Thermo Fisher Scientific MSFileReader 3.0 Reference guide

Type
Reference guide
MSFileReader
Reference Guide
Software Version 3.0
XCALI-97542 Revision A April 2013
© 2013 Thermo Fisher Scientific Inc. All rights reserved.
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.
Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-
free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might
result from any use of this document, even if the information in the document is followed properly.
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 April 2013
Software version: MSFileReader Version 3.0
For Research Use Only. Not for use in diagnostic procedures.
Thermo Scientific MSFileReader Reference Guide iii
C
Chapter 1 Library Definitions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Enumerated Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Sample Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Controller Type. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Cutoff Type. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Chromatogram Type. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Chromatogram Operator. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Smoothing Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Error Codes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Chapter 2 Function Reference. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Open. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Close . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
GetFileName. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
GetCreatorID . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
GetVersionNumber. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
GetCreationDate. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
IsError. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
IsNewFile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
GetErrorCode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
GetErrorMessage. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
GetWarningMessage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
GetSeqRowNumber . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
GetSeqRowSampleType . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
GetSeqRowDataPath. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
GetSeqRowRawFileName . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
GetSeqRowSampleName . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
GetSeqRowSampleID . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
GetSeqRowComment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
GetSeqRowLevelName . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
GetSeqRowUserText. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
GetSeqRowInstrumentMethod . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
GetSeqRowProcessingMethod. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
GetSetRowCalibrationFile. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
GetSeqRowVial. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
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GetSeqRowInjectionVolume. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
GetSeqRowSampleWeight . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
GetSeqRowSampleVolume . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
GetSeqRowISTDAmount . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
GetSeqRowDilutionFactor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
GetSeqRowUserLabel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
InAcquisition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
GetNumberOfControllers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
GetNumberOfControllersOfType. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
GetControllerType . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
SetCurrentController . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
GetCurrentController . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
GetNumSpectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
GetNumStatusLog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
GetNumErrorLog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
GetNumTuneData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
GetMassResolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
GetExpectedRunTime. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
GetNumTrailerExtra. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
GetLowMass . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
GetHighMass . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
GetStartTime . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
GetEndTime . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
GetMaxIntegratedIntensity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
GetMaxIntensity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
GetFirstSpectrumNumber. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
GetLastSpectrumNumber . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
GetInstrumentID . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
GetInletID . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
GetErrorFlag . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
GetSampleVolume . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
GetSampleWeight . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
GetVialNumber . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
GetInjectionVolume . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
GetFlags . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
GetAcquisitionFileName. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
GetInstrumentDescription . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
GetAcquisitionDate. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
GetOperator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
GetComment1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
GetComment2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
GetSampleAmountUnits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
GetInjectionAmountUnits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
GetSampleVolumeUnits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
GetInstName. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
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GetInstModel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
GetInstSerialNumber . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
GetInstSoftwareVersion. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
GetInstHardwareVersion. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
GetInstFlags . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
GetInstNumChannelLabels. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
GetInstChannelLabel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
GetFilters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
ScanNumFromRT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
RTFromScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
GetFilterForScanNum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
GetFilterForScanRT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
GetMassListFromScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
GetMassListFromRT. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
GetNextMassListFromScanNum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
GetPrevMassListFromScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
GetMassListRangeFromScanNum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
GetMassListRangeFromRT. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
GetNextMassListRangeFromScanNum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
GetPrecursorInfoFromScanNum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
GetPrevMassListRangeFromScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
GetAverageMassList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
GetAveragedMassSpectrum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
GetSummedMassSpectrum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
GetLabelData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
GetAveragedLabelData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
GetNoiseData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
IsProfileScanForScanNum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
IsCentroidScanForScanNum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
GetScanHeaderInfoForScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
GetStatusLogForScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
GetStatusLogForRT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
GetStatusLogLabelsForScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
GetStatusLogLabelsForRT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
GetStatusLogValueForScanNum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
GetStatusLogValueForRT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
GetTrailerExtraForScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
GetTrailerExtraForRT. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
GetTrailerExtraLabelsForScanNum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
GetTrailerExtraLabelsForRT. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
GetTrailerExtraValueForScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
GetTrailerExtraValueForRT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
GetErrorLogItem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
GetTuneData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
GetTuneDataValue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
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GetTuneDataLabels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
GetNumInstMethods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
GetInstMethod . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
GetChroData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
GetMassListRangeFromScanNum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
GetMassListRangeFromRT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
GetPrecursorInfoFromScanNum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
RefreshViewOfFile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
ExtractInstMethodFromRaw. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
GetActivationTypeForScanNum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
GetMassAnalyzerTypeForScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
GetDetectorTypeForScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
GetScanTypeForScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
GetMSOrderForScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
GetPrecursorMassForScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
Version . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
IsThereMSData. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
HasExpMethod . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
GetFilterMassPrecision . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
GetStatusLogForPos . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
GetStatusLogPlottableIndex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
GetInstMethodNames. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
SetMassTolerance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
GetChros. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
GetSegmentedMassListFromRT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
GetSegmentedMassListFromScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
GetScanEventForScanNum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
GetSeqRowUserTextEx. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
GetSeqRowBarcode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
GetSeqRowBarcodeStatus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
GetSegmentAndScanEventForScanNum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
GetMassPrecisionEstimate. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
GetNumberOfMassRangesFromScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
GetNumberOfMSOrdersFromScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
GetNumberOfMassCalibratorsFromScanNum . . . . . . . . . . . . . . . . . . . . . . . . 193
GetCycleNumberFromScanNumber. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
GetUniqueCompoundNames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194
GetCompoundNameFromScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
GetAValueFromScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
GetBValueFromScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
GetFValueFromScanNum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
GetKValueFromScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
GetRValueFromScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
GetVValueFromScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
GetMSXMultiplexValueFromScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
Contents
Thermo Scientific MSFileReader Reference Guide vii
GetMassCalibrationValueFromScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
GetFullMSOrderPrecursorDataFromScanNum . . . . . . . . . . . . . . . . . . . . . . . 202
GetMassRangeFromScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
GetMassTolerance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206
GetNumberOfSourceFragmentsFromScanNum . . . . . . . . . . . . . . . . . . . . . . . 206
GetSourceFragmentValueFromScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
GetNumberOfSourceFragmentationMassRangesFromScanNum . . . . . . . . . . 208
GetSourceFragmentationMassRangeFromScanNum. . . . . . . . . . . . . . . . . . . . 209
GetIsolationWidthForScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 210
GetCollisionEnergyForScanNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
GetPrecursorRangeForScanNum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212
GetAllMSOrderData. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
GetChroByCompoundName . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
IsQExactive . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .275
Thermo Scientific MSFileReader Reference Guide 1
1
Library Definitions
MSFileReader is designed to support read access to Xcalibur™ raw files with a simple-to-use
Component Object Model (COM) standard without requiring installation of the Xcalibur
data system. It is designed to be used with C++-based applications, but since it is a COM
object, you can use any language that supports the COM interface.
Most of the functions described in this document are simple data access functions, but the
manual also includes a number of higher-level functions that extract and manipulate the data
in commonly used ways.
The description of each function includes the following information:
The function calling sequence
Return values
Definitions of both input and output parameters
An example using the function
The enumeration types described in this chapter standardize the handling of the following
components: the variables set by the instrument (or instruments) during acquisition, and
algorithms in the post-acquisition processing of data. Using these variables, you can determine
the instrument type (mass spectrometer, analog signal, and so on), and you can select the
number of the instrument (with a multiple instrument configuration) used to generate data to
the raw file. The described enumerators also handle access to selected channels from
multiple-channel data.
All of the described methods provide for systematic error checking and handling. This chapter
also provides descriptions related to the error codes returned as a result of trapped errors (see
Table 1 on page 6).
Contents
Enumerated Types
Error Codes
1 Library Definitions
Enumerated Types
2MSFileReader Reference Guide Thermo Scientific
Enumerated Types
Several functions expect or return a parameter of type “long” that generally defines a type
parameter.
Sample Type
Controller Type
Cutoff Type
Chromatogram Type
Chromatogram Operator
Smoothing Type
Sample Type
Sample type is returned in the GetSeqRowSampleType(…) function. The returned value has
the following meaning.
Value Sample type
0 Unknown
1Blank
2QC
3Standard Clear (None)
4 Standard Update (None)
5 Standard Bracket (Open)
6 Standard Bracket Start (multiple brackets)
7 Standard Bracket End (multiple brackets)
1 Library Definitions
Enumerated Types
Thermo Scientific MSFileReader Reference Guide 3
Controller Type
Controller type determines the type of data being accessed. This type is set or returned in the
calls to Get or Set controller information. This value has the following meaning.
Cutoff Type
Cutoff type is specified in calls to GetMassListXYZ(…). The purpose of this cutoff type is to
determine how the cutoff value is interpreted. This value has the following meaning.
Chromatogram Type
Chromatogram type is specified in the GetChroData(…) function. The value of this field
depends on the current controller and whether or not this is the first chromatogram type
parameter or the second chromatogram type parameter to this function. This value has the
following meaning:
For MS devices (chromatogram trace type values are in parentheses).
Value Controller type
–1 No device
0MS
1Analog
2A/D card
3PDA
4UV
Value Cutoff type
0 None (all values returned)
1 Absolute (in intensity units)
2 Relative (to base peak)
Chro type 1 Chro operator Chro type 2
Mass Range (0) + or – Mass Range (0)
TIC (1) Mass Range (0)
TIC (1) Base Peak (1)
Base Peak (2) + or – Mass Range (0)
1 Library Definitions
Enumerated Types
4MSFileReader Reference Guide Thermo Scientific
For PDA devices (chromatogram trace type values are in parentheses).
For UV devices (chromatogram trace type values are in parentheses).
Chro type 1 Chro operator Chro type 2
Wavelength Range (0) + or – Wavelength Range (0)
Total Scan (1) Wavelength Range (0)
Total Scan (1) Spectrum Maximum (1)
Spectrum Maximum (2) + or – Wavelength Range (0)
Chro type 1 Chro operator Chro type 2
Channel A (0) + or – Channel B (0)
Channel A (0) + or – Channel C (1)
Channel A (0) + or – Channel D (2)
Channel B (1) + or – Channel A (0)
Channel B (1) + or – Channel C (1)
Channel B (1) + or – Channel D (2)
Channel C (2) + or – Channel A (0)
Channel C (2) + or – Channel B (1)
Channel C (2) + or – Channel D (2)
Channel D (3) + or – Channel A (0)
Channel D (3) + or – Channel B (1)
Channel D (3) + or – Channel C (2)
1 Library Definitions
Enumerated Types
Thermo Scientific MSFileReader Reference Guide 5
For Analog devices (chromatogram trace type values are in parentheses).
For A/D card devices (chromatogram trace type values are in parentheses).
Chro type 1 Chro operator Chro type 2
Analog 1 (0) + or – Analog 2 (0)
Analog 1 (0) + or – Analog 3 (1)
Analog 1 (0) + or – Analog 4 (2)
Analog 2 (1) + or – Analog 1 (0)
Analog 2 (1) + or – Analog 3 (1)
Analog 2 (1) + or – Analog 4 (2)
Analog 3 (2) + or – Analog 1 (0)
Analog 3 (2) + or – Analog 2 (1)
Analog 3 (2) + or – Analog 4 (2)
Analog 4 (3) + or – Analog 1 (0)
Analog 4 (3) + or – Analog 2 (1)
Analog 4 (3) + or – Analog 3 (2)
Chro type 1 Chro operator Chro type 2
A/D Card Ch. 1 (0) + or – A/D Card Ch. 2 (0)
A/D Card Ch. 1 (0) + or – A/D Card Ch. 3 (1)
A/D Card Ch. 1 (0) + or – A/D Card Ch. 4 (2)
A/D Card Ch. 2 (1) + or – A/D Card Ch. 1 (0)
A/D Card Ch. 2 (1) + or – A/D Card Ch. 3 (1)
A/D Card Ch. 2 (1) + or – A/D Card Ch. 4 (2)
A/D Card Ch. 3 (2) + or – A/D Card Ch. 1 (0)
A/D Card Ch. 3 (2) + or – A/D Card Ch. 2 (1)
A/D Card Ch. 3 (2) + or – A/D Card Ch. 4 (2)
A/D Card Ch. 4 (3) + or – A/D Card Ch. 1 (0)
A/D Card Ch. 4 (3) + or – A/D Card Ch. 2 (1)
A/D Card Ch. 4 (3) + or – A/D Card Ch. 3 (2)
1 Library Definitions
Error Codes
6MSFileReader Reference Guide Thermo Scientific
Chromatogram Operator
The chromatogram operator type is specified in the GetChroData(…) function. This value
has the following meaning.
Smoothing Type
The smoothing type is specified in the GetChroData(…) function. This value has the
following meaning.
Error Codes
Value Chro operator
0 None (single chro only)
1 Minus (subtract chro 2 from chro 1)
2 Plus (add chro 1 and chro 2)
Value Smoothing type
0 None (no smoothing)
1Boxcar
2 Gaussian
Table 1. Error Codes (Sheet 1 of 6)
List of error codes
clNO_DATA_PRESENT = 0x80002101;
Does not typically indicate an error. This code may be returned
if optional data is not contained in the current raw file.
clSUCCESS = 0;
Indicates that the function call to the dll was processed without error.
clFAILED = 0x80004005;
Indicates that a general error has occurred. This code may be returned
whenever an error of indeterminate origin occurs.
1 Library Definitions
Error Codes
Thermo Scientific MSFileReader Reference Guide 7
clCOL_INDEX_OUT_OF_RANGE = 0x80002206;
Returns if the column index is out of the range.
clUSER_INDEX_OUT_OF_RANGE = 0x80002205;
Returns if the user index is out of the range.
clSEQ_ROW_INVALID = 0x80002204;
Returns if the sequence row is invalid.
clSEQ_FILE_READONLY = 0x80002203;
Returns if the sequence file is read only.
clNEW_FILE_READONLY = 0x80002202;
Returns if the file to be created is read only.
clSEQ_FILE_INVALID = 0x80002201;
Returns if the sequence file is invalid.
clINCOMPLETE_PARAMETER_SET = 0x80002117;
Returns if the parameter set is wrong.
clFILE_CRC_CHECK_FAILED = 0x80002116;
Returns if the CRC check fails.
clFILE_ALREADY_EXISTS = 0x80002115;
Returns if creating a file that already exists.
clFILE_NOT_FOUND = 0x80002114;
Returns if the file specified is not found.
Table 1. Error Codes (Sheet 2 of 6)
List of error codes
1 Library Definitions
Error Codes
8MSFileReader Reference Guide Thermo Scientific
clFILE_INVALID = 0x80002113;
Returns if no valid raw file is currently open.
clMETHOD_SCAN_EVENTS_NOT_INITIALIZED = 0x80002112;
Returns if the scan event in the method file is not initialized.
clTUNE_DATA_HEADER_NOT_INITIALIZED = 0x80002111;
Returns if the tune data header is not initialized.
clSTATUS_LOG_HEADER_NOT_INITIALIZED = 0x80002110;
Returns if the status log header is not initialized.
clTRAILER_HEADER_NOT_INITIALIZED = 0x8000210f;
Returns if the trailer header is not initialized.
clVIRUV_CREATION_FAILED = 0x8000210e;
Returns if the UV file creation fails.
clVIRUV_INVALID = 0x8000210d;
Returns if the UV data is invalid.
clVIRMS_CREATION_FAILED = 0x8000210c;
Returns if the MS data creation fails.
clVIRMS_INVALID = 0x8000210b;
Returns if the MS data is invalid.
clRAW_FILE_SAVE_FAILED = 0x8000210a;
Returns if the raw file saving fails.
Table 1. Error Codes (Sheet 3 of 6)
List of error codes
1 Library Definitions
Error Codes
Thermo Scientific MSFileReader Reference Guide 9
clRAW_FILE_CREATION_FAILED = 0x80002109;
Returns if the raw file creation fails.
clMASS_RANGE_FORMAT_INCORRECT = 0x80002108;
Returns if an incorrectly formatted mass range is passed in a function
call. Mass ranges should have the same format as entered in Xcalibur
applications.
clFILTER_FORMAT_INCORRECT = 0x80002107;
Returns if an incorrectly formatted scan filter is passed in a function
call. See the topic scan filters – format, definition in Xcalibur Help
for scan filter format specifications.
clOPERATION_NOT_SUPPORTED_ON_CURRENT_CONTROLLER = 0x80002105;
Returns if the requested action is inappropriate for the currently
defined controller. Some functions only apply to specific controllers.
This code might also be returned if a parameter is passed in a call that
is not supported by the current controller. For example, scan filters
may only be passed in calls when the current controller is of mass
spectrometer type (MS_DEVICE).
clCURRENT_CONTROLLER_INVALID = 0x80002104;
Returns if no current controller has been specified.
clRAW_FILE_INVALID = 0x80002103;
Returns if the raw file is invalid.
clNO_DATA_PRESENT = 0x80002101;
Returns if there is no data in the specified file.
clRAW_FILE_OPEN_FAIL = 0x80002100;
Returns if the raw file cannot be opened.
Table 1. Error Codes (Sheet 4 of 6)
List of error codes
1 Library Definitions
Error Codes
10 MSFileReader Reference Guide Thermo Scientific
clINSTMETHOD_NOT_EMBEDDED = 0x80002099;
Returns if there is no emebedded instrument method in the raw file.
clRAW_FILE_TOOOLDVER = 0x80002098;
Returns if the raw file version is so old that it is not supported by Xcalibur.
clINSTMETHOD_CREATE_FAIL = 0x80002097;
Returns if the instrument method file creation fails.
const long clMPE_SCANFILTER = 0x80002117;
Empty scan filters.
const long clMPE_EMPTY_SCANHEADER = 0x80002118;
Scan header is empty.
const long clMPE_FILTER = 0x80002119;
The filter format is not supported.
const long clRAW_FILE_OPEN_FAIL = 0x80002100;
Failed to open raw file.
const long clMPE_RESOLUTIONERROR = 0x80002101;
The resolution value is wrong with the raw file.
const long clINSTMETHOD_NOT_EMBEDDED = 0x80002099;
In the raw file, the instrument method is not embedded.
const long clRAW_FILE_TOOOLDVER = 0x80002098;
The version of the raw file is too old or is not supported.
const long clINSTMETHOD_CREATE_FAIL = 0x80002097;
Table 1. Error Codes (Sheet 5 of 6)
List of error codes
1 Library Definitions
Error Codes
Thermo Scientific MSFileReader Reference Guide 11
Failed to create instrument method extracted from the raw file.
const long clMPE_INVALID_SCANHEADER = 0x8000211a;
Returns when the scan header is invalid.
const long clMPE_INVALID_SCANTRAIL = 0x8000211b;
Returns when the scan trail data is invalid.
const long clMPE_INVALID_RAWDATA = 0x8000211c;
Returns when the raw data is invalid.
const long clMPE_INVALID_LABELDATA = 0x8000211d;
Returns when the label data is invalid.
Table 1. Error Codes (Sheet 6 of 6)
List of error codes
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Thermo Fisher Scientific MSFileReader 3.0 Reference guide

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