HP Data Explorer 4 manuals
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HP Data Explorer 4 Manual
447 pages 3.68 Mb
1 Data Explorer™ Software3 How to Use This GuideChapter 1 Data Explorer™ Basics 4 Chapter 2 Using Chromatogram and Spectrum Windows5 Chapter 3 Peak Detection and Labeling6 Chapter 4 Examining Chromatogram DataChapter 5 Examining Spectrum Data 7 Chapter 6 Using Tools and Applications8 Chapter 7 Data Explorer ExamplesChapter 8 Viewing Voyager PSD Data Chapter 9 Troubleshooting 9 Appendix C Data Explorer ToolboxIndex 11 How to Use This Guide15 Chapter1Data Explorer™ BasicsThis chapter contains the following sections: 16 11.1 Overview19 1.2.1Software Applications Compatibility1.2.2 Data (.DAT) File Format 25 1.3 Parts of theData Explorer Window 37 1.5.1 Changing Background Color38 1 1.5.2 Customizing Graphic Options43 1.5.3 Reverting to Previous Graphic Options44 1.6.1Converting .SPC File Format to .DAT File Format (Mariner Data Only)47 1.6.2 Converting Data fromProfile to Centroid (Mariner Data Only) 48 1 1.6.3 Converting to and Exporting ASCII Data49 1.6.4 Importing a Trace in ASCII Format50 1.6.5Extracting and Saving Information from .DAT, .RSD, and .RCD Files52 1.6.6 Copying from Data Files57 2Using Chromatogram and Spectrum Windows58 Opening Data Files62 2.1.2 Displaying Mariner DAD Traces63 Displaying Voyager ChromatogramsViewing Read-OnlyFiles 64 2.1.5 Moving Between Open Files66 Closing Data Files67 2.2 Adjusting the Display Range69 2.3 Organizing WindowsLinking views Organizing windows 70 2.4.1Zooming, Centering, and Customizing a Trace71 2.4.2 Duplicating a Trace2.4.3Dividing the Active Trace 72 2.4.4Adding Traces fromthe Same Data File to a Window 77 2.4.5 Removing Traces2.4.6 Expanding and Linking Traces 78 2.4.7Recalling and Rearranging Traces (Processing History)80 2.4.8 Overlaying Traces84 2.4.9 Annotating Traces86 2.4.10 Viewing Trace Labels89 2.4.11 Printing Traces92 2.5.1 Working with Separate Data Files93 2.5.2 Copying Traces fromMultiple Data Files to a Window 94 2.6 Saving, Opening, andDeleting .DAT ResultsSaving results for Opening results for .DAT files Deleting results for .DAT files 95 Exporting results for .RCD and.RSD files Opening results for .RCD and Deleting results for .RCD and .RSD files 96 Saving, Opening, and Deleting.SPC Results Files (Mariner Data Only) 99 3Peak Detection and Labeling100 3.1.1Default Peak Detection101 3.1.2The Resolution-BasedPeak Detection Routine104 3.2.1Strategy for Mariner Peak Detection106 3.2.2 Strategy for Voyager Peak Detection109 3.2.3 Setting Peak Detection Parameters117 3.2.4Peak Detection Parameter Descriptions130 3.2.5Charge StateDetermination and Examples 135 3.3.1Displaying the Peak List137 3.3.2 Inserting Peaks in the Peak List138 3.3.3 Saving the Peak List140 3.3.4Sorting, Filteringand Printing the Peak List 143 3.4 Deisotoping a Spectrum150 3.5 Peak Labeling165 3.6Process that Occurs During Peak Detection, Centroiding, and Integration169 3.7 Default Peak Detection Settings173 4Examining Chromatogram Data174 4.1 Overview177 4.2.1Creating an ExtractedIon Chromatogram (XIC) 181 4.2.2Creating a ConstantNeutral Loss (CNL) Chromatogram 185 4.3Creating an Extracted Absorbance Chromatogram (XAC) (Mariner Data Only)189 4.4 Noise Filtering/Smoothing192 4.5Adding and SubtractingRaw Spectra Within a Data FileAdding and subtracting spectra 195 4.6Displaying MS Method Data (Mariner Data Only)199 4.7.1Using Baseline Offset201 4.7.2 Using Baseline Correction202 4.8Using UV Trace Offset (Mariner Data Only)205 5Examining Spectrum Data206 5.1 OverviewTypes of spectra you can display Voyager PSD spectra 208 5.2 Creating a Combined Spectrum209 5.3.1 Overview of Manual Calibration211 5.3.2 Manually Calibrating221 5.3.3Creating or Modifying a Calibration Reference File (.REF)226 5.3.4 Reverting to Instrument Calibration228 5.3.5 Hints for Calibrating Mariner Data229 5.3.6 Hints for Calibrating Voyager Data230 5.4.1 Overview of Automatic Calibration233 5.4.2Importing and Specifying Automatic Calibration Settings238 5.4.3Automatically Calibrating (Mariner Data Only)240 5.5 Centroiding241 5.6Mass Deconvolution (Mariner Data Only)246 5.7 Noise Filtering/Smoothing249 5.8.1Using Baseline Offset251 5.8.2 Using Baseline Correction252 5.8.3 Using Advanced Baseline Correction260 5.9 Truncating a Spectrum263 5.10Converting to a Singly Charged Spectrum (Mariner Data Only)266 5.11AutoSaturation Correction (Mariner Data Only)271 6Using Tools and Applications272 6.1.1Determining Elemental Composition277 6.1.2 Setting Limits283 6.2 Using the Isotope Calculator290 6.3 Using theMass Resolution Calculator 293 6.4 Using the Signal-to-NoiseRatioCalculatorCalculating signal-to-noiseratio 295 6.5 Using theIon Fragmentation CalculatorUsing the Ion Fragmentation calculator 300 Labeling peaksCreating a calibration reference file (.REF) 301 6.6 Using the ElementalTargeting Application 304 6.7.1Before Using the Macro Recorder307 6.7.2 Recording a Macro308 6.7.3 Assigning Macros to Buttons309 6.7.4 Running a Macro311 6.7.5 Deleting a Macro312 6.7.6 Advanced Macro Editing313 6.7.7 Importing or Exporting Macrosin DATAEXPLORER.VB6 315 6.7.8 Running Macros AutomaticallyWhen Opening and Closing Files 317 7Data Explorer Examples318 Improving Signal-To-NoiseRatio320 7.1.2Deconvoluting and Evaluating Unresolved Chromatographic Peaks324 7.1.3Determining if a Peak is Background Noise327 7.2.1 Detecting and LabelingPartially Resolved Peaks 330 7.2.2Processing Before Calibrating to Optimize Mass Accuracy334 7.2.3Detecting Peaksfrom Complex Digests 339 8ViewingVoyager PSD Data 340 8.1 Displaying PSD Data346 8.2 Applying Fragment Labels348 8.3 Calibrating a PSD Spectrum363 9 Troubleshooting364 9.1 Overview365 9.2 General Troubleshooting368 9.3Processing, Tools, and Applications Troubleshooting372 9.4 Calibration Troubleshooting376 9.5 Printing Troubleshooting377 9.6Peak Detection and Labeling Troubleshooting385 A Warranty386 Warranty period effective dateWarranty claims Warranty exceptions 387 Warranties limitations389 BOverview of Isotopes390 B.1 Isotopes394 B.2 Monoisotopicand Average Masses 396 B.3 Isotopes of Common Elements398 C.1 OverviewModifying the macros References required 399 C.2 Preparing DataBefore Accessing Macros 400 C.3 Accessing the Macros401 C.4 Using theLadder Sequencing Toolbox 405 C.5 Using the PeptideFragmentation Toolbox 411 C.6 Using thePolymer Analysis Toolbox 414 C.7 Using MS Fit/MS Tag ToolboxPreparing data before accessing Running MS Fit/MS tag 417 Index
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