 Default Number of Recently Used Files Page . 115 Default Directory of Raw Files Page . 115 Default Elemental Composition Search Parameters Page. 116 Factory Default Template Page . 117 Default Library Search Parameters Page. 118 Appendix B Scan Filters and Scan Headers . .119 Scan Filter Parameters . 119 Scan Headers and Scan Header Abbreviations . 122 Appendix C One- and Three-Letter Abbreviations for Amino Acid Residues . .125 Index . .129 iv FreeStyle User Guide Thermo Scientific P Preface This guide describes how to use the FreeStyle™ application to view and analyze raw data. It provides information about functionality using the multiple FreeStyle toolbar commands. Contents • Related Documentation • System Requirements • License Activation and Deactivation • Cautions and Special Notices • Contacting Us To open the FreeStyle application From the Microsoft™ Windows™ taskbar, choose Start > All Programs > Thermo FreeStyle > FreeStyle. –or– Click the FreeStyle icon, , on the desktop. Thermo Scientific FreeStyle User Guide v Preface Related Documentation The FreeStyle application includes complete documentation. In addition to this guide, you can also access the application Help. To view the product manuals From the taskbar, choose Start > All Programs > Thermo FreeStyle > Manual. To view application-specific Help • From the FreeStyle window, click the Help icon, , in the upper-right corner. • If information about setting parameters is available for a specific view, page, or dialog box, click Help or press the F1 key for information about setting parameters. For more information, visit www.thermoscientific.com. System Requirements The FreeStyle application requires a license. In addition, your system must meet the minimum requirements as stated in the following table. System Minimum requirements Computer • 1.7 GHz dual core processor with 3.0 GB RAM • CD/R-ROM or DVD drive • 30 GB or greater available on drive C • Video card and monitor capable of 1280 × 1024 resolution Software • Adobe™ Flash™ Player 11 •Adobe Reader™ 9 • Microsoft .NET Framework 4.0 Extended • Microsoft Office 2007 • Microsoft Windows 7 SP1 (32-bit or 64-bit) • Thermo Foundation™ 3.0 vi FreeStyle User Guide Thermo Scientific Preface License Activation and Deactivation Use the Thermo Scientific Product Licensing wizard to activate or deactivate the FreeStyle application. To activate the FreeStyle application, you must have an activation code from Thermo Fisher Scientific. You must deactivate the FreeStyle application before you transfer the license to another computer. To open the Product Licensing wizard 1. Open the FreeStyle application. 2. Choose File > About FreeStyle to display the License Activation wizard. 3. Click Activate (Deactivate) to start the activation or deactivation processes, as applicable. Cautions and Special Notices Make sure you follow the cautions and special notices presented in this guide. Cautions and special notices appear in boxes; those concerning safety or possible system damage also have corresponding caution symbols. This guide uses the following types of cautions and special notices. CAUTION Highlights hazards to humans, property, or the environment. Each CAUTION notice is accompanied by an appropriate CAUTION symbol. IMPORTANT Highlights.
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