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™
Data Explorer Software
Version 4 Series Software
User Guide
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© Copyright 2001, Applied Biosystems. All rights reserved. For Research Use Only. Not for use in diagnostic procedures. Information in this document is subject to change without notice. Applied Biosystems assumes no responsibility for any errors that may appear in this document. This document is believed to be complete and accurate at the time of publication. In no event shall Applied Biosystems be liable for incidental, special, multiple, or consequential damages in connection with or arising
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Table of Contents Table of Contents How to Use This Guide .............................................................. xi Chapter 1 Data Explorer™ Basics 1.1 Overview .............................................................................. 1-2 1.2 File Formats and Types ............................................................ 1-5 1.2.1 Software Applications Compatibility ....................................... 1-5 1.2.2 Data (.DAT) File Format .......................................
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Table of Contents Chapter 2 Using Chromatogram and Spectrum Windows 2.1 Opening and Closing Data Files ................................................. 2-2 2.1.1 Opening Data Files ................................................................ 2-2 2.1.2 Displaying Mariner DAD Traces ............................................. 2-6 2.1.3 Displaying Voyager Chromatograms ...................................... 2-7 2.1.4 Viewing Read-Only Files ...................................................
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Table of Contents Chapter 3 Peak Detection and Labeling 3.1 Overview .............................................................................. 3-2 3.1.1 Default Peak Detection .......................................................... 3-2 3.1.2 The Resolution-Based Peak Detection Routine ...................... 3-3 3.2 Peak Detection....................................................................... 3-6 3.2.1 Strategy for Mariner Peak Detection ....................................... 3-6
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Table of Contents Chapter 4 Examining Chromatogram Data 4.1 Overview .............................................................................. 4-2 4.2 Creating an Extracted Ion Chromatogram ..................................... 4-5 4.2.1 Creating an Extracted Ion Chromatogram (XIC) ..................... 4-5 4.2.2 Creating a Constant Neutral Loss (CNL) Chromatogram ........ 4-9 4.3 Creating an Extracted Absorbance Chromatogram (XAC) (Mariner Data Only) ......................................
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Table of Contents 5.5 Centroiding .......................................................................... 5-36 5.6 Mass Deconvolution (Mariner Data Only)..................................... 5-37 5.7 Noise Filtering/Smoothing ........................................................ 5-42 5.8 Adjusting the Baseline ............................................................ 5-45 5.8.1 Using Baseline Offset ...........................................................5-45 5.8.2 Using Baseline Cor
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Table of Contents Chapter 7 Data Explorer Examples 7.1 Mariner Data Examples ............................................................ 7-2 7.1.1 Improving Signal-To-Noise Ratio ............................................ 7-2 7.1.2 Deconvoluting and Evaluating Unresolved Chromatographic Peaks .......................................7-4 7.1.3 Determining if a Peak is Background Noise ............................ 7-8 7.2 Voyager Data Examples .....................................................
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Table of Contents Appendix A Warranty Information........................................ A-1 Appendix B Overview of Isotopes........................................ B-1 Appendix C Data Explorer Toolbox (Visual Basic Macros) ......................................................... C-1 C.1 Overview .............................................................................. C-2 C.2 Preparing Data Before Accessing Macros ..................................... C-3 C.3 Accessing the Macros ......
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Table of Contents x Applied Biosystems
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How to Use This Guide 1 How to Use This Guide ™ Purpose of The Applied Biosystems Data Explorer Software User’s Guide describes processing and analyzing data with the this guide Data Explorer software. You can use the Data Explorer software to analyze data collected on: ™ Mariner Workstations with Version 3.0 and later software ™ ™ Voyager -DE Biospectrometry Workstations with Version 5.0 and later software Audience This guide is intended for novice and experienced Mariner or Voyager
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How to Use This Guide 1 Chapter/Appendix Content Chapter 5, Examining Spectrum Describes processing and analyzing mass Data spectral data. Chapter 6, Using Tools and Describes how to generate results using Applications several tools and applications: the Centroid calculator, Elemental Composition calculator, Isotope calculator, Mass Resolution calculator, Ion Fragmentation calculator and Signal-to-Noise calculator. Also describes using the Macro Recorder and the Elemental Targeting Appli
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How to Use This Guide 1 Conventions This guide uses the following conventions to make text easier to understand. Bold indicates user action. For example: Type 0 and press Enter for the remaining fields. Italic text denotes new or important words, and is also used for emphasis. For example: Before analyzing, always prepare fresh matrix. Notes, Cautions, A note provides important information to the operator. For example: Warnings, and Hints NOTE: If you are prompted to insert the boot disk
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How to Use This Guide 1 Related The related documents shipped with your system include: ™ documentation Mariner Workstation User’s Guide—Use this document to learn detailed information about the Mariner Workstation. ™ Voyager -DE Biospectrometry Workstation User’s Guide—Use this document to learn detailed information about the Voyager-DE Workstation. Printer documentation (depends on the printer you purchase)—Use this documentation to set up and service your printer. ® ® Microsoft
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Chapter 1 ™ 1 Data Explorer Basics This chapter contains the following sections: 1.1 Overview ................................................... 1-2 1.2 File Formats and Types ............................. 1-5 1.3 Parts of the Data Explorer Window .......... 1-11 1.4 Customizing the Data Explorer Window ... 1-17 1.5 Setting Graphic Options .......................... 1-23 1.6 Managing Files ........................................ 1-30 ™ Data Explorer Software User’s Guide 1-1
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Chapter 1 Data Explorer™ Basics 1.1 Overview 1 ™ Description The Data Explorer Version 4.0 processing software is graphical software that you use to analyze, calibrate, and report data. You can use the Data Explorer software to analyze data collected on: ™ Mariner Workstations ™ ™ Voyager -DE Biospectrometry Workstations NOTE: Application systems that automatically acquire and process data, such as Mariner High Throughput ™ Analysis Option (CombiSolve ) and Proteomics ™ Solution
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Overview Starting and To start the Data Explorer software from the Windows NT desktop, double-click the Data Explorer icon on the desktop. exiting the 1 The Data Explorer window opens. software The Data Explorer window is blank with only a few menus displayed until you open a data file. Figure 1-1 shows the Data Explorer main window with a Mariner data file open. Figure 1-2 shows the Data Explorer main window with a Voyager data file open. To exit the software, select Exit from the File
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Chapter 1 Data Explorer™ Basics 1 Figure 1-2 Data Explorer Window with Voyager Data Default colors The default colors are different for Mariner and Voyager: Mariner—Black background, yellow traces, and green labels Voyager—White background, blue traces, and red labels You can customize the default colors as needed. See Section 1.5.1, Changing Background Color. NOTE: For consistency, all Mariner and Voyager screen examples in the following sections of this User’s Guide are shown wit
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File Formats and Types 1.2 File Formats and Types 1 This section describes: Software applications compatibility Data (.DAT) file format 1.2.1 Software Applications Compatibility You can use the Data Explorer Macro Recorder function to create Visual Basic scripts to automate tasks. You can also use the Visual Basic Editor directly to create more complex programs customized to suit your needs. For more information, see Section 6.7, Using the Macro Recorder. Additionally, you can convert
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Chapter 1 Data Explorer™ Basics Mariner .SPC file In Mariner software versions earlier than version 3.0, data files are stored in .SPC format. You can view and process .SPC format 1 files in Data Explorer, or you can convert these files to .DAT format. For information about the differences between the ™ .DAT and the .SPC formats, see the Mariner Workstation User’s Guide. Voyager .MS file In Voyager software versions earlier than version 5.0, data files are stored in .MS, .MSF, .MSA, an
