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Freestyle 1.4 – User Guide

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Freestyle 1.4 – User Guide Thermo FreeStyle User Guide Software Version 1.4 XCALI-97962 Revision A February 2018 © 2018 Thermo Fisher Scientific Inc. All rights reserved. Foundation, FreeStyle, and mzVault are trademarks, and Orbitrap, Thermo Scientific, TSQ Endura, TSQ Quantiva, 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 Incorporated. Microsoft, Windows, Outlook, and Excel are registered trademarks of Microsoft Corporation. NIST is a registered trademark of the National Institute of Standards and Technology. mzCloud is a registered trademark of HighChem, Ltd. in Slovakia. 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. 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 February 2018 Software version: (Thermo) Foundation 3.1 SP4 and later; FreeStyle 1.4 and later For Research Use Only. Not for use in diagnostic procedures. C Contents Preface . ix Related Documentation . x System Requirements . x Special Notices . .xi Contacting Us . xii Chapter 1 Introduction . .1 Mass Spectra . 1 Base Peak. 2 Neutral Losses . 3 Effect of Ionization Modes . 4 Adduct Formation. 5 Effect of Isotopes. 6 Isotope Patterns in High-Resolution Data . 6 Analysis Modes for the Mass Spectrometer . 7 Full Scan . 7 Selected Ion Monitoring (SIM) . 7 MS/MS . 8 Qualitative Analysis Tools . 8 New Features. 9 Chapter 2 Using the FreeStyle Window . .11 Startup Window . 12 File Menu . 12 Communicator Bar . 14 Opening Raw Data Files or Sequence Files . 15 Factory Default Layout . 16 Creating, Positioning, Previewing, and Closing Workspaces . 17 Selecting the Columns to Display in a View or Dialog Box with Tabular Data . 20 Saving and Applying Layout Templates. 21 Restoring the Default Settings . 22 Zooming In and Out of a Graphical View. 23 Adding Text and Graphic Annotations to a Graphical View . 24 Thermo Scientific FreeStyle User Guide iii Contents Copying, Exporting, and Printing Graphical Images and Tabular Data. 26 Copying an Image of a Graphical View to the Clipboard. 26 Copying Tabular Data to the Clipboard . 26 Exporting or Printing the Contents of a View or Workspace . 27 Setting FreeStyle as the Default Data Visualization Application . 28 Toolbars . 29 Workspace Options Toolbar . 29 Workspace Processing Toolbar . 33 Display Options Toolbar. 33 Zoom Options Toolbar. 33 Text and Graphic Annotation Toolbar . 34 Views. 36 Arranging Views . 38 Using the Pointer to Update the Timebase or Rescale a Graph . 40 Selecting How You Open the Floating Toolboxes . 40 Info Bar Pages . 41 Chapter 3 Reviewing Chromatographic Data. .43 Adding and Deleting Chromatogram Traces . 44 Adding Chromatogram Traces Manually. 44 Adding Chromatogram Traces with the Auto Filter Feature . 46 Deleting Chromatogram Traces . 47 Defining the Range of a Chromatogram Trace . 48 Defining Chromatogram Ranges Manually . 49 Setting Up Instrument Status Traces with the MS Trending Feature. 52 Defining Chromatogram Ranges by Using a Spreadsheet File . 53 Using the Scan Filters Page to Display a Filtered Chromatogram . 54 Setting Up the Display Options for a Chromatogram Trace . 54 Formatting Chromatogram Plots. 55 Labeling Chromatogram Peaks or Local Maxima. 56 Normalizing Chromatogram Traces . 57 Applying Local Normalization . 57 Applying Global Normalization . 58 Turning Off Normalization . 59 Changing the Y-Axis Range . 61 Changing the Y-Axis Scale of the Chromatogram View. 62 Automatically Detecting and Integrating Chromatographic Peaks. 63 Selecting the Manual Noise Region for the Genesis and ICIS Algorithms . 66 Manually Adding and Deleting Chromatographic Peaks . 67 Manually Adding Chromatographic Peaks. 67 Deleting Chromatographic Peaks . 68 Working with Sequences . 69 Creating a New Sequence . 69 Comparing Chromatogram Traces in a Sequence . 70 iv FreeStyle User Guide Thermo Scientific Contents Chromatogram-Specific Toolbars . 71 Chromatogram – Display Options Toolbar. 71 Chromatogram – Workspace Processing Toolbar . 76 Sequence Toolbar . 77 Chromatogram-Specific Views . 78 Chromatogram View. 78 Chromatogram Ranges View. 80 Peaks List View . 87 Chromatogram View Toolbox. 91 Chromatogram-Specific Pages in the Info Bar . 93 Detector Type Page ..
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