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Copy pathmqpar_for_PS_Script.xml
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mqpar_for_PS_Script.xml
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<?xml version="1.0" encoding="utf-8"?>
<MaxQuantParams xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" aifSilWeight="0" aifIsoWeight="0" aifTopx="0" aifCorrelation="0" aifCorrelationFirstPass="0" aifMinMass="0" aifMsmsTol="0" aifSecondPass="false" aifIterative="false" aifThresholdFdr="0" writeMsScansTable="true" writeMsmsScansTable="true" writePasefMsmsScansTable="true" writeAccumulatedPasefMsmsScansTable="true" writeMs3ScansTable="true" writeAllPeptidesTable="true" writeMzRangeTable="true" writeMzTab="false" disableMd5="false" connected="false" cacheBinInds="true" etdIncludeB="false" complementaryTmtCollapseNplets="true" connectedScore0="0.800000011920929" connectedScore1="0.800000011920929" connectedScore2="0.800000011920929">
<name>Session1</name>
<maxQuantVersion>1.6.0.16</maxQuantVersion>
<tempFolder />
<numThreads>4</numThreads>
<sendEmail>false</sendEmail>
<fixedCombinedFolder />
<ionCountIntensities>false</ionCountIntensities>
<verboseColumnHeaders>false</verboseColumnHeaders>
<fullMinMz>-1.7976931348623157E+308</fullMinMz>
<fullMaxMz>1.7976931348623157E+308</fullMaxMz>
<calcPeakProperties>true</calcPeakProperties>
<showCentroidMassDifferences>false</showCentroidMassDifferences>
<showIsotopeMassDifferences>false</showIsotopeMassDifferences>
<filePaths>
<string>C:\Users\G.Huffman\Documents\RAW_FILES\QC38b\180123AMRSAM03554_SC_QC38B.raw</string>
</filePaths>
<experiments>
<string />
</experiments>
<fractions>
<short>32767</short>
</fractions>
<ptms>
<boolean>false</boolean>
</ptms>
<paramGroupIndices>
<int>0</int>
</paramGroupIndices>
<parameterGroups>
<parameterGroup>
<maxCharge>7</maxCharge>
<minPeakLen>2</minPeakLen>
<useMs1Centroids>false</useMs1Centroids>
<useMs2Centroids>false</useMs2Centroids>
<cutPeaks>true</cutPeaks>
<gapScans>1</gapScans>
<minTime>NaN</minTime>
<maxTime>NaN</maxTime>
<matchType>MatchFromAndTo</matchType>
<centroidMatchTol>8</centroidMatchTol>
<centroidMatchTolInPpm>true</centroidMatchTolInPpm>
<centroidHalfWidth>35</centroidHalfWidth>
<centroidHalfWidthInPpm>true</centroidHalfWidthInPpm>
<valleyFactor>1.4</valleyFactor>
<isotopeValleyFactor>1.2</isotopeValleyFactor>
<advancedPeakSplitting>false</advancedPeakSplitting>
<intensityThreshold>0</intensityThreshold>
<msInstrument>0</msInstrument>
<intensityDetermination>0</intensityDetermination>
<labelMods>
<string />
</labelMods>
<reQuantify>false</reQuantify>
<lfqSkipNorm>false</lfqSkipNorm>
<lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
<lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
<lfqMaxFeatures>100000</lfqMaxFeatures>
<neucodeMaxPpm>0</neucodeMaxPpm>
<neucodeResolution>0</neucodeResolution>
<neucodeResolutionInMda>false</neucodeResolutionInMda>
<neucodeInSilicoLowRes>false</neucodeInSilicoLowRes>
<fastLfq>true</fastLfq>
<lfqRestrictFeatures>false</lfqRestrictFeatures>
<lfqMinRatioCount>2</lfqMinRatioCount>
<useNormRatiosForHybridLfq>true</useNormRatiosForHybridLfq>
<maxLabeledAa>0</maxLabeledAa>
<maxNmods>3</maxNmods>
<maxMissedCleavages>2</maxMissedCleavages>
<multiplicity>1</multiplicity>
<enzymes>
<string>Trypsin/P</string>
</enzymes>
<enzymesFirstSearch />
<useEnzymeFirstSearch>false</useEnzymeFirstSearch>
<useVariableModificationsFirstSearch>false</useVariableModificationsFirstSearch>
<variableModifications>
<string>Oxidation (M)</string>
<string>Acetyl (Protein N-term)</string>
</variableModifications>
<useMultiModification>false</useMultiModification>
<multiModifications />
<isobaricLabels>
<string>TMT10plex-Nter126C</string>
<string>TMT10plex-Nter127N</string>
<string>TMT10plex-Nter127C</string>
<string>TMT10plex-Nter128N</string>
<string>TMT10plex-Nter128C</string>
<string>TMT10plex-Nter129N</string>
<string>TMT10plex-Nter129C</string>
<string>TMT10plex-Nter130N</string>
<string>TMT10plex-Nter130C</string>
<string>TMT10plex-Nter131N</string>
<string>TMT10plex-Lys126C</string>
<string>TMT10plex-Lys127N</string>
<string>TMT10plex-Lys127C</string>
<string>TMT10plex-Lys128N</string>
<string>TMT10plex-Lys128C</string>
<string>TMT10plex-Lys129N</string>
<string>TMT10plex-Lys129C</string>
<string>TMT10plex-Lys130N</string>
<string>TMT10plex-Lys130C</string>
<string>TMT10plex-Lys131N</string>
</isobaricLabels>
<neucodeLabels />
<variableModificationsFirstSearch />
<hasAdditionalVariableModifications>false</hasAdditionalVariableModifications>
<additionalVariableModifications />
<additionalVariableModificationProteins />
<doMassFiltering>true</doMassFiltering>
<firstSearchTol>20</firstSearchTol>
<mainSearchTol>4.5</mainSearchTol>
<searchTolInPpm>true</searchTolInPpm>
<isotopeMatchTol>2</isotopeMatchTol>
<isotopeMatchTolInPpm>true</isotopeMatchTolInPpm>
<isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
<theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
<recalibrationInPpm>true</recalibrationInPpm>
<intensityDependentCalibration>false</intensityDependentCalibration>
<minScoreForCalibration>70</minScoreForCalibration>
<matchLibraryFile>false</matchLibraryFile>
<libraryFile />
<matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
<matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
<matchLabelTimeTolMin>0</matchLabelTimeTolMin>
<reporterMassTolerance>0.01</reporterMassTolerance>
<reporterPif>0</reporterPif>
<filterPif>false</filterPif>
<reporterFraction>0</reporterFraction>
<reporterBasePeakRatio>0</reporterBasePeakRatio>
<timsHalfWidth>0</timsHalfWidth>
<timsStep>0</timsStep>
<timsResolution>0</timsResolution>
<timsMinMsmsIntensity>0</timsMinMsmsIntensity>
<timsRemovePrecursor>true</timsRemovePrecursor>
<timsIsobaricLabels>false</timsIsobaricLabels>
<timsCollapseMsms>true</timsCollapseMsms>
<crosslinkSearch>false</crosslinkSearch>
<crosslinkOnlyIntraProtein>false</crosslinkOnlyIntraProtein>
<crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
<crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
<crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
<crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
<crosslinkUseSeparateFasta>false</crosslinkUseSeparateFasta>
<crosslinkFastaFiles />
<crosslinkMode>PeptidesWithCleavedLinker</crosslinkMode>
<lcmsRunType>Reporter ion MS2</lcmsRunType>
<lfqMode>0</lfqMode>
<enzymeMode>0</enzymeMode>
<complementaryReporterType>0</complementaryReporterType>
<neucodeIntensityMode>0</neucodeIntensityMode>
<enzymeModeFirstSearch>0</enzymeModeFirstSearch>
</parameterGroup>
</parameterGroups>
<fixedModifications />
<fastaFiles>
<string>C:\Users\G.Huffman\Documents\RAW_FILES\SwissProt_human_09042017.fasta</string>
</fastaFiles>
<fastaFilesProteogenomics />
<fastaFilesFirstSearch />
<fixedSearchFolder />
<andromedaCacheSize>350000</andromedaCacheSize>
<advancedRatios>true</advancedRatios>
<pvalThres>0.005</pvalThres>
<neucodeRatioBasedQuantification>true</neucodeRatioBasedQuantification>
<neucodeStabilizeLargeRatios>true</neucodeStabilizeLargeRatios>
<rtShift>false</rtShift>
<separateLfq>false</separateLfq>
<lfqStabilizeLargeRatios>true</lfqStabilizeLargeRatios>
<lfqRequireMsms>true</lfqRequireMsms>
<decoyMode>revert</decoyMode>
<boxCarMode>all</boxCarMode>
<includeContaminants>false</includeContaminants>
<maxPeptideMass>4600</maxPeptideMass>
<epsilonMutationScore>true</epsilonMutationScore>
<mutatedPeptidesSeparately>true</mutatedPeptidesSeparately>
<proteogenomicPeptidesSeparately>true</proteogenomicPeptidesSeparately>
<minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>
<minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>
<minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>
<minScoreModifiedPeptides>40</minScoreModifiedPeptides>
<secondPeptide>false</secondPeptide>
<matchBetweenRuns>false</matchBetweenRuns>
<matchUnidentifiedFeatures>false</matchUnidentifiedFeatures>
<matchBetweenRunsFdr>false</matchBetweenRunsFdr>
<dependentPeptides>false</dependentPeptides>
<dependentPeptideFdr>0</dependentPeptideFdr>
<dependentPeptideMassBin>0</dependentPeptideMassBin>
<msmsConnection>false</msmsConnection>
<ibaq>false</ibaq>
<top3>false</top3>
<independentEnzymes>false</independentEnzymes>
<useDeltaScore>false</useDeltaScore>
<splitProteinGroupsByTaxonomy>false</splitProteinGroupsByTaxonomy>
<taxonomyLevel>Species</taxonomyLevel>
<avalon>false</avalon>
<nModColumns>3</nModColumns>
<ibaqLogFit>false</ibaqLogFit>
<razorProteinFdr>true</razorProteinFdr>
<deNovoSequencing>false</deNovoSequencing>
<deNovoVarMods>true</deNovoVarMods>
<massDifferenceSearch>false</massDifferenceSearch>
<minPepLen>6</minPepLen>
<peptideFdr>1</peptideFdr>
<proteinFdr>1</proteinFdr>
<siteFdr>1</siteFdr>
<lfqSitePeptide>false</lfqSitePeptide>
<minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>
<maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>
<useNormRatiosForOccupancy>true</useNormRatiosForOccupancy>
<minPeptides>1</minPeptides>
<minRazorPeptides>1</minRazorPeptides>
<minUniquePeptides>0</minUniquePeptides>
<useCounterparts>false</useCounterparts>
<advancedSiteIntensities>true</advancedSiteIntensities>
<customProteinQuantification>false</customProteinQuantification>
<customProteinQuantificationFile />
<minRatioCount>2</minRatioCount>
<restrictProteinQuantification>true</restrictProteinQuantification>
<restrictMods>
<string>Oxidation (M)</string>
<string>Acetyl (Protein N-term)</string>
</restrictMods>
<matchingTimeWindow>0</matchingTimeWindow>
<alignmentTimeWindow>0</alignmentTimeWindow>
<numberOfCandidatesMultiplexedMsms>25</numberOfCandidatesMultiplexedMsms>
<numberOfCandidatesMsms>15</numberOfCandidatesMsms>
<massDifferenceMods />
<mainSearchMaxCombinations>200</mainSearchMaxCombinations>
<stackPeaks>false</stackPeaks>
<ms2PrecursorShift>0</ms2PrecursorShift>
<complementaryIonPpm>20</complementaryIonPpm>
<variationParseRule />
<msmsParamsArray>
<msmsParams Name="FTMS" MatchToleranceInPpm="true" DeisotopeToleranceInPpm="true" DeNovoToleranceInPpm="true" Deisotope="true" Topx="12" TopxInterval="100" HigherCharges="true" IncludeWater="true" IncludeAmmonia="true" DependentLosses="true" Recalibration="false">
<MatchTolerance>20</MatchTolerance>
<DeisotopeTolerance>7</DeisotopeTolerance>
<DeNovoTolerance>10</DeNovoTolerance>
</msmsParams>
<msmsParams Name="ITMS" MatchToleranceInPpm="false" DeisotopeToleranceInPpm="false" DeNovoToleranceInPpm="false" Deisotope="false" Topx="8" TopxInterval="100" HigherCharges="true" IncludeWater="true" IncludeAmmonia="true" DependentLosses="true" Recalibration="false">
<MatchTolerance>1.5</MatchTolerance>
<DeisotopeTolerance>0.15</DeisotopeTolerance>
<DeNovoTolerance>0.25</DeNovoTolerance>
</msmsParams>
<msmsParams Name="TOF" MatchToleranceInPpm="true" DeisotopeToleranceInPpm="false" DeNovoToleranceInPpm="false" Deisotope="true" Topx="10" TopxInterval="100" HigherCharges="true" IncludeWater="true" IncludeAmmonia="true" DependentLosses="true" Recalibration="false">
<MatchTolerance>40</MatchTolerance>
<DeisotopeTolerance>0.01</DeisotopeTolerance>
<DeNovoTolerance>0.02</DeNovoTolerance>
</msmsParams>
<msmsParams Name="Unknown" MatchToleranceInPpm="false" DeisotopeToleranceInPpm="false" DeNovoToleranceInPpm="false" Deisotope="false" Topx="8" TopxInterval="100" HigherCharges="true" IncludeWater="true" IncludeAmmonia="true" DependentLosses="true" Recalibration="false">
<MatchTolerance>0.5</MatchTolerance>
<DeisotopeTolerance>0.15</DeisotopeTolerance>
<DeNovoTolerance>0.25</DeNovoTolerance>
</msmsParams>
</msmsParamsArray>
<compositionPrediction>0</compositionPrediction>
<quantMode>1</quantMode>
<variationMode>none</variationMode>
</MaxQuantParams>