Thermo Xcalibur Qual Browser User Guide Software Version 3.1 XCALI-97617 Revision A August 2014 © 2014 Thermo Fisher Scientific Inc. All rights reserved. Accela, Xcalibur, and Q Exactive are registered trademarks of Thermo Fisher Scientific Inc. in the United States. Microsoft, Windows, and Excel are registered trademarks of Microsoft Corporation in the United States and other countries. Adobe, Acrobat, and Reader are registered trademarks of Adobe Systems Incorporated in the United States and other countries. 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, August 2014 Software version: Xcalibur 3.1 and later For Research Use Only. Not for use in diagnostic procedures. C Contents Preface . ix About This Guide. .ix Related Documentation . x Safety and Special Notices . .xi Contacting Us . xii Chapter 1 Introduction . .1 Understanding Mass Spectra . 1 Base Peak. 2 Neutral Losses . 2 Effect of Ionization Modes . 3 Adduct Formation. 5 Effect of Isotopes. 5 Analysis Modes for the Mass Spectrometer . 6 Full Scan . 6 Selected Ion Monitoring (SIM) . 7 MS/MS . 7 Chapter 2 Using the Qual Browser Window . .9 Opening the Qual Browser Window . 10 Using the Qual Browser Toolbars . 11 Displaying Toolbars . 12 Customizing the Toolbar. 13 Using the Info Bar. 16 Working with Windows . 17 Identifying Inactive, Active, and Pinned Cells . 18 Changing the Cell State. 19 Using the Cursor. 20 Viewing Data Files in Qual Browser . 21 Opening Single Raw Files in Qual Browser . 22 Opening a Sequence Set of Raw Data Files in Qual Browser . 23 Opening and Viewing Result Files in Qual Browser . 26 Thermo Scientific Xcalibur Qual Browser User Guide iii Contents Working with Cells . 29 Making a View Active . 29 Inserting and Deleting Cells . 31 Adjusting the Cell Size. 32 Amplifying Regions of a Plot. 34 Adding Text to a Plot . 35 Adding Graphics to a Plot . 37 Removing Text and Graphics from a Plot . 39 Opening or Changing Views in Cells. 40 Scaling a Plot. 42 Managing Layouts. 43 Creating and Saving a Layout . 43 Opening and Applying a Layout . 44 Displaying Layout Summary Information . 45 Using the Cell Information Page . 46 Chromatogram Information . 47 Spectrum Information. 48 Setting the Global Mass Options for the Qual Browser Window. 48 Chapter 3 Using Views Interactively . .51 Selecting a Point on a Plot. 52 Selecting a Point on a Plot: Example 1 . 54 Selecting a Point on a Plot: Example 2 . 55 Selecting a Point on a Plot: Example 3 . 55 Selecting a One-Dimensional Range on a Plot. 56 Selecting a One-Dimensional Range: Example 1 . 58 Selecting a One-Dimensional Range: Example 2 . 59 Selecting a Two-Dimensional Range on a Plot . 60 Using Scan Filters . 62 Scan Filter Format. 64 Applying a Scan Filter to a Plot . 67 Displaying Multiple Magnifications of a Plot . 69 Chapter 4 Working with a Chromatogram View . .73 Inserting and Deleting Chromatogram Plots . 74 Setting the Chromatogram Ranges and Processing Options . 74 Setting Chromatogram Ranges . 74 Setting Automatic Processing for Chromatograms. 77 Adding Plots to a Chromatogram View with the Autofilter Command . 81 iv Xcalibur Qual Browser User Guide Thermo Scientific Contents Setting the Chromatogram Display Options . 82 Setting the Chromatogram Axis Options. 82 Setting the Chromatogram Color Options . 84 Setting the Chromatogram Label Options. 85 Setting the Chromatogram Normalization Options. 86 Setting the Chromatogram Style Options . 88 Detecting Peaks. 89 Automatic Detection of One Plot . 90 Automatic Detection of All Plots. 90 Manual Detection . 90 Reviewing the Effect of Different Peak Detection Settings . 92 Chapter 5 Working with a Spectrum View. .95 Setting Spectrum Display Options . 95 Setting the Spectrum Axis Options . ..