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HP Data Explorer 4 manual 316

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Chapter 6 Using Tools and Applications

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6-46 Applied Biosystems

Contents

Data Explorer™ Software Page How to Use This Guide Chapter 1 Data Explorer™ Basics Chapter 2 Using Chromatogram and Spectrum Windows Chapter 3 Peak Detection and Labeling Chapter 4 Examining Chromatogram Data Chapter 5 Examining Spectrum Data Chapter 6 Using Tools and Applications Chapter 7 Data Explorer Examples Chapter 8 Viewing Voyager PSD Data Chapter 9 Troubleshooting Appendix C Data Explorer Toolbox Index Page How to Use This Guide Purpose of this guide Audience Structure of this guide Page Conventions Notes, Cautions Warnings, and Hints Related documentation Send us your comments Chapter 1Data Explorer™ Basics This chapter contains the following sections: 11.1 Overview Features Starting and exiting the software Default colors 1.2.1Software Applications Compatibility 1.2.2 Data (.DAT) File Format Mariner .SPC file 1 format Voyager .MS file format Extracting information from .DAT files Page Additional files types Page Page 1.3 Parts of the Data Explorer Window Toolbar and Spectrum windows Page Tabs for data files Data file names Output window Page Page Page Page Page Page Page 1.5.1 Changing Background Color 1 1.5.2 Customizing Graphic Options Setting colors Setting line widths Setting data cursors Setting traces in 1 Line or Vertical Bar mode Setting graphic compression 1.5.3 Reverting to Previous Graphic Options 1.6.1Converting .SPC File Format to .DAT File Format (Mariner Data Only) Converting Viewing file properties Searching file properties 1.6.2 Converting Data from Profile to Centroid (Mariner Data Only) 1 1.6.3 Converting to and Exporting ASCII Data 1.6.4 Importing a Trace in ASCII Format 1.6.5Extracting and Saving Information from .DAT, .RSD, and .RCD Files Saving .SET files 1.6.6 Copying from Data Files Copy trace data Copy displayed peaks Copy all peaks Copy mass list Page 2Using Chromatogram and Spectrum Windows Opening Data Files Page Page Page 2.1.2 Displaying Mariner DAD Traces Displaying Voyager Chromatograms Viewing Read-OnlyFiles 2.1.5 Moving Between Open Files Page Closing Data Files 2.2 Adjusting the Display Range Page 2.3 Organizing Windows Linking views Organizing windows 2.4.1Zooming, Centering, and Customizing a Trace 2.4.2 Duplicating a Trace 2.4.3Dividing the Active Trace 2.4.4Adding Traces from the Same Data File to a Window Setting the Replace mode Adding a trace Page Page 2.4.5 Removing Traces 2.4.6 Expanding and Linking Traces 2.4.7Recalling and Rearranging Traces (Processing History) Setting Processing History options 2.4.8 Overlaying Traces Overlaying traces in a single data file Changing the active trace Sequentially activating overlaid spectra Setting overlay attributes Page 2.4.9 Annotating Traces Annotating the trace 2.4.10 Viewing Trace Labels Spectrum trace labels Page 2.4.11 Printing Traces Page Dedicating a printer to landscape orientation Print Setup 2.5.1 Working with Separate Data Files 2.5.2 Copying Traces from Multiple Data Files to a Window Comparing copied traces 2.6 Saving, Opening, and Deleting .DAT Results Saving results for Opening results for .DAT files Deleting results for .DAT files Exporting results for .RCD and .RSD files Opening results for .RCD and Deleting results for .RCD and .RSD files Saving, Opening, and Deleting .SPC Results Files (Mariner Data Only) .SPC files Opening results: for .SPC files Deleting results for .SPC files Page 3Peak Detection and Labeling 3.1.1Default Peak Detection 3.1.2The Resolution-BasedPeak Detection Routine Detection ranges PSD peak detection for Voyager data 3.2.1Strategy for Mariner Peak Detection Page 3.2.2 Strategy for Voyager Peak Detection Page Page 3.2.3 Setting Peak Detection Parameters Page Setting Basic Settings (spectrum data) Page Page Setting Peak Processing parameters (spectrum data only) Setting Advanced Settings (spectrum data only) Resetting Basic Settings 3.2.4Peak Detection Parameter Descriptions Page Page Basic Settings (spectrum data only) Page Page Page Peak Processing parameters (spectrum data only) Page Advanced Settings (spectrum data only) Page Page Page 3.2.5Charge State Determination and Examples Page Page Page Charge state determination troubleshooting 3.3.1Displaying the Peak List Contents of peak list 3.3.2 Inserting Peaks in the Peak List 3.3.3 Saving the Peak List Importing and saving in Excel 3.3.4Sorting, Filtering and Printing the Peak List Page Printing the peak list Deleting items from the peak list 3.4 Deisotoping a Spectrum During peak deisotoping Page Requirements Deisotope function Page Page Page 3.5 Peak Labeling Factors affecting peak labeling Labeling peaks manually 3.5.1 Charge State Labels 3.5.2Setting Chromatogram and Spectrum Peak Labels Page Setting spectrum labels Page Page Deleting labels Labels not displayed Charge state not displayed 3.5.3 Setting Custom Peak Labels Page Page Page Applying user labels from .LBC or .LBS files Displaying user labels User labels not displayed 3.6Process that Occurs During Peak Detection, Centroiding, and Integration Peak detection Page Centroiding Integration 3.7 Default Peak Detection Settings Default .SET files provided Page Additional Voyager .SET files provided Page 4Examining Chromatogram Data 4.1 Overview Types of Mariner data Types of Voyager data Creating macros to combine processing functions Returning to the original trace 4.2.1Creating an Extracted Ion Chromatogram (XIC) Page Page Page 4.2.2Creating a Constant Neutral Loss (CNL) Chromatogram Labeling spectrum peaks with mass difference (optional) Page Page 4.3Creating an Extracted Absorbance Chromatogram (XAC) (Mariner Data Only) Page Page Page 4.4 Noise Filtering/Smoothing Page Page 4.5Adding and Subtracting Raw Spectra Within a Data File Adding and subtracting spectra Page Page 4.6Displaying MS Method Data (Mariner Data Only) In this section Example applications Displaying acquisition conditions and event tags Setting Trace Replace mode Filtering event tags Page Evaluating filtered traces Displaying additional filtered traces 4.7.1Using Baseline Offset Page 4.7.2 Using Baseline Correction 4.8Using UV Trace Offset (Mariner Data Only) Page Page 5Examining Spectrum Data 5.1 Overview Types of spectra you can display Voyager PSD spectra Page 5.2 Creating a Combined Spectrum 5.3.1 Overview of Manual Calibration Calibration references files (.REF) provided When to use manual calibration Accurate mass 5 measurements 5.3.2 Manually Calibrating Manually calibrating a single spectrum Page Page Page Page Page Page Page Exporting calibration constants (.CAL file) Applying new constants to additional files 5.3.3Creating or Modifying a Calibration Reference File (.REF) Definition .REF files provided Calibration reference file contents Creating and saving a calibration reference file Page Modifying a calibration reference file Specifying mass type for highly charged, narrow peaks 5.3.4 Reverting to Instrument Calibration Page 5.3.5 Hints for Calibrating Mariner Data 5.3.6 Hints for Calibrating Voyager Data 5.4.1 Overview of Automatic Calibration Automatic calibration for Mariner data Automatic calibration for Voyager data 5.4.2Importing and Specifying Automatic Calibration Settings Page Page Page Saving the .SET file 5.4.3Automatically Calibrating (Mariner Data Only) Calibration results Applying auto calibration settings to other files 5.5 Centroiding 5.6Mass Deconvolution (Mariner Data Only) Mass Deconvolution Page Page Converting to zero-charge Page 5.7 Noise Filtering/Smoothing Page Page 5.8.1Using Baseline Offset Page 5.8.2 Using Baseline Correction 5.8.3 Using Advanced Baseline Correction Page Page Page Page Page General guidelines for setting parameters Page 5.9 Truncating a Spectrum Truncating Page Page 5.10Converting to a Singly Charged Spectrum (Mariner Data Only) Page Page 5.11AutoSaturation Correction (Mariner Data Only) Function Hardware 5 requirements Effect on Mariner .RST files Trace label Page Page Page 6Using Tools and Applications 6.1.1Determining Elemental Composition Page Page Calculating 14. Click Calculate If no results are displayed 6.1.2 Setting Limits Page Adding new elements and setting limits Page Page Setting limits for other result types 6.2 Using the Isotope Calculator Using the Isotope Calculator Page Page Add and subtract examples Page Evaluating traces If results are not calculated 6.3 Using the Mass Resolution Calculator Calculating mass Page Page 6.4 Using the Signal-to-NoiseRatio Calculator Calculating signal-to-noiseratio Page 6.5 Using the Ion Fragmentation Calculator Using the Ion Fragmentation calculator Page Page Page Page Labeling peaks Creating a calibration reference file (.REF) 6.6 Using the Elemental Targeting Application Elemental application Page Displaying results 6.7.1Before Using the Macro Recorder Location of macros Displaying the macro toolbar Functions not supported Page 6.7.2 Recording a Macro 6.7.3 Assigning Macros to Buttons 6.7.4 Running a Macro If the macro contains a syntax error 6.7.5 Deleting a Macro 6.7.6 Advanced Macro Editing 6.7.7 Importing or Exporting Macros in DATAEXPLORER.VB6 Exporting 6.7.8 Running Macros Automatically When Opening and Closing Files Page 7Data Explorer Examples Improving Signal-To-NoiseRatio Page 7.1.2Deconvoluting and Evaluating Unresolved Chromatographic Peaks Creating extracted ion chromatograms Creating combined spectra Page 7.1.3Determining if a Peak is Background Noise Page Creating extracted ion chromatogram 7.2.1 Detecting and Labeling Partially Resolved Peaks Adjusting peak detection Page 7.2.2Processing Before Calibrating to Optimize Mass Accuracy Before calibrating Page Page 7.2.3Detecting Peaks from Complex Digests Page Page Page Page 8Viewing Voyager PSD Data 8.1 Displaying PSD Data Displaying the composite spectrum Advancing through segment traces Displaying multiple segment traces Page Redisplaying the composite spectrum How the composite spectrum is generated Page 8.2 Applying Fragment Labels Applying labels Page 8.3 Calibrating a PSD Spectrum When to use this procedure Overview of creating a PSD .CAL file 8.3.1 Checking Peak Detection 8.3.2 Calibrating Page Page Matching peaks automatically Selecting peaks manually Page Solving and plotting Selecting calibration peaks for optimum mass accuracy 8.3.3Creating PSD Calibration (.CAL) Files and Applying to Other Data Files 8.3.4Creating PSD Calibration Reference (.REF) Files Page 8.3.5 Changing the Precursor Mass Changing 9 Troubleshooting 9.1 Overview 9.2 General Troubleshooting Page Page 9.3Processing, Tools, and Applications Troubleshooting Page Page Page 9.4 Calibration Troubleshooting Page Page Page 9.5 Printing Troubleshooting 9.6Peak Detection and Labeling Troubleshooting Page Page Page Page Page Page Page A Warranty Warranty period effective date Warranty claims Warranty exceptions Warranties limitations Page BOverview of Isotopes B.1 Isotopes Isotopic pattern in mass spectra Isotope-limitedresolution Page B.2 Monoisotopic and Average Masses Page B.3 Isotopes of Common Elements This appendix includes: C.1 Overview Modifying the macros References required C.2 Preparing Data Before Accessing Macros C.3 Accessing the Macros C.4 Using the Ladder Sequencing Toolbox Running the macro Page Page Displaying the original labels C.5 Using the Peptide Fragmentation Toolbox Setup Pairs Sequence Page Correlation Displaying the original labels C.6 Using the Polymer Analysis Toolbox Using Polymer Analysis Page Calculations C.7 Using MS Fit/MS Tag Toolbox Preparing data before accessing Running MS Fit/MS tag Page Page Index

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