diff --git a/MaxQuant/mqpar.xml b/MaxQuant/mqpar.xml deleted file mode 100644 index 04a4140d06c6e8eb1f55917edc7d71e1129f3f35..0000000000000000000000000000000000000000 --- a/MaxQuant/mqpar.xml +++ /dev/null @@ -1,563 +0,0 @@ -<?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"> - <fastaFiles> - <FastaFileInfo> - <fastaFilePath>/MaxQuant/TUM_isoform_118_01_01.fasta</fastaFilePath> - <identifierParseRule>>([^\s]*)</identifierParseRule> - <descriptionParseRule>>(.*)</descriptionParseRule> - <taxonomyParseRule></taxonomyParseRule> - <variationParseRule></variationParseRule> - <modificationParseRule></modificationParseRule> - <taxonomyId></taxonomyId> - </FastaFileInfo> - </fastaFiles> - <fastaFilesProteogenomics> - </fastaFilesProteogenomics> - <fastaFilesFirstSearch> - </fastaFilesFirstSearch> - <fixedSearchFolder></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>revert</decoyMode> - <includeContaminants>True</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>True</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> - <deNovoMassClusterTolDa>0</deNovoMassClusterTolDa> - <deNovoScalingFactor>0</deNovoScalingFactor> - <massDifferenceSearch>False</massDifferenceSearch> - <isotopeCalc>False</isotopeCalc> - <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></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> - <writeAccumulatedMsmsScansTable>True</writeAccumulatedMsmsScansTable> - <writeMs3ScansTable>True</writeMs3ScansTable> - <writeAllPeptidesTable>False</writeAllPeptidesTable> - <writeMzRangeTable>True</writeMzRangeTable> - <writeDiaFragmentTable>False</writeDiaFragmentTable> - <writeDiaFragmentQuantTable>False</writeDiaFragmentQuantTable> - <writeMzTab>False</writeMzTab> - <writeSdrf>False</writeSdrf> - <disableMd5>False</disableMd5> - <cacheBinInds>True</cacheBinInds> - <etdIncludeB>False</etdIncludeB> - <ms2PrecursorShift>0</ms2PrecursorShift> - <complementaryIonPpm>20</complementaryIonPpm> - <variationParseRule></variationParseRule> - <variationMode>none</variationMode> - <useSeriesReporters>False</useSeriesReporters> - <name>session1</name> - <maxQuantVersion>2.5.1.0</maxQuantVersion> - <pluginFolder></pluginFolder> - <numThreads>4</numThreads> - <emailAddress></emailAddress> - <smtpHost></smtpHost> - <emailFromAddress></emailFromAddress> - <fixedCombinedFolder>/gpfswork/rech/ute/ucg81ws/these/LC-MS-RT-prediction/MaxQuant</fixedCombinedFolder> - <fullMinMz>-1.7976931348623157E+308</fullMinMz> - <fullMaxMz>1.7976931348623157E+308</fullMaxMz> - <sendEmail>False</sendEmail> - <ionCountIntensities>False</ionCountIntensities> - <verboseColumnHeaders>False</verboseColumnHeaders> - <calcPeakProperties>False</calcPeakProperties> - <showCentroidMassDifferences>False</showCentroidMassDifferences> - <showIsotopeMassDifferences>False</showIsotopeMassDifferences> - <profilePerformance>False</profilePerformance> - <filePaths> - <string>/MaxQuant/02080d_GB10-TUM_isoform_118_01_01-2xIT_2xHCD-1h-R1.raw</string> - </filePaths> - <experiments> - <string></string> - </experiments> - <fractions> - <short>32767</short> - </fractions> - <ptms> - <boolean>False</boolean> - </ptms> - <paramGroupIndices> - <int>0</int> - </paramGroupIndices> - <referenceChannel> - <string></string> - </referenceChannel> - <lfqTopNPeptides>0</lfqTopNPeptides> - <diaJoinPrecChargesForLfq>False</diaJoinPrecChargesForLfq> - <diaFragChargesForQuant>1</diaFragChargesForQuant> - <gridSpacing>0.7</gridSpacing> - <proteinGroupingFile></proteinGroupingFile> - <simplePepCalculation>False</simplePepCalculation> - <useAndromeda20>False</useAndromeda20> - <useAndromeda20DefaultModel>False</useAndromeda20DefaultModel> - <andromeda20AltModelPath></andromeda20AltModelPath> - <intensityPredictionFolder></intensityPredictionFolder> - <encoding>0</encoding> - <parameterGroups> - <parameterGroup> - <andromeda20AltModelPath></andromeda20AltModelPath> - <andromeda20DefaultModel>False</andromeda20DefaultModel> - <useAndromeda20>False</useAndromeda20> - <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> - <intensityThresholdMs1Dda>0</intensityThresholdMs1Dda> - <intensityThresholdMs1Dia>0</intensityThresholdMs1Dia> - <intensityThresholdMs2>0</intensityThresholdMs2> - <labelMods> - <string></string> - </labelMods> - <lcmsRunType>Standard</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> - <lfqMinRatioCountDia>2</lfqMinRatioCountDia> - <lfqPrioritizeMs1Dia>True</lfqPrioritizeMs1Dia> - <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></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> - <crossLinkingType>0</crossLinkingType> - <crossLinker></crossLinker> - <minMatchXl>3</minMatchXl> - <minPairedPepLenXl>6</minPairedPepLenXl> - <minScoreDipeptide>40</minScoreDipeptide> - <minScoreMonopeptide>0</minScoreMonopeptide> - <minScorePartialCross>10</minScorePartialCross> - <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></crosslinkMode> - <peakRefinement>False</peakRefinement> - <peakRefinementCrosslinking>False</peakRefinementCrosslinking> - <isobaricSumOverWindow>True</isobaricSumOverWindow> - <isobaricWeightExponent>0.75</isobaricWeightExponent> - <collapseMsmsOnIsotopePatterns>False</collapseMsmsOnIsotopePatterns> - <diaLibraryType>0</diaLibraryType> - <diaLibraryPaths> - </diaLibraryPaths> - <diaEvidencePaths> - </diaEvidencePaths> - <diaMsmsPaths> - </diaMsmsPaths> - <diaLabelIndsForLibraryMatch> - </diaLabelIndsForLibraryMatch> - <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm> - <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm> - <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering> - <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> - <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> - <diaScoreN>12</diaScoreN> - <diaScoreNAdditional>5</diaScoreNAdditional> - <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>12</diaTopNForQuant> - <diaTopNCorrelationForQuant>7</diaTopNCorrelationForQuant> - <diaFragmentCorrelationForQuant>0.78</diaFragmentCorrelationForQuant> - <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant> - <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant> - <diaMinFragmentOverlapScore>0</diaMinFragmentOverlapScore> - <diaMinPrecursorScore>0</diaMinPrecursorScore> - <diaUseProfileCorrelation>False</diaUseProfileCorrelation> - <diaMinPrecProfileCorrelation>0</diaMinPrecProfileCorrelation> - <diaMinFragProfileCorrelation>0</diaMinFragProfileCorrelation> - <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> - <diaNoMl>False</diaNoMl> - <diaPermuteRt>False</diaPermuteRt> - <diaPermuteCcs>False</diaPermuteCcs> - <diaBackgroundSubtraction>False</diaBackgroundSubtraction> - <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> - <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> - <diaLfqRatioType>0</diaLfqRatioType> - <diaTransferQvalue>0.3</diaTransferQvalue> - <diaTransferQvalueBetweenLabels>0.01</diaTransferQvalueBetweenLabels> - <diaTransferQvalueBetweenFractions>0.01</diaTransferQvalueBetweenFractions> - <diaTransferQvalueBetweenFaims>0.01</diaTransferQvalueBetweenFaims> - <diaOnlyIsosForRecal>True</diaOnlyIsosForRecal> - <diaMinPeaks>5</diaMinPeaks> - <diaUseFragIntensForMl>False</diaUseFragIntensForMl> - <diaUseFragMassesForMl>False</diaUseFragMassesForMl> - <diaMaxTrainInstances>500000</diaMaxTrainInstances> - <diaMaxFragmentCharge>3</diaMaxFragmentCharge> - <diaAdaptiveMlScoring>False</diaAdaptiveMlScoring> - <diaDynamicScoringMaxInstances>25000</diaDynamicScoringMaxInstances> - <diaMaxPrecursorMz>0</diaMaxPrecursorMz> - <diaHardRtFilter>True</diaHardRtFilter> - <diaConvertLibraryCharge2Fragments>False</diaConvertLibraryCharge2Fragments> - <diaChargeNormalizationLibrary>True</diaChargeNormalizationLibrary> - <diaChargeNormalizationSample>True</diaChargeNormalizationSample> - <diaDeleteIntermediateResults>True</diaDeleteIntermediateResults> - <diaScoreWeightScanIndex>-1</diaScoreWeightScanIndex> - <diaScoreWeightScanValue>1</diaScoreWeightScanValue> - <diaNumNonleadingMatches>1</diaNumNonleadingMatches> - <diaUseDefaultFragmentModel>True</diaUseDefaultFragmentModel> - <diaAltFragmentModelPath></diaAltFragmentModelPath> - <diaUseDefaultRtModel>True</diaUseDefaultRtModel> - <diaAltRtModelPath></diaAltRtModelPath> - <diaUseDefaultCcsModel>True</diaUseDefaultCcsModel> - <diaAltCcsModelPath></diaAltCcsModelPath> - <diaBatchProcessing>True</diaBatchProcessing> - <diaBatchSize>25</diaBatchSize> - <diaFirstBatch>-1</diaFirstBatch> - <diaLastBatch>-1</diaLastBatch> - <diaOnlyPreprocess>False</diaOnlyPreprocess> - <diaMultiplexQuantMethod>1</diaMultiplexQuantMethod> - <diaOnlyPostprocess>False</diaOnlyPostprocess> - <diaRequirePrecursor>False</diaRequirePrecursor> - <diaFuturePeptides>False</diaFuturePeptides> - <diaOverrideRtWithPrediction>False</diaOverrideRtWithPrediction> - <diaMaxModifications>0</diaMaxModifications> - <diaMaxPositionings>0</diaMaxPositionings> - <diaUseProbScore>False</diaUseProbScore> - <diaProbScoreP>0.055</diaProbScoreP> - <diaProbScoreG>1.2</diaProbScoreG> - <diaProbScoreStep>0.1</diaProbScoreStep> - <isM2FragTypeOverride>False</isM2FragTypeOverride> - <ms2FragTypeOverride>0</ms2FragTypeOverride> - <classicLfqForSingleShots>True</classicLfqForSingleShots> - <sequenceBasedModifier>False</sequenceBasedModifier> - <diaRtFromSamplesForExport>True</diaRtFromSamplesForExport> - <diaCcsFromSamplesForExport>True</diaCcsFromSamplesForExport> - <diaLibraryExport>0</diaLibraryExport> - <diaUseApexWeightsForPtmLoc>False</diaUseApexWeightsForPtmLoc> - <diaSecondScoreForMultiplex>True</diaSecondScoreForMultiplex> - <diaPtmLocMethod>0</diaPtmLocMethod> - </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> - <IncludeWaterCross>False</IncludeWaterCross> - <IncludeAmmoniaCross>False</IncludeAmmoniaCross> - <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> - <IncludeWaterCross>False</IncludeWaterCross> - <IncludeAmmoniaCross>False</IncludeAmmoniaCross> - <DependentLosses>True</DependentLosses> - <Recalibration>False</Recalibration> - </msmsParams> - <msmsParams> - <Name>TOF</Name> - <MatchTolerance>25</MatchTolerance> - <MatchToleranceInPpm>True</MatchToleranceInPpm> - <DeisotopeTolerance>0.01</DeisotopeTolerance> - <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> - <DeNovoTolerance>25</DeNovoTolerance> - <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm> - <Deisotope>True</Deisotope> - <Topx>16</Topx> - <TopxInterval>100</TopxInterval> - <HigherCharges>True</HigherCharges> - <IncludeWater>True</IncludeWater> - <IncludeAmmonia>True</IncludeAmmonia> - <IncludeWaterCross>False</IncludeWaterCross> - <IncludeAmmoniaCross>False</IncludeAmmoniaCross> - <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> - <IncludeWaterCross>False</IncludeWaterCross> - <IncludeAmmoniaCross>False</IncludeAmmoniaCross> - <DependentLosses>True</DependentLosses> - <Recalibration>False</Recalibration> - </msmsParams> - </msmsParamsArray> - <fragmentationParamsArray> - <fragmentationParams> - <Name>HCD</Name> - <UseIntensityPrediction>False</UseIntensityPrediction> - <UseSequenceBasedModifier>False</UseSequenceBasedModifier> - <InternalFragments>False</InternalFragments> - <InternalFragmentWeight>1</InternalFragmentWeight> - <InternalFragmentAas>KRH</InternalFragmentAas> - </fragmentationParams> - <fragmentationParams> - <Name>CID</Name> - <UseIntensityPrediction>False</UseIntensityPrediction> - <UseSequenceBasedModifier>False</UseSequenceBasedModifier> - <InternalFragments>False</InternalFragments> - <InternalFragmentWeight>1</InternalFragmentWeight> - <InternalFragmentAas>KRH</InternalFragmentAas> - </fragmentationParams> - <fragmentationParams> - <Name>ETD</Name> - <UseIntensityPrediction>False</UseIntensityPrediction> - <UseSequenceBasedModifier>False</UseSequenceBasedModifier> - <InternalFragments>False</InternalFragments> - <InternalFragmentWeight>1</InternalFragmentWeight> - <InternalFragmentAas>KRH</InternalFragmentAas> - </fragmentationParams> - <fragmentationParams> - <Name>PQD</Name> - <UseIntensityPrediction>False</UseIntensityPrediction> - <UseSequenceBasedModifier>False</UseSequenceBasedModifier> - <InternalFragments>False</InternalFragments> - <InternalFragmentWeight>1</InternalFragmentWeight> - <InternalFragmentAas>KRH</InternalFragmentAas> - </fragmentationParams> - <fragmentationParams> - <Name>ETHCD</Name> - <UseIntensityPrediction>False</UseIntensityPrediction> - <UseSequenceBasedModifier>False</UseSequenceBasedModifier> - <InternalFragments>False</InternalFragments> - <InternalFragmentWeight>1</InternalFragmentWeight> - <InternalFragmentAas>KRH</InternalFragmentAas> - </fragmentationParams> - <fragmentationParams> - <Name>ETCID</Name> - <UseIntensityPrediction>False</UseIntensityPrediction> - <UseSequenceBasedModifier>False</UseSequenceBasedModifier> - <InternalFragments>False</InternalFragments> - <InternalFragmentWeight>1</InternalFragmentWeight> - <InternalFragmentAas>KRH</InternalFragmentAas> - </fragmentationParams> - <fragmentationParams> - <Name>UVPD</Name> - <UseIntensityPrediction>False</UseIntensityPrediction> - <UseSequenceBasedModifier>False</UseSequenceBasedModifier> - <InternalFragments>False</InternalFragments> - <InternalFragmentWeight>1</InternalFragmentWeight> - <InternalFragmentAas>KRH</InternalFragmentAas> - </fragmentationParams> - <fragmentationParams> - <Name>Unknown</Name> - <UseIntensityPrediction>False</UseIntensityPrediction> - <UseSequenceBasedModifier>False</UseSequenceBasedModifier> - <InternalFragments>False</InternalFragments> - <InternalFragmentWeight>1</InternalFragmentWeight> - <InternalFragmentAas>KRH</InternalFragmentAas> - </fragmentationParams> - </fragmentationParamsArray> -</MaxQuantParams> diff --git a/data/Custom dataset/msms.txt b/data/Custom dataset/msms.txt new file mode 100644 index 0000000000000000000000000000000000000000..d3934f6642c1e8f73a9982f84f2419d36a95615f Binary files /dev/null and b/data/Custom dataset/msms.txt differ