Document Outline

• Table of Contents
• How to Use This Guide
• 1 Data Explorer™ Basics
  • 1.1 Overview
  • 1.2 File Formats and Types
    • 1.2.1 Software Applications Compatibility
    • 1.2.2 Data (.DAT) File Format
  • 1.3 Parts of the DataExplorerWindow
  • 1.4 Customizing the Data Explorer Window
    • 1.4.1 Setting Default Values
    • 1.4.2 Customizing Processing andGraphicSettings (.SET)
    • 1.4.3 Customizing Toolbars
  • 1.5 Setting Graphic Options
    • 1.5.1 Changing Background Color
    • 1.5.2 Customizing Graphic Options
    • 1.5.3 Reverting to Previous Graphic Options
  • 1.6 Managing Files
    • 1.6.1 Converting .SPC File Format to .DAT File Format (Mariner Data Only)
    • 1.6.2 Converting Data from ProfiletoCentroid (Mariner Data Only)
    • 1.6.3 Converting to and ExportingASCIIData
    • 1.6.4 Importing a Trace in ASCII Format
    • 1.6.5 Extracting and Saving Information from .DAT, .RSD, and .RCD Files
    • 1.6.6 Copying from Data Files
• 2 Using Chromatogram andSpectrum Windows
  • 2.1 Opening and Closing Data Files
    • 2.1.1 Opening Data Files
    • 2.1.2 Displaying Mariner DAD Traces
    • 2.1.3 Displaying Voyager Chromatograms
    • 2.1.4 Viewing Read-Only Files
    • 2.1.5 Moving Between Open Files
    • 2.1.6 Closing Data Files
  • 2.2 Adjusting the Display Range
  • 2.3 Organizing Windows
  • 2.4 Manipulating Traces
    • 2.4.1 Zooming, Centering, andCustomizinga Trace
    • 2.4.2 Duplicating a Trace
    • 2.4.3 Dividing the Active Trace
    • 2.4.4 Adding Traces from the Same Data File to a Window
    • 2.4.5 Removing Traces
    • 2.4.6 Expanding and Linking Traces
    • 2.4.7 Recalling and Rearranging Traces (Processing History)
    • 2.4.8 Overlaying Traces
    • 2.4.9 Annotating Traces
    • 2.4.10 Viewing TraceLabels
    • 2.4.11 Printing Traces
  • 2.5 Working with Multiple Data Files
    • 2.5.1 Working with Separate Data Files
    • 2.5.2 Copying Traces from Multiple Data Files to a Window
  • 2.6 Saving, Opening, and Deleting.DAT Results
  • 2.7 Exporting, Opening, and Deleting .RCD and .RSD Results Files (MarinerData Only)
  • 2.8 Saving, Opening, and Deleting .SPC ResultsFiles (MarinerData Only)
• 3 Peak Detection andLabeling
  • 3.1 Overview
    • 3.1.1 Default Peak Detection
    • 3.1.2 The Resolution-Based Peak Detection Routine
  • 3.2 Peak Detection
    • 3.2.1 Strategy for Mariner Peak Detection
    • 3.2.2 Strategy for Voyager Peak Detection
    • 3.2.3 Setting Peak Detection Parameters
    • 3.2.4 Peak Detection ParameterDescriptions
    • 3.2.5 Charge State Determination and Examples
  • 3.3 Peak List
    • 3.3.1 Displaying the Peak List
    • 3.3.2 Inserting Peaks in the Peak List
    • 3.3.3 Saving the Peak List
    • 3.3.4 Sorting, Filtering, andPrintingthePeak List
  • 3.4 Deisotoping a Spectrum
  • 3.5 Peak Labeling
    • 3.5.1 Charge State Labels
    • 3.5.2 Setting Chromatogram andSpectrumPeak Labels
    • 3.5.3 Setting Custom Peak Labels
  • 3.6 Process that Occurs DuringPeak Detection, Centroiding, andIntegration
  • 3.7 Default Peak Detection Settings
• 4 Examining Chromatogram Data
  • 4.1 Overview
  • 4.2 Creating an ExtractedIonChromatogram
    • 4.2.1 Creating an Extracted Ion Chromatogram (XIC)
    • 4.2.2 Creating a Constant NeutralLoss(CNL) Chromatogram
  • 4.3 Creating an Extracted Absorbance Chromatogram (XAC) (Mariner Data Only)
  • 4.4 Noise Filtering/Smoothing
  • 4.5 Adding and Subtracting Raw Spectra Within a Data File
  • 4.6 Displaying MSMethodData (Mariner Data Only)
  • 4.7 Adjusting the Baseline
    • 4.7.1 Using Baseline Offset
    • 4.7.2 Using Baseline Correction
  • 4.8 Using UV Trace Offset (Mariner Data Only)
• 5 Examining Spectrum Data
  • 5.1 Overview
  • 5.2 Creating a Combined Spectrum
  • 5.3 Manual Calibration
    • 5.3.1 Overview of ManualCalibration
    • 5.3.2 Manually Calibrating
    • 5.3.3 Creating or Modifying a CalibrationReference File (.REF)
    • 5.3.4 Reverting to Instrument Calibration
    • 5.3.5 Hints for Calibrating Mariner Data
    • 5.3.6 Hints for Calibrating Voyager Data
  • 5.4 Automatic Calibration
    • 5.4.1 Overview of Automatic Calibration
    • 5.4.2 Importing and Specifying AutomaticCalibrationSettings
    • 5.4.3 Automatically Calibrating (MarinerData Only)
  • 5.5 Centroiding
  • 5.6 Mass Deconvolution (MarinerData Only)
  • 5.7 Noise Filtering/Smoothing
  • 5.8 Adjusting the Baseline
    • 5.8.1 Using Baseline Offset
    • 5.8.2 Using Baseline Correction
    • 5.8.3 Using Advanced Baseline Correction
  • 5.9 Truncating a Spectrum
  • 5.10 Converting to a Singly Charged Spectrum (Mariner Data Only)
  • 5.11 AutoSaturation Correction (MarinerData Only)
  • 5.12 Adding and Subtracting Raw or Processed Spectra from the Same or Different Data Files (Dual ...
• 6 UsingTools and Applications
  • 6.1 Using the Elemental CompositionCalculator
    • 6.1.1 Determining Elemental Composition
    • 6.1.2 Setting Limits
  • 6.2 Using the Isotope Calculator
  • 6.3 Using the MassResolutionCalculator
  • 6.4 Using the SignaltoNoiseRatio Calculator
  • 6.5 Using the IonFragmentationCalculator
  • 6.6 Using the Elemental TargetingApplication
  • 6.7 Using the Macro Recorder
    • 6.7.1 Before Using the Macro Recorder
    • 6.7.2 Recording a Macro
    • 6.7.3 Assigning Macros to Buttons
    • 6.7.4 Running a Macro
    • 6.7.5 Deleting a Macro
    • 6.7.6 Advanced Macro Editing
    • 6.7.7 Importing or Exporting Macros inDATAEXPLORER.VB6
    • 6.7.8 Running Macros Automatically WhenOpening and Closing Files
• 7 Data Explorer Examples
  • 7.1 Mariner Data Examples
    • 7.1.1 Improving SignalToNoiseRatio
    • 7.1.2 Deconvoluting and EvaluatingUnresolved Chromatographic Peaks
    • 7.1.3 Determining if a Peak isBackgroundNoise
  • 7.2 Voyager Data Examples
    • 7.2.1 Detecting and Labeling PartiallyResolvedPeaks
    • 7.2.2 Processing Before Calibrating to OptimizeMassAccuracy
    • 7.2.3 Detecting Peaks fromComplexDigests
• 8 Viewing VoyagerPSD Data
  • 8.1 Displaying PSD Data
  • 8.2 Applying Fragment Labels
  • 8.3 Calibrating a PSD Spectrum
    • 8.3.1 Checking Peak Detection
    • 8.3.2 Calibrating
    • 8.3.3 Creating PSD Calibration (.CAL) Files and Applying to Other Data Files
    • 8.3.4 Creating PSD CalibrationReference(.REF) Files
    • 8.3.5 Changing the Precursor Mass
• 9 Troubleshooting
  • 9.1 Overview
  • 9.2 General Troubleshooting
  • 9.3 Processing, Tools, and Applications Troubleshooting
  • 9.4 Calibration Troubleshooting
  • 9.5 Printing Troubleshooting
  • 9.6 Peak Detection and LabelingTroubleshooting
• A Warranty
• B Overview of Isotopes
  • B.1 Isotopes
  • B.2 Monoisotopic and Average Masses
  • B.3 Isotopes of Common Elements
• C Data Explorer Toolbox (Visual Basic Macros)
  • C.1 Overview
  • C.2 Preparing Data BeforeAccessing Macros
  • C.3 Accessing the Macros
  • C.4 Using the LadderSequencingToolbox
  • C.5 Using the Peptide FragmentationToolbox
  • C.6 Using the PolymerAnalysisToolbox
  • C.7 Using MS Fit/MS Tag Toolbox
• Index