annotate test-data/02/mqpar.xml @ 22:9c52362ae7bb draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit c810d2eaedfcad1edf1a84cab8296dcd7b35f5bc

<?xml version="1.0" ?>
<MaxQuantParams>
	<fastaFiles>
		<FastaFileInfo>
			<fastaFilePath>/tmp/tmpyzym30dx/files/d/3/1/dataset_d314bbcd-5f08-4e93-b285-2ad6e4739fc9.dat</fastaFilePath>
			<identifierParseRule>&gt;([^\s]*)</identifierParseRule>
			<descriptionParseRule>&gt;(.*)</descriptionParseRule>
			<taxonomyParseRule/>
			<variationParseRule/>
			<modificationParseRule/>
			<taxonomyId/>
		</FastaFileInfo>
	</fastaFiles>
	<fastaFilesProteogenomics>
   </fastaFilesProteogenomics>
	<fastaFilesFirstSearch>
   </fastaFilesFirstSearch>
	<fixedSearchFolder/>
	<andromedaCacheSize>350000</andromedaCacheSize>
	<advancedRatios>True</advancedRatios>
	<pvalThres>0.005</pvalThres>
	<rtShift>False</rtShift>
	<separateLfq>False</separateLfq>
	<lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>
	<lfqRequireMsms>True</lfqRequireMsms>
	<lfqBayesQuant>False</lfqBayesQuant>
	<decoyMode>randomize</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>
	<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>
	<ibaqChargeNormalization>False</ibaqChargeNormalization>
	<razorProteinFdr>True</razorProteinFdr>
	<deNovoSequencing>False</deNovoSequencing>
	<deNovoVarMods>False</deNovoVarMods>
	<deNovoCompleteSequence>False</deNovoCompleteSequence>
	<deNovoCalibratedMasses>False</deNovoCalibratedMasses>
	<deNovoMaxIterations>0</deNovoMaxIterations>
	<deNovoProteaseReward>0</deNovoProteaseReward>
	<deNovoProteaseRewardTof>0</deNovoProteaseRewardTof>
	<deNovoAgPenalty>0</deNovoAgPenalty>
	<deNovoGgPenalty>0</deNovoGgPenalty>
	<deNovoUseComplementScore>True</deNovoUseComplementScore>
	<deNovoUseProteaseScore>True</deNovoUseProteaseScore>
	<deNovoUseWaterLossScore>True</deNovoUseWaterLossScore>
	<deNovoUseAmmoniaLossScore>True</deNovoUseAmmoniaLossScore>
	<deNovoUseA2Score>True</deNovoUseA2Score>
	<massDifferenceSearch>False</massDifferenceSearch>
	<isotopeCalc>False</isotopeCalc>
	<writePeptidesForSpectrumFile/>
	<intensityPredictionsFile>
   </intensityPredictionsFile>
	<minPepLen>7</minPepLen>
	<psmFdrCrosslink>0.01</psmFdrCrosslink>
	<peptideFdr>0.5</peptideFdr>
	<proteinFdr>0.4</proteinFdr>
	<siteFdr>0.01</siteFdr>
	<minPeptideLengthForUnspecificSearch>7</minPeptideLengthForUnspecificSearch>
	<maxPeptideLengthForUnspecificSearch>24</maxPeptideLengthForUnspecificSearch>
	<useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>
	<minPeptides>1</minPeptides>
	<minRazorPeptides>1</minRazorPeptides>
	<minUniquePeptides>0</minUniquePeptides>
	<useCounterparts>True</useCounterparts>
	<advancedSiteIntensities>True</advancedSiteIntensities>
	<customProteinQuantification>False</customProteinQuantification>
	<customProteinQuantificationFile/>
	<minRatioCount>2</minRatioCount>
	<restrictProteinQuantification>True</restrictProteinQuantification>
	<restrictMods>
		<string>Pro5</string>
		<string>Pro6</string>
	</restrictMods>
	<matchingTimeWindow>0</matchingTimeWindow>
	<matchingIonMobilityWindow>0</matchingIonMobilityWindow>
	<alignmentTimeWindow>0</alignmentTimeWindow>
	<alignmentIonMobilityWindow>0</alignmentIonMobilityWindow>
	<numberOfCandidatesMsms>15</numberOfCandidatesMsms>
	<compositionPrediction>0</compositionPrediction>
	<quantMode>0</quantMode>
	<massDifferenceMods>
   </massDifferenceMods>
	<mainSearchMaxCombinations>200</mainSearchMaxCombinations>
	<writeMsScansTable>False</writeMsScansTable>
	<writeMsmsScansTable>True</writeMsmsScansTable>
	<writePasefMsmsScansTable>True</writePasefMsmsScansTable>
	<writeAccumulatedMsmsScansTable>True</writeAccumulatedMsmsScansTable>
	<writeMs3ScansTable>True</writeMs3ScansTable>
	<writeAllPeptidesTable>True</writeAllPeptidesTable>
	<writeMzRangeTable>True</writeMzRangeTable>
	<writeDiaFragmentTable>False</writeDiaFragmentTable>
	<writeDiaFragmentQuantTable>False</writeDiaFragmentQuantTable>
	<writeMzTab>True</writeMzTab>
	<disableMd5>False</disableMd5>
	<cacheBinInds>True</cacheBinInds>
	<etdIncludeB>False</etdIncludeB>
	<ms2PrecursorShift>0</ms2PrecursorShift>
	<complementaryIonPpm>20</complementaryIonPpm>
	<variationParseRule/>
	<variationMode>none</variationMode>
	<useSeriesReporters>False</useSeriesReporters>
	<name>templateSession</name>
	<maxQuantVersion>2.0.3.0</maxQuantVersion>
	<pluginFolder/>
	<numThreads>1</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>True</useDotNetCore>
	<profilePerformance>False</profilePerformance>
	<filePaths>
		<string>/tmp/tmpyzym30dx/job_working_directory/000/7/working/BSA_min_23.mzXML</string>
		<string>/tmp/tmpyzym30dx/job_working_directory/000/7/working/BSA_min_22.mzxml</string>
	</filePaths>
	<experiments>
		<string>BSA_min_23.mzXML</string>
		<string>BSA_min_22.mzxml</string>
	</experiments>
	<fractions>
		<short>32767</short>
		<short>32767</short>
	</fractions>
	<ptms>
		<boolean>False</boolean>
		<boolean>False</boolean>
	</ptms>
	<paramGroupIndices>
		<int>0</int>
		<int>1</int>
	</paramGroupIndices>
	<referenceChannel>
		<string/>
		<string/>
	</referenceChannel>
	<intensPred>False</intensPred>
	<intensPredModelReTrain>False</intensPredModelReTrain>
	<lfqTopNPeptides>0</lfqTopNPeptides>
	<diaJoinPrecChargesForLfq>False</diaJoinPrecChargesForLfq>
	<diaFragChargesForQuant>1</diaFragChargesForQuant>
	<timsRearrangeSpectra>False</timsRearrangeSpectra>
	<gridSpacing>0.5</gridSpacing>
	<proteinGroupingFile/>
	<parameterGroups>
		<parameterGroup>
			<msInstrument>0</msInstrument>
			<maxCharge>7</maxCharge>
			<minPeakLen>2</minPeakLen>
			<diaMinPeakLen>1</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>
			<intensityThresholdMs1>0</intensityThresholdMs1>
			<intensityThresholdMs2>0</intensityThresholdMs2>
			<labelMods>
				<string/>
			</labelMods>
			<lcmsRunType>Reporter ion MS2</lcmsRunType>
			<reQuantify>False</reQuantify>
			<lfqMode>0</lfqMode>
			<lfqNormClusterSize>80</lfqNormClusterSize>
			<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/>
			<enzymes>
				<string>Trypsin/P</string>
			</enzymes>
			<enzymesFirstSearch>
         </enzymesFirstSearch>
			<enzymeModeFirstSearch>0</enzymeModeFirstSearch>
			<useEnzymeFirstSearch>False</useEnzymeFirstSearch>
			<useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
			<variableModifications>
				<string>Oxidation (M)</string>
			</variableModifications>
			<useMultiModification>False</useMultiModification>
			<multiModifications>
         </multiModifications>
			<isobaricLabels>
				<IsobaricLabelInfo>
					<internalLabel>TMT2plex-Lys126</internalLabel>
					<terminalLabel>TMT2plex-Nter126</terminalLabel>
					<correctionFactorM2>0</correctionFactorM2>
					<correctionFactorM1>0</correctionFactorM1>
					<correctionFactorP1>6.7</correctionFactorP1>
					<correctionFactorP2>3</correctionFactorP2>
					<tmtLike>True</tmtLike>
				</IsobaricLabelInfo>
				<IsobaricLabelInfo>
					<internalLabel>TMT2plex-Lys127</internalLabel>
					<terminalLabel>TMT2plex-Nter127</terminalLabel>
					<correctionFactorM2>0</correctionFactorM2>
					<correctionFactorM1>0</correctionFactorM1>
					<correctionFactorP1>0</correctionFactorP1>
					<correctionFactorP2>0</correctionFactorP2>
					<tmtLike>True</tmtLike>
				</IsobaricLabelInfo>
			</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>0.003</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>
			<crossLinkingType>0</crossLinkingType>
			<crossLinker/>
			<minMatchXl>3</minMatchXl>
			<minPairedPepLenXl>6</minPairedPepLenXl>
			<minScore_Dipeptide>40</minScore_Dipeptide>
			<minScore_Monopeptide>0</minScore_Monopeptide>
			<minScore_PartialCross>10</minScore_PartialCross>
			<crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
			<crosslinkIntensityBasedPrecursor>True</crosslinkIntensityBasedPrecursor>
			<isHybridPrecDetermination>False</isHybridPrecDetermination>
			<topXcross>3</topXcross>
			<doesSeparateInterIntraProteinCross>False</doesSeparateInterIntraProteinCross>
			<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>
			<collapseMsmsOnIsotopePatterns>False</collapseMsmsOnIsotopePatterns>
			<diaLibraryType>0</diaLibraryType>
			<diaLibraryPaths>
         </diaLibraryPaths>
			<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>1.99</diaMinScore>
			<diaXgBoostBaseScore>0.4</diaXgBoostBaseScore>
			<diaXgBoostSubSample>0.9</diaXgBoostSubSample>
			<centroidPosition>0</centroidPosition>
			<diaQuantMethod>7</diaQuantMethod>
			<diaFeatureQuantMethod>2</diaFeatureQuantMethod>
			<lfqNormType>1</lfqNormType>
			<diaTopNForQuant>10</diaTopNForQuant>
			<diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant>
			<diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant>
			<diaPrecursorFilterType>0</diaPrecursorFilterType>
			<diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore>
			<diaMinPrecursorScore>0.5</diaMinPrecursorScore>
			<diaMinProfileCorrelation>0</diaMinProfileCorrelation>
			<diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight>
			<diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth>
			<diaXgBoostEstimators>580</diaXgBoostEstimators>
			<diaXgBoostGamma>0.9</diaXgBoostGamma>
			<diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep>
			<diaGlobalMl>True</diaGlobalMl>
			<diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy>
			<diaMassWindowFactor>3.3</diaMassWindowFactor>
			<diaRtPrediction>False</diaRtPrediction>
			<diaRtPredictionSecondRound>False</diaRtPredictionSecondRound>
			<diaNoMl>False</diaNoMl>
			<diaPermuteRt>False</diaPermuteRt>
			<diaPermuteCcs>False</diaPermuteCcs>
			<diaBackgroundSubtraction>False</diaBackgroundSubtraction>
			<diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile>
			<diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>
			<diaLfqWeightedMedian>False</diaLfqWeightedMedian>
			<diaTransferQvalue>0.3</diaTransferQvalue>
			<diaOnlyIsosForRecal>True</diaOnlyIsosForRecal>
			<diaMinPeaksForRecal>5</diaMinPeaksForRecal>
			<diaUseFragIntensForMl>False</diaUseFragIntensForMl>
			<diaUseFragMassesForMl>False</diaUseFragMassesForMl>
			<diaMaxTrainInstances>1000000</diaMaxTrainInstances>
		</parameterGroup>
		<parameterGroup>
			<msInstrument>0</msInstrument>
			<maxCharge>7</maxCharge>
			<minPeakLen>2</minPeakLen>
			<diaMinPeakLen>1</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>
			<intensityThresholdMs1>0</intensityThresholdMs1>
			<intensityThresholdMs2>0</intensityThresholdMs2>
			<labelMods>
				<string/>
			</labelMods>
			<lcmsRunType>Reporter ion MS2</lcmsRunType>
			<reQuantify>False</reQuantify>
			<lfqMode>0</lfqMode>
			<lfqNormClusterSize>80</lfqNormClusterSize>
			<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/>
			<enzymes/>
			<enzymesFirstSearch>
         </enzymesFirstSearch>
			<enzymeModeFirstSearch>0</enzymeModeFirstSearch>
			<useEnzymeFirstSearch>False</useEnzymeFirstSearch>
			<useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
			<variableModifications/>
			<useMultiModification>False</useMultiModification>
			<multiModifications>
         </multiModifications>
			<isobaricLabels>
				<IsobaricLabelInfo>
					<internalLabel>iTRAQ4plex-Lys114</internalLabel>
					<terminalLabel>iTRAQ4plex-Nter114</terminalLabel>
					<correctionFactorM2>0</correctionFactorM2>
					<correctionFactorM1>0</correctionFactorM1>
					<correctionFactorP1>0</correctionFactorP1>
					<correctionFactorP2>0</correctionFactorP2>
					<tmtLike>False</tmtLike>
				</IsobaricLabelInfo>
				<IsobaricLabelInfo>
					<internalLabel>iTRAQ4plex-Lys115</internalLabel>
					<terminalLabel>iTRAQ4plex-Nter115</terminalLabel>
					<correctionFactorM2>0</correctionFactorM2>
					<correctionFactorM1>0</correctionFactorM1>
					<correctionFactorP1>0</correctionFactorP1>
					<correctionFactorP2>0</correctionFactorP2>
					<tmtLike>False</tmtLike>
				</IsobaricLabelInfo>
				<IsobaricLabelInfo>
					<internalLabel>iTRAQ4plex-Lys116</internalLabel>
					<terminalLabel>iTRAQ4plex-Nter116</terminalLabel>
					<correctionFactorM2>0</correctionFactorM2>
					<correctionFactorM1>0</correctionFactorM1>
					<correctionFactorP1>0</correctionFactorP1>
					<correctionFactorP2>0</correctionFactorP2>
					<tmtLike>False</tmtLike>
				</IsobaricLabelInfo>
				<IsobaricLabelInfo>
					<internalLabel>iTRAQ4plex-Lys117</internalLabel>
					<terminalLabel>iTRAQ4plex-Nter117</terminalLabel>
					<correctionFactorM2>0</correctionFactorM2>
					<correctionFactorM1>0</correctionFactorM1>
					<correctionFactorP1>0</correctionFactorP1>
					<correctionFactorP2>0</correctionFactorP2>
					<tmtLike>False</tmtLike>
				</IsobaricLabelInfo>
			</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>0.003</reporterMassTolerance>
			<reporterPif>0.8</reporterPif>
			<filterPif>True</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>
			<crossLinkingType>0</crossLinkingType>
			<crossLinker/>
			<minMatchXl>3</minMatchXl>
			<minPairedPepLenXl>6</minPairedPepLenXl>
			<minScore_Dipeptide>40</minScore_Dipeptide>
			<minScore_Monopeptide>0</minScore_Monopeptide>
			<minScore_PartialCross>10</minScore_PartialCross>
			<crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
			<crosslinkIntensityBasedPrecursor>True</crosslinkIntensityBasedPrecursor>
			<isHybridPrecDetermination>False</isHybridPrecDetermination>
			<topXcross>3</topXcross>
			<doesSeparateInterIntraProteinCross>False</doesSeparateInterIntraProteinCross>
			<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>
			<collapseMsmsOnIsotopePatterns>False</collapseMsmsOnIsotopePatterns>
			<diaLibraryType>0</diaLibraryType>
			<diaLibraryPaths>
         </diaLibraryPaths>
			<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>1.99</diaMinScore>
			<diaXgBoostBaseScore>0.4</diaXgBoostBaseScore>
			<diaXgBoostSubSample>0.9</diaXgBoostSubSample>
			<centroidPosition>0</centroidPosition>
			<diaQuantMethod>7</diaQuantMethod>
			<diaFeatureQuantMethod>2</diaFeatureQuantMethod>
			<lfqNormType>1</lfqNormType>
			<diaTopNForQuant>10</diaTopNForQuant>
			<diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant>
			<diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant>
			<diaPrecursorFilterType>0</diaPrecursorFilterType>
			<diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore>
			<diaMinPrecursorScore>0.5</diaMinPrecursorScore>
			<diaMinProfileCorrelation>0</diaMinProfileCorrelation>
			<diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight>
			<diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth>
			<diaXgBoostEstimators>580</diaXgBoostEstimators>
			<diaXgBoostGamma>0.9</diaXgBoostGamma>
			<diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep>
			<diaGlobalMl>True</diaGlobalMl>
			<diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy>
			<diaMassWindowFactor>3.3</diaMassWindowFactor>
			<diaRtPrediction>False</diaRtPrediction>
			<diaRtPredictionSecondRound>False</diaRtPredictionSecondRound>
			<diaNoMl>False</diaNoMl>
			<diaPermuteRt>False</diaPermuteRt>
			<diaPermuteCcs>False</diaPermuteCcs>
			<diaBackgroundSubtraction>False</diaBackgroundSubtraction>
			<diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile>
			<diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>
			<diaLfqWeightedMedian>False</diaLfqWeightedMedian>
			<diaTransferQvalue>0.3</diaTransferQvalue>
			<diaOnlyIsosForRecal>True</diaOnlyIsosForRecal>
			<diaMinPeaksForRecal>5</diaMinPeaksForRecal>
			<diaUseFragIntensForMl>False</diaUseFragIntensForMl>
			<diaUseFragMassesForMl>False</diaUseFragMassesForMl>
			<diaMaxTrainInstances>1000000</diaMaxTrainInstances>
		</parameterGroup>
	</parameterGroups>
	<msmsParamsArray>
		<msmsParams>
			<Name>FTMS</Name>
			<MatchTolerance>20</MatchTolerance>
			<MatchToleranceInPpm>True</MatchToleranceInPpm>
			<DeisotopeTolerance>7</DeisotopeTolerance>
			<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
			<DeNovoTolerance>25</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>0.5</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>25</DeNovoTolerance>
			<DeNovoToleranceInPpm>True</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>25</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>