<?xml version="1.0" ?><MaxQuantParams xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<fastaFiles>
<FastaFileInfo>
<fastaFilePath>F:\fasta\proteome_human-crap-20536_20200915.fasta</fastaFilePath>
<identifierParseRule>>([^\s]*)</identifierParseRule>
<descriptionParseRule>>(.*)</descriptionParseRule>
<taxonomyParseRule/>
<variationParseRule/>
<modificationParseRule/>
<taxonomyId/>
</FastaFileInfo>
</fastaFiles>
<fastaFilesProteogenomics>
</fastaFilesProteogenomics>
<fastaFilesFirstSearch>
</fastaFilesFirstSearch>
<fixedSearchFolder/>
<andromedaCacheSize>350000</andromedaCacheSize>
<advancedRatios>True</advancedRatios>
<pvalThres>0.005</pvalThres>
<neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification>
<neucodeStabilizeLargeRatios>False</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>True</secondPeptide>
<matchBetweenRuns>False</matchBetweenRuns>
<matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>
<matchBetweenRunsFdr>False</matchBetweenRunsFdr>
<dependentPeptides>False</dependentPeptides>
<dependentPeptideFdr>0</dependentPeptideFdr>
<dependentPeptideMassBin>0</dependentPeptideMassBin>
<dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>
<dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>
<dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>
<dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>
<dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>
<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>
<isotopeCalc>False</isotopeCalc>
<writePeptidesForSpectrumFile/>
<intensityPredictionsFile>
</intensityPredictionsFile>
<minPepLen>7</minPepLen>
<psmFdrCrosslink>0.01</psmFdrCrosslink>
<peptideFdr>0.01</peptideFdr>
<proteinFdr>0.01</proteinFdr>
<siteFdr>0.01</siteFdr>
<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>
<matchingIonMobilityWindow>0</matchingIonMobilityWindow>
<alignmentTimeWindow>0</alignmentTimeWindow>
<alignmentIonMobilityWindow>0</alignmentIonMobilityWindow>
<numberOfCandidatesMsms>15</numberOfCandidatesMsms>
<compositionPrediction>0</compositionPrediction>
<quantMode>1</quantMode>
<massDifferenceMods>
</massDifferenceMods>
<mainSearchMaxCombinations>200</mainSearchMaxCombinations>
<writeMsScansTable>False</writeMsScansTable>
<writeMsmsScansTable>True</writeMsmsScansTable>
<writePasefMsmsScansTable>True</writePasefMsmsScansTable>
<writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable>
<writeMs3ScansTable>True</writeMs3ScansTable>
<writeAllPeptidesTable>True</writeAllPeptidesTable>
<writeMzRangeTable>True</writeMzRangeTable>
<writeMzTab>False</writeMzTab>
<disableMd5>False</disableMd5>
<cacheBinInds>True</cacheBinInds>
<etdIncludeB>False</etdIncludeB>
<ms2PrecursorShift>0</ms2PrecursorShift>
<complementaryIonPpm>20</complementaryIonPpm>
<variationParseRule/>
<variationMode>none</variationMode>
<useSeriesReporters>False</useSeriesReporters>
<name>session1</name>
<maxQuantVersion>1.6.10.43</maxQuantVersion>
<tempFolder/>
<pluginFolder/>
<numThreads>8</numThreads>
<emailAddress/>
<smtpHost/>
<emailFromAddress/>
<fixedCombinedFolder/>
<fullMinMz>-1.79769313486232E+308</fullMinMz>
<fullMaxMz>1.79769313486232E+308</fullMaxMz>
<sendEmail>False</sendEmail>
<ionCountIntensities>False</ionCountIntensities>
<verboseColumnHeaders>False</verboseColumnHeaders>
<calcPeakProperties>False</calcPeakProperties>
<showCentroidMassDifferences>False</showCentroidMassDifferences>
<showIsotopeMassDifferences>False</showIsotopeMassDifferences>
<useDotNetCore>False</useDotNetCore>
<filePaths>
<string>E:\pel_staff\lfq_p97\ctl_51.raw</string>
<string>E:\pel_staff\lfq_p97\ctl_52.raw</string>
<string>E:\pel_staff\lfq_p97\ctl_53.raw</string>
<string>E:\pel_staff\lfq_p97\p97kd_54.raw</string>
<string>E:\pel_staff\lfq_p97\p97kd_55.raw</string>
<string>E:\pel_staff\lfq_p97\p97kd_56.raw</string>
</filePaths>
<experiments>
<string>ctrl_1</string>
<string>ctrl_2</string>
<string>ctrl_3</string>
<string>p97_kd_1</string>
<string>p97_kd_2</string>
<string>p97_kd_3</string>
</experiments>
<fractions>
<short>32767</short>
<short>32767</short>
<short>32767</short>
<short>32767</short>
<short>32767</short>
<short>32767</short>
</fractions>
<ptms>
<boolean>False</boolean>
<boolean>False</boolean>
<boolean>False</boolean>
<boolean>False</boolean>
<boolean>False</boolean>
<boolean>False</boolean>
</ptms>
<paramGroupIndices>
<int>0</int>
<int>0</int>
<int>0</int>
<int>0</int>
<int>0</int>
<int>0</int>
</paramGroupIndices>
<referenceChannel>
<string/>
<string/>
<string/>
<string/>
<string/>
<string/>
</referenceChannel>
<intensPred>False</intensPred>
<intensPredModelReTrain>False</intensPredModelReTrain>
<parameterGroups>
<parameterGroup>
<msInstrument>0</msInstrument>
<maxCharge>7</maxCharge>
<minPeakLen>2</minPeakLen>
<diaMinPeakLen>2</diaMinPeakLen>
<useMs1Centroids>False</useMs1Centroids>
<useMs2Centroids>False</useMs2Centroids>
<cutPeaks>True</cutPeaks>
<gapScans>1</gapScans>
<minTime>NaN</minTime>
<maxTime>NaN</maxTime>
<matchType>MatchFromAndTo</matchType>
<intensityDetermination>0</intensityDetermination>
<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>
<labelMods>
<string/>
</labelMods>
<lcmsRunType>Standard</lcmsRunType>
<reQuantify>False</reQuantify>
<lfqMode>1</lfqMode>
<lfqSkipNorm>True</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>
<maxLabeledAa>0</maxLabeledAa>
<maxNmods>5</maxNmods>
<maxMissedCleavages>2</maxMissedCleavages>
<multiplicity>1</multiplicity>
<enzymeMode>0</enzymeMode>
<complementaryReporterType>0</complementaryReporterType>
<reporterNormalization>0</reporterNormalization>
<neucodeIntensityMode>0</neucodeIntensityMode>
<fixedModifications>
<string>Carbamidomethyl (C)</string>
</fixedModifications>
<enzymes>
<string>Trypsin/P</string>
</enzymes>
<enzymesFirstSearch>
</enzymesFirstSearch>
<enzymeModeFirstSearch>0</enzymeModeFirstSearch>
<useEnzymeFirstSearch>False</useEnzymeFirstSearch>
<useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
<variableModifications>
<string>Oxidation (M)</string>
<string>Acetyl (Protein N-term)</string>
</variableModifications>
<useMultiModification>False</useMultiModification>
<multiModifications>
</multiModifications>
<isobaricLabels>
</isobaricLabels>
<neucodeLabels>
</neucodeLabels>
<variableModificationsFirstSearch>
</variableModificationsFirstSearch>
<hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
<additionalVariableModifications>
</additionalVariableModifications>
<additionalVariableModificationProteins>
</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>
<checkMassDeficit>True</checkMassDeficit>
<recalibrationInPpm>True</recalibrationInPpm>
<intensityDependentCalibration>False</intensityDependentCalibration>
<minScoreForCalibration>70</minScoreForCalibration>
<matchLibraryFile>False</matchLibraryFile>
<libraryFile/>
<matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
<matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
<matchLabelTimeTolMin>0</matchLabelTimeTolMin>
<reporterMassTolerance>NaN</reporterMassTolerance>
<reporterPif>NaN</reporterPif>
<filterPif>False</filterPif>
<reporterFraction>NaN</reporterFraction>
<reporterBasePeakRatio>NaN</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>
<crossLinker/>
<minMatchXl>0</minMatchXl>
<minPairedPepLenXl>6</minPairedPepLenXl>
<crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
<crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
<crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
<crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
<crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
<crosslinkModifications>
</crosslinkModifications>
<crosslinkFastaFiles>
</crosslinkFastaFiles>
<crosslinkSites>
</crosslinkSites>
<crosslinkNetworkFiles>
</crosslinkNetworkFiles>
<crosslinkMode/>
<peakRefinement>False</peakRefinement>
<isobaricSumOverWindow>True</isobaricSumOverWindow>
<isobaricWeightExponent>0.75</isobaricWeightExponent>
<diaLibraryType>0</diaLibraryType>
<diaLibraryPath/>
<diaPeptidePaths>
</diaPeptidePaths>
<diaEvidencePaths>
</diaEvidencePaths>
<diaMsmsPaths>
</diaMsmsPaths>
<diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
<diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
<diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
<diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
<diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
<diaScoreN>7</diaScoreN>
<diaMinScore>2.99</diaMinScore>
<diaPrecursorQuant>False</diaPrecursorQuant>
<diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>
</parameterGroup>
</parameterGroups>
<msmsParamsArray>
<msmsParams>
<Name>FTMS</Name>
<MatchTolerance>20</MatchTolerance>
<MatchToleranceInPpm>True</MatchToleranceInPpm>
<DeisotopeTolerance>7</DeisotopeTolerance>
<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
<DeNovoTolerance>10</DeNovoTolerance>
<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
<Deisotope>True</Deisotope>
<Topx>12</Topx>
<TopxInterval>100</TopxInterval>
<HigherCharges>True</HigherCharges>
<IncludeWater>True</IncludeWater>
<IncludeAmmonia>True</IncludeAmmonia>
<DependentLosses>True</DependentLosses>
<Recalibration>False</Recalibration>
</msmsParams>
<msmsParams>
<Name>ITMS</Name>
<MatchTolerance>0.5</MatchTolerance>
<MatchToleranceInPpm>False</MatchToleranceInPpm>
<DeisotopeTolerance>0.15</DeisotopeTolerance>
<DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
<DeNovoTolerance>0.25</DeNovoTolerance>
<DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
<Deisotope>False</Deisotope>
<Topx>8</Topx>
<TopxInterval>100</TopxInterval>
<HigherCharges>True</HigherCharges>
<IncludeWater>True</IncludeWater>
<IncludeAmmonia>True</IncludeAmmonia>
<DependentLosses>True</DependentLosses>
<Recalibration>False</Recalibration>
</msmsParams>
<msmsParams>
<Name>TOF</Name>
<MatchTolerance>40</MatchTolerance>
<MatchToleranceInPpm>True</MatchToleranceInPpm>
<DeisotopeTolerance>0.01</DeisotopeTolerance>
<DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
<DeNovoTolerance>0.02</DeNovoTolerance>
<DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
<Deisotope>True</Deisotope>
<Topx>10</Topx>
<TopxInterval>100</TopxInterval>
<HigherCharges>True</HigherCharges>
<IncludeWater>True</IncludeWater>
<IncludeAmmonia>True</IncludeAmmonia>
<DependentLosses>True</DependentLosses>
<Recalibration>False</Recalibration>
</msmsParams>
<msmsParams>
<Name>Unknown</Name>
<MatchTolerance>20</MatchTolerance>
<MatchToleranceInPpm>True</MatchToleranceInPpm>
<DeisotopeTolerance>7</DeisotopeTolerance>
<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
<DeNovoTolerance>10</DeNovoTolerance>
<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
<Deisotope>True</Deisotope>
<Topx>12</Topx>
<TopxInterval>100</TopxInterval>
<HigherCharges>True</HigherCharges>
<IncludeWater>True</IncludeWater>
<IncludeAmmonia>True</IncludeAmmonia>
<DependentLosses>True</DependentLosses>
<Recalibration>False</Recalibration>
</msmsParams>
</msmsParamsArray>
<fragmentationParamsArray>
<fragmentationParams>
<Name>CID</Name>
<Connected>False</Connected>
<ConnectedScore0>1</ConnectedScore0>
<ConnectedScore1>1</ConnectedScore1>
<ConnectedScore2>1</ConnectedScore2>
<InternalFragments>False</InternalFragments>
<InternalFragmentWeight>1</InternalFragmentWeight>
<InternalFragmentAas>KRH</InternalFragmentAas>
</fragmentationParams>
<fragmentationParams>
<Name>HCD</Name>
<Connected>False</Connected>
<ConnectedScore0>1</ConnectedScore0>
<ConnectedScore1>1</ConnectedScore1>
<ConnectedScore2>1</ConnectedScore2>
<InternalFragments>False</InternalFragments>
<InternalFragmentWeight>1</InternalFragmentWeight>
<InternalFragmentAas>KRH</InternalFragmentAas>
</fragmentationParams>
<fragmentationParams>
<Name>ETD</Name>
<Connected>False</Connected>
<ConnectedScore0>1</ConnectedScore0>
<ConnectedScore1>1</ConnectedScore1>
<ConnectedScore2>1</ConnectedScore2>
<InternalFragments>False</InternalFragments>
<InternalFragmentWeight>1</InternalFragmentWeight>
<InternalFragmentAas>KRH</InternalFragmentAas>
</fragmentationParams>
<fragmentationParams>
<Name>PQD</Name>
<Connected>False</Connected>
<ConnectedScore0>1</ConnectedScore0>
<ConnectedScore1>1</ConnectedScore1>
<ConnectedScore2>1</ConnectedScore2>
<InternalFragments>False</InternalFragments>
<InternalFragmentWeight>1</InternalFragmentWeight>
<InternalFragmentAas>KRH</InternalFragmentAas>
</fragmentationParams>
<fragmentationParams>
<Name>ETHCD</Name>
<Connected>False</Connected>
<ConnectedScore0>1</ConnectedScore0>
<ConnectedScore1>1</ConnectedScore1>
<ConnectedScore2>1</ConnectedScore2>
<InternalFragments>False</InternalFragments>
<InternalFragmentWeight>1</InternalFragmentWeight>
<InternalFragmentAas>KRH</InternalFragmentAas>
</fragmentationParams>
<fragmentationParams>
<Name>ETCID</Name>
<Connected>False</Connected>
<ConnectedScore0>1</ConnectedScore0>
<ConnectedScore1>1</ConnectedScore1>
<ConnectedScore2>1</ConnectedScore2>
<InternalFragments>False</InternalFragments>
<InternalFragmentWeight>1</InternalFragmentWeight>
<InternalFragmentAas>KRH</InternalFragmentAas>
</fragmentationParams>
<fragmentationParams>
<Name>UVPD</Name>
<Connected>False</Connected>
<ConnectedScore0>1</ConnectedScore0>
<ConnectedScore1>1</ConnectedScore1>
<ConnectedScore2>1</ConnectedScore2>
<InternalFragments>False</InternalFragments>
<InternalFragmentWeight>1</InternalFragmentWeight>
<InternalFragmentAas>KRH</InternalFragmentAas>
</fragmentationParams>
<fragmentationParams>
<Name>Unknown</Name>
<Connected>False</Connected>
<ConnectedScore0>1</ConnectedScore0>
<ConnectedScore1>1</ConnectedScore1>
<ConnectedScore2>1</ConnectedScore2>
<InternalFragments>False</InternalFragments>
<InternalFragmentWeight>1</InternalFragmentWeight>
<InternalFragmentAas>KRH</InternalFragmentAas>
</fragmentationParams>
</fragmentationParamsArray>
</MaxQuantParams>