From b0239c7b493da3c304a11e84a23dc5f78632a246 Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Fri, 9 Aug 2024 10:27:51 +0200 Subject: [PATCH] :bug: Close 338 parsing MQ 2.6 (minPepLen) - MaxQuant 2.6 changed the a relevant parameter name: - minPepLen -> minPeptideLength --- proteobench/io/params/maxquant.py | 8 +- test/params/mqpar1.5.3.30_MBR_sel.json | 2 +- test/params/mqpar_mq2.6.2.0_1mc_MBR.csv | 525 ++++++++ test/params/mqpar_mq2.6.2.0_1mc_MBR.json | 1156 ++++++++++++++++++ test/params/mqpar_mq2.6.2.0_1mc_MBR.xml | 603 +++++++++ test/params/mqpar_mq2.6.2.0_1mc_MBR_sel.json | 22 + test/test_parse_params_maxquant.py | 1 + 7 files changed, 2315 insertions(+), 2 deletions(-) create mode 100644 test/params/mqpar_mq2.6.2.0_1mc_MBR.csv create mode 100644 test/params/mqpar_mq2.6.2.0_1mc_MBR.json create mode 100644 test/params/mqpar_mq2.6.2.0_1mc_MBR.xml create mode 100644 test/params/mqpar_mq2.6.2.0_1mc_MBR_sel.json diff --git a/proteobench/io/params/maxquant.py b/proteobench/io/params/maxquant.py index 8d8b8382..b3fd9fcd 100644 --- a/proteobench/io/params/maxquant.py +++ b/proteobench/io/params/maxquant.py @@ -154,7 +154,12 @@ def extract_params(fname, ms2frac="FTMS") -> ProteoBenchParameters: params.allowed_miscleavages = record.loc[ pd.IndexSlice["parameterGroups", "parameterGroup", "maxMissedCleavages", :] ].squeeze() - params.min_peptide_length = record.loc["minPepLen"].squeeze() + try: + params.min_peptide_length = record.loc["minPepLen"].squeeze() + except KeyError: + # Version 2.6 and above + params.minPeptideLength = record.loc["minPeptideLength"].squeeze() + # minPeptideLengthForUnspecificSearch (what is it?) params.max_peptide_length = None # fixed mods if params.software_version > "1.6.0.0": @@ -192,6 +197,7 @@ def extract_params(fname, ms2frac="FTMS") -> ProteoBenchParameters: "../../../test/params/mqpar_MQ1.6.3.3_MBR.xml", "../../../test/params/mqpar_MQ2.1.3.0_noMBR.xml", "../../../test/params/mqpar1.5.3.30_MBR.xml", + "../../../test/params/mqpar_mq2.6.2.0_1mc_MBR.xml", ]: print(f"{test_file = }") record = read_file(test_file) diff --git a/test/params/mqpar1.5.3.30_MBR_sel.json b/test/params/mqpar1.5.3.30_MBR_sel.json index ff5e3e0a..1f2a86db 100644 --- a/test/params/mqpar1.5.3.30_MBR_sel.json +++ b/test/params/mqpar1.5.3.30_MBR_sel.json @@ -18,4 +18,4 @@ "max_mods": "5", "min_precursor_charge": null, "max_precursor_charge": "7" -} +} \ No newline at end of file diff --git a/test/params/mqpar_mq2.6.2.0_1mc_MBR.csv b/test/params/mqpar_mq2.6.2.0_1mc_MBR.csv new file mode 100644 index 00000000..3c8fcf16 --- /dev/null +++ b/test/params/mqpar_mq2.6.2.0_1mc_MBR.csv @@ -0,0 +1,525 @@ +,,,,run_identifier +fastaFiles,FastaFileInfo,fastaFilePath,,\\unicph.domain\users\abc123\proteobench_202407\mq2.6.2.0_1mc_MBR\ProteoBenchFASTA_DDAQuantification.fasta +fastaFiles,FastaFileInfo,identifierParseRule,,>([^\s]*) +fastaFiles,FastaFileInfo,descriptionParseRule,,>(.*) +fastaFiles,FastaFileInfo,taxonomyParseRule,, +fastaFiles,FastaFileInfo,variationParseRule,, +fastaFiles,FastaFileInfo,modificationParseRule,, +fastaFiles,FastaFileInfo,taxonomyId,, +fastaFilesProteogenomics,,,, +fastaFilesFirstSearch,,,, +fixedSearchFolder,,,, +andromedaCacheSize,,,,350000 +advancedRatios,,,,True +pvalThres,,,,0.005 +rtShift,,,,False +separateLfq,,,,False +lfqStabilizeLargeRatios,,,,True +lfqRequireMsms,,,,True +lfqBayesQuant,,,,False +decoyMode,,,,revert +includeContaminants,,,,False +maxPeptideMass,,,,4600 +epsilonMutationScore,,,,True +mutatedPeptidesSeparately,,,,True +proteogenomicPeptidesSeparately,,,,True +minDeltaScoreUnmodifiedPeptides,,,,0 +minDeltaScoreModifiedPeptides,,,,6 +minScoreUnmodifiedPeptides,,,,0 +minScoreModifiedPeptides,,,,40 +secondPeptide,,,,True +matchBetweenRuns,,,,True +matchUnidentifiedFeatures,,,,False +matchBetweenRunsFdr,,,,False +dependentPeptides,,,,False +dependentPeptideFdr,,,,0 +dependentPeptideMassBin,,,,0 +dependentPeptidesBetweenRuns,,,,False +dependentPeptidesWithinExperiment,,,,False +dependentPeptidesWithinParameterGroup,,,,False +dependentPeptidesRestrictFractions,,,,False +dependentPeptidesFractionDifference,,,,0 +ibaq,,,,False +top3,,,,False +independentEnzymes,,,,False +useDeltaScore,,,,False +splitProteinGroupsByTaxonomy,,,,True +taxonomyLevel,,,,Species +avalon,,,,False +nModColumns,,,,3 +ibaqLogFit,,,,False +ibaqChargeNormalization,,,,False +razorProteinFdr,,,,True +deNovoSequencing,,,,False +deNovoVarMods,,,,False +deNovoCompleteSequence,,,,False +deNovoCalibratedMasses,,,,False +deNovoMaxIterations,,,,0 +deNovoProteaseReward,,,,0 +deNovoProteaseRewardTof,,,,0 +deNovoAgPenalty,,,,0 +deNovoGgPenalty,,,,0 +deNovoUseComplementScore,,,,True +deNovoUseProteaseScore,,,,True +deNovoUseWaterLossScore,,,,True +deNovoUseAmmoniaLossScore,,,,True +deNovoUseA2Score,,,,True +deNovoMassClusterTolDa,,,,0 +deNovoScalingFactor,,,,0 +massDifferenceSearch,,,,False +isotopeCalc,,,,False +minPeptideLength,,,,7 +psmFdrCrosslink,,,,0.01 +peptideFdr,,,,0.01 +proteinFdr,,,,0.01 +siteFdr,,,,0.01 +minPeptideLengthForUnspecificSearch,,,,8 +maxPeptideLengthForUnspecificSearch,,,,25 +useNormRatiosForOccupancy,,,,True +minPeptides,,,,1 +minRazorPeptides,,,,1 +minUniquePeptides,,,,0 +useCounterparts,,,,False +advancedSiteIntensities,,,,True +customProteinQuantification,,,,False +customProteinQuantificationFile,,,, +minRatioCount,,,,2 +restrictProteinQuantification,,,,True +restrictMods,string,,,Oxidation (M) +restrictMods,string,,,Acetyl (Protein N-term) +matchingTimeWindow,,,,0.4 +matchingIonMobilityWindow,,,,0.05 +alignmentTimeWindow,,,,20 +alignmentIonMobilityWindow,,,,1 +numberOfCandidatesMsms,,,,15 +compositionPrediction,,,,0 +quantMode,,,,1 +massDifferenceMods,,,, +mainSearchMaxCombinations,,,,200 +writeMsScansTable,,,,False +writeMsmsScansTable,,,,True +writePasefMsmsScansTable,,,,True +writeAccumulatedMsmsScansTable,,,,True +writeMs3ScansTable,,,,True +writeAllPeptidesTable,,,,False +writeMzRangeTable,,,,True +writeDiaFragmentTable,,,,False +writeDiaFragmentQuantTable,,,,False +writeMzTab,,,,False +writeSdrf,,,,False +disableMd5,,,,False +cacheBinInds,,,,True +etdIncludeB,,,,False +ms2PrecursorShift,,,,0 +complementaryIonPpm,,,,20 +variationParseRule,,,, +variationMode,,,,none +useSeriesReporters,,,,False +name,,,,session1 +maxQuantVersion,,,,2.6.2.0 +pluginFolder,,,, +numThreads,,,,4 +emailAddress,,,, +smtpHost,,,, +emailFromAddress,,,, +fullMinMz,,,,-1.7976931348623157E+308 +fullMaxMz,,,,1.7976931348623157E+308 +sendEmail,,,,False +ionCountIntensities,,,,False +verboseColumnHeaders,,,,False +calcPeakProperties,,,,False +showCentroidMassDifferences,,,,False +showIsotopeMassDifferences,,,,False +profilePerformance,,,,False +filePaths,string,,,\\unicph.domain\users\abc123\proteobench_202407\mq2.6.2.0_1mc_MBR\LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.raw +filePaths,string,,,\\unicph.domain\users\abc123\proteobench_202407\mq2.6.2.0_1mc_MBR\LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.raw +filePaths,string,,,\\unicph.domain\users\abc123\proteobench_202407\mq2.6.2.0_1mc_MBR\LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.raw +filePaths,string,,,\\unicph.domain\users\abc123\proteobench_202407\mq2.6.2.0_1mc_MBR\LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.raw +filePaths,string,,,\\unicph.domain\users\abc123\proteobench_202407\mq2.6.2.0_1mc_MBR\LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.raw +filePaths,string,,,\\unicph.domain\users\abc123\proteobench_202407\mq2.6.2.0_1mc_MBR\LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.raw +experiments,string,,,A_Sample_Alpha_01 +experiments,string,,,A_Sample_Alpha_02 +experiments,string,,,A_Sample_Alpha_03 +experiments,string,,,B_Sample_Alpha_01 +experiments,string,,,B_Sample_Alpha_02 +experiments,string,,,B_Sample_Alpha_03 +fractions,short,,,32767 +fractions,short,,,32767 +fractions,short,,,32767 +fractions,short,,,32767 +fractions,short,,,32767 +fractions,short,,,32767 +ptms,boolean,,,False +ptms,boolean,,,False +ptms,boolean,,,False +ptms,boolean,,,False +ptms,boolean,,,False +ptms,boolean,,,False +paramGroupIndices,int,,,0 +paramGroupIndices,int,,,0 +paramGroupIndices,int,,,0 +paramGroupIndices,int,,,0 +paramGroupIndices,int,,,0 +paramGroupIndices,int,,,0 +referenceChannel,string,,, +referenceChannel,string,,, +referenceChannel,string,,, +referenceChannel,string,,, +referenceChannel,string,,, +referenceChannel,string,,, +lfqTopNPeptides,,,,0 +diaJoinPrecChargesForLfq,,,,False +diaFragChargesForQuant,,,,1 +gridSpacing,,,,0.7 +proteinGroupingFile,,,, +simplePepCalculation,,,,False +useAndromeda20,,,,False +useAndromeda20DefaultModel,,,,False +andromeda20AltModelPath,,,, +intensityPredictionFolder,,,, +encoding,,,,0 +parameterGroups,parameterGroup,andromeda20AltModelPath,, +parameterGroups,parameterGroup,andromeda20DefaultModel,,False +parameterGroups,parameterGroup,useAndromeda20,,False +parameterGroups,parameterGroup,msInstrument,,0 +parameterGroups,parameterGroup,maxCharge,,7 +parameterGroups,parameterGroup,minPeakLen,,2 +parameterGroups,parameterGroup,diaMinPeakLen,,1 +parameterGroups,parameterGroup,useMs1Centroids,,False +parameterGroups,parameterGroup,useMs2Centroids,,False +parameterGroups,parameterGroup,cutPeaks,,True +parameterGroups,parameterGroup,gapScans,,1 +parameterGroups,parameterGroup,minTime,,NaN +parameterGroups,parameterGroup,maxTime,,NaN +parameterGroups,parameterGroup,matchType,,MatchFromAndTo +parameterGroups,parameterGroup,intensityDetermination,,0 +parameterGroups,parameterGroup,centroidMatchTol,,8 +parameterGroups,parameterGroup,centroidMatchTolInPpm,,True +parameterGroups,parameterGroup,centroidHalfWidth,,35 +parameterGroups,parameterGroup,centroidHalfWidthInPpm,,True +parameterGroups,parameterGroup,valleyFactor,,1.4 +parameterGroups,parameterGroup,isotopeValleyFactor,,1.2 +parameterGroups,parameterGroup,advancedPeakSplitting,,False +parameterGroups,parameterGroup,intensityThresholdMs1Dda,,0 +parameterGroups,parameterGroup,intensityThresholdMs1Dia,,0 +parameterGroups,parameterGroup,intensityThresholdMs2,,0 +parameterGroups,parameterGroup,labelMods,string, +parameterGroups,parameterGroup,lcmsRunType,,Standard +parameterGroups,parameterGroup,reQuantify,,False +parameterGroups,parameterGroup,lfqMode,,0 +parameterGroups,parameterGroup,lfqNormClusterSize,,80 +parameterGroups,parameterGroup,lfqMinEdgesPerNode,,3 +parameterGroups,parameterGroup,lfqAvEdgesPerNode,,6 +parameterGroups,parameterGroup,lfqMaxFeatures,,100000 +parameterGroups,parameterGroup,neucodeMaxPpm,,0 +parameterGroups,parameterGroup,neucodeResolution,,0 +parameterGroups,parameterGroup,neucodeResolutionInMda,,False +parameterGroups,parameterGroup,neucodeInSilicoLowRes,,False +parameterGroups,parameterGroup,fastLfq,,True +parameterGroups,parameterGroup,lfqRestrictFeatures,,False +parameterGroups,parameterGroup,lfqMinRatioCount,,2 +parameterGroups,parameterGroup,lfqMinRatioCountDia,,2 +parameterGroups,parameterGroup,lfqPrioritizeMs1Dia,,True +parameterGroups,parameterGroup,maxLabeledAa,,0 +parameterGroups,parameterGroup,maxNmods,,5 +parameterGroups,parameterGroup,maxMissedCleavages,,1 +parameterGroups,parameterGroup,maxMissedCleavagesDia,,1 +parameterGroups,parameterGroup,multiplicity,,1 +parameterGroups,parameterGroup,enzymeMode,,0 +parameterGroups,parameterGroup,complementaryReporterType,,0 +parameterGroups,parameterGroup,reporterNormalization,,0 +parameterGroups,parameterGroup,neucodeIntensityMode,,0 +parameterGroups,parameterGroup,fixedModifications,string,Carbamidomethyl (C) +parameterGroups,parameterGroup,enzymes,string,Trypsin/P +parameterGroups,parameterGroup,enzymesFirstSearch,, +parameterGroups,parameterGroup,enzymeModeFirstSearch,,0 +parameterGroups,parameterGroup,useEnzymeFirstSearch,,False +parameterGroups,parameterGroup,useVariableModificationsFirstSearch,,False +parameterGroups,parameterGroup,variableModifications,string,Oxidation (M) +parameterGroups,parameterGroup,variableModifications,string,Acetyl (Protein N-term) +parameterGroups,parameterGroup,useMultiModification,,False +parameterGroups,parameterGroup,multiModifications,, +parameterGroups,parameterGroup,isobaricLabels,, +parameterGroups,parameterGroup,neucodeLabels,, +parameterGroups,parameterGroup,variableModificationsFirstSearch,, +parameterGroups,parameterGroup,hasAdditionalVariableModifications,,False +parameterGroups,parameterGroup,additionalVariableModifications,, +parameterGroups,parameterGroup,additionalVariableModificationProteins,, +parameterGroups,parameterGroup,doMassFiltering,,True +parameterGroups,parameterGroup,firstSearchTol,,20 +parameterGroups,parameterGroup,mainSearchTol,,4.5 +parameterGroups,parameterGroup,searchTolInPpm,,True +parameterGroups,parameterGroup,isotopeMatchTol,,2 +parameterGroups,parameterGroup,isotopeMatchTolInPpm,,True +parameterGroups,parameterGroup,isotopeTimeCorrelation,,0.6 +parameterGroups,parameterGroup,theorIsotopeCorrelation,,0.6 +parameterGroups,parameterGroup,checkMassDeficit,,True +parameterGroups,parameterGroup,recalibrationInPpm,,True +parameterGroups,parameterGroup,intensityDependentCalibration,,False +parameterGroups,parameterGroup,minScoreForCalibration,,70 +parameterGroups,parameterGroup,matchLibraryFile,,False +parameterGroups,parameterGroup,libraryFile,, +parameterGroups,parameterGroup,matchLibraryMassTolPpm,,0 +parameterGroups,parameterGroup,matchLibraryTimeTolMin,,0 +parameterGroups,parameterGroup,matchLabelTimeTolMin,,0 +parameterGroups,parameterGroup,reporterMassTolerance,,NaN +parameterGroups,parameterGroup,reporterPif,,NaN +parameterGroups,parameterGroup,filterPif,,False +parameterGroups,parameterGroup,reporterFraction,,NaN +parameterGroups,parameterGroup,reporterBasePeakRatio,,NaN +parameterGroups,parameterGroup,timsHalfWidth,,0 +parameterGroups,parameterGroup,timsStep,,0 +parameterGroups,parameterGroup,timsResolution,,0 +parameterGroups,parameterGroup,timsMinMsmsIntensity,,0 +parameterGroups,parameterGroup,timsRemovePrecursor,,True +parameterGroups,parameterGroup,timsIsobaricLabels,,False +parameterGroups,parameterGroup,timsCollapseMsms,,True +parameterGroups,parameterGroup,crossLinkingType,,0 +parameterGroups,parameterGroup,crossLinker,, +parameterGroups,parameterGroup,minMatchXl,,3 +parameterGroups,parameterGroup,minPairedPepLenXl,,6 +parameterGroups,parameterGroup,minScoreDipeptide,,40 +parameterGroups,parameterGroup,minScoreMonopeptide,,0 +parameterGroups,parameterGroup,minScorePartialCross,,10 +parameterGroups,parameterGroup,crosslinkOnlyIntraProtein,,False +parameterGroups,parameterGroup,crosslinkIntensityBasedPrecursor,,True +parameterGroups,parameterGroup,isHybridPrecDetermination,,False +parameterGroups,parameterGroup,topXcross,,3 +parameterGroups,parameterGroup,doesSeparateInterIntraProteinCross,,False +parameterGroups,parameterGroup,crosslinkMaxMonoUnsaturated,,0 +parameterGroups,parameterGroup,crosslinkMaxMonoSaturated,,0 +parameterGroups,parameterGroup,crosslinkMaxDiUnsaturated,,0 +parameterGroups,parameterGroup,crosslinkMaxDiSaturated,,0 +parameterGroups,parameterGroup,crosslinkModifications,, +parameterGroups,parameterGroup,crosslinkFastaFiles,, +parameterGroups,parameterGroup,crosslinkSites,, +parameterGroups,parameterGroup,crosslinkNetworkFiles,, +parameterGroups,parameterGroup,crosslinkMode,, +parameterGroups,parameterGroup,peakRefinement,,False +parameterGroups,parameterGroup,peakRefinementCrosslinking,,False +parameterGroups,parameterGroup,isobaricSumOverWindow,,True +parameterGroups,parameterGroup,isobaricWeightExponent,,0.75 +parameterGroups,parameterGroup,collapseMsmsOnIsotopePatterns,,False +parameterGroups,parameterGroup,diaLibraryType,,0 +parameterGroups,parameterGroup,diaLibraryPaths,, +parameterGroups,parameterGroup,diaEvidencePaths,, +parameterGroups,parameterGroup,diaMsmsPaths,, +parameterGroups,parameterGroup,diaLabelIndsForLibraryMatch,, +parameterGroups,parameterGroup,diaInitialPrecMassTolPpm,,20 +parameterGroups,parameterGroup,diaInitialFragMassTolPpm,,20 +parameterGroups,parameterGroup,diaCorrThresholdFeatureClustering,,0.85 +parameterGroups,parameterGroup,diaPrecTolPpmFeatureClustering,,2 +parameterGroups,parameterGroup,diaFragTolPpmFeatureClustering,,2 +parameterGroups,parameterGroup,diaScoreN,,12 +parameterGroups,parameterGroup,diaScoreNAdditional,,5 +parameterGroups,parameterGroup,diaMinScore,,1.99 +parameterGroups,parameterGroup,diaXgBoostBaseScore,,0.4 +parameterGroups,parameterGroup,diaXgBoostSubSample,,0.9 +parameterGroups,parameterGroup,centroidPosition,,0 +parameterGroups,parameterGroup,diaQuantMethod,,7 +parameterGroups,parameterGroup,diaFeatureQuantMethod,,2 +parameterGroups,parameterGroup,lfqNormType,,1 +parameterGroups,parameterGroup,diaTopNForQuant,,12 +parameterGroups,parameterGroup,diaTopNCorrelatingFragmentsForQuant,,7 +parameterGroups,parameterGroup,diaFragmentCorrelationForQuant,,0.78 +parameterGroups,parameterGroup,lfqUsePeptideCorrelation,,True +parameterGroups,parameterGroup,lfqTopNCorrelatingPeptides,,3 +parameterGroups,parameterGroup,lfqPeptideCorrelation,,3 +parameterGroups,parameterGroup,diaMinMsmsIntensityForQuant,,0 +parameterGroups,parameterGroup,diaTopMsmsIntensityQuantileForQuant,,0.85 +parameterGroups,parameterGroup,diaMinFragmentOverlapScore,,0 +parameterGroups,parameterGroup,diaMinPrecursorScore,,0 +parameterGroups,parameterGroup,diaUseProfileCorrelation,,False +parameterGroups,parameterGroup,diaMinPrecProfileCorrelation,,0 +parameterGroups,parameterGroup,diaMinFragProfileCorrelation,,0 +parameterGroups,parameterGroup,diaXgBoostMinChildWeight,,9 +parameterGroups,parameterGroup,diaXgBoostMaximumTreeDepth,,12 +parameterGroups,parameterGroup,diaXgBoostEstimators,,580 +parameterGroups,parameterGroup,diaXgBoostGamma,,0.9 +parameterGroups,parameterGroup,diaXgBoostMaxDeltaStep,,3 +parameterGroups,parameterGroup,diaGlobalMl,,True +parameterGroups,parameterGroup,diaAdaptiveMassAccuracy,,False +parameterGroups,parameterGroup,diaMassWindowFactor,,3.3 +parameterGroups,parameterGroup,diaNoMl,,False +parameterGroups,parameterGroup,diaPermuteRt,,False +parameterGroups,parameterGroup,diaPermuteCcs,,False +parameterGroups,parameterGroup,diaBackgroundSubtraction,,False +parameterGroups,parameterGroup,diaBackgroundSubtractionQuantile,,0.5 +parameterGroups,parameterGroup,diaBackgroundSubtractionFactor,,4 +parameterGroups,parameterGroup,diaLfqRatioType,,0 +parameterGroups,parameterGroup,diaTransferQvalue,,0.3 +parameterGroups,parameterGroup,diaTransferQvalueBetweenLabels,,0.01 +parameterGroups,parameterGroup,diaTransferQvalueBetweenFractions,,0.01 +parameterGroups,parameterGroup,diaTransferQvalueBetweenFaims,,0.01 +parameterGroups,parameterGroup,diaOnlyIsosForRecal,,True +parameterGroups,parameterGroup,diaMinPeaks,,5 +parameterGroups,parameterGroup,diaUseFragIntensForMl,,False +parameterGroups,parameterGroup,diaUseFragMassesForMl,,False +parameterGroups,parameterGroup,diaMaxTrainInstances,,500000 +parameterGroups,parameterGroup,diaMaxFragmentCharge,,3 +parameterGroups,parameterGroup,diaAdaptiveMlScoring,,False +parameterGroups,parameterGroup,diaDynamicScoringMaxInstances,,25000 +parameterGroups,parameterGroup,diaMaxPrecursorMz,,0 +parameterGroups,parameterGroup,diaHardRtFilter,,True +parameterGroups,parameterGroup,diaConvertLibraryCharge2Fragments,,False +parameterGroups,parameterGroup,diaChargeNormalizationLibrary,,True +parameterGroups,parameterGroup,diaChargeNormalizationSample,,True +parameterGroups,parameterGroup,diaDeleteIntermediateResults,,True +parameterGroups,parameterGroup,diaScoreWeightScanIndex,,-1 +parameterGroups,parameterGroup,diaScoreWeightScanValue,,1 +parameterGroups,parameterGroup,diaNumNonleadingMatches,,0 +parameterGroups,parameterGroup,diaFragmentModelType,,0 +parameterGroups,parameterGroup,diaAltFragmentModelPath,, +parameterGroups,parameterGroup,diaUseDefaultRtModel,,True +parameterGroups,parameterGroup,diaAltRtModelPath,, +parameterGroups,parameterGroup,diaUseDefaultCcsModel,,True +parameterGroups,parameterGroup,diaAltCcsModelPath,, +parameterGroups,parameterGroup,diaBatchProcessing,,True +parameterGroups,parameterGroup,diaBatchSize,,25 +parameterGroups,parameterGroup,diaFirstBatch,,-1 +parameterGroups,parameterGroup,diaLastBatch,,-1 +parameterGroups,parameterGroup,diaOnlyPreprocess,,False +parameterGroups,parameterGroup,diaMultiplexQuantMethod,,1 +parameterGroups,parameterGroup,diaOnlyPostprocess,,False +parameterGroups,parameterGroup,diaRequirePrecursor,,False +parameterGroups,parameterGroup,diaFuturePeptides,,False +parameterGroups,parameterGroup,diaOverrideRtWithPrediction,,False +parameterGroups,parameterGroup,diaMaxModifications,,0 +parameterGroups,parameterGroup,diaMaxPositionings,,0 +parameterGroups,parameterGroup,diaPredictCharges,,False +parameterGroups,parameterGroup,diaUseProbScore,,False +parameterGroups,parameterGroup,diaProbScoreP,,0.055 +parameterGroups,parameterGroup,diaProbScoreG,,1.2 +parameterGroups,parameterGroup,diaProbScoreStep,,0.1 +parameterGroups,parameterGroup,isM2FragTypeOverride,,False +parameterGroups,parameterGroup,ms2FragTypeOverride,,0 +parameterGroups,parameterGroup,classicLfqForSingleShots,,True +parameterGroups,parameterGroup,sequenceBasedModifier,,False +parameterGroups,parameterGroup,diaRtFromSamplesForExport,,True +parameterGroups,parameterGroup,diaCcsFromSamplesForExport,,True +parameterGroups,parameterGroup,diaLibraryExport,,0 +parameterGroups,parameterGroup,diaUseApexWeightsForPtmLoc,,False +parameterGroups,parameterGroup,diaSecondScoreForMultiplex,,True +parameterGroups,parameterGroup,diaBestPrecursorChargeForQuant,,False +parameterGroups,parameterGroup,diaBestPrecursorMassRangeForQuant,,False +parameterGroups,parameterGroup,diaBestPrecursorIntensityForQuant,,False +parameterGroups,parameterGroup,diaPtmLocMethod,,0 +parameterGroups,parameterGroup,diaIndexedSearch,,True +parameterGroups,parameterGroup,diaIncreaseSequenceCoverage,,True +parameterGroups,parameterGroup,diaSequenceCoverageFdr,,0.03 +msmsParamsArray,msmsParams,Name,,FTMS +msmsParamsArray,msmsParams,MatchTolerance,,20 +msmsParamsArray,msmsParams,MatchToleranceInPpm,,True +msmsParamsArray,msmsParams,DeisotopeTolerance,,7 +msmsParamsArray,msmsParams,DeisotopeToleranceInPpm,,True +msmsParamsArray,msmsParams,DeNovoTolerance,,25 +msmsParamsArray,msmsParams,DeNovoToleranceInPpm,,True +msmsParamsArray,msmsParams,Deisotope,,True +msmsParamsArray,msmsParams,Topx,,12 +msmsParamsArray,msmsParams,TopxInterval,,100 +msmsParamsArray,msmsParams,HigherCharges,,True +msmsParamsArray,msmsParams,IncludeWater,,True +msmsParamsArray,msmsParams,IncludeAmmonia,,True +msmsParamsArray,msmsParams,IncludeWaterCross,,False +msmsParamsArray,msmsParams,IncludeAmmoniaCross,,False +msmsParamsArray,msmsParams,DependentLosses,,True +msmsParamsArray,msmsParams,Recalibration,,False +msmsParamsArray,msmsParams,Name,,ITMS +msmsParamsArray,msmsParams,MatchTolerance,,0.5 +msmsParamsArray,msmsParams,MatchToleranceInPpm,,False +msmsParamsArray,msmsParams,DeisotopeTolerance,,0.15 +msmsParamsArray,msmsParams,DeisotopeToleranceInPpm,,False +msmsParamsArray,msmsParams,DeNovoTolerance,,0.5 +msmsParamsArray,msmsParams,DeNovoToleranceInPpm,,False +msmsParamsArray,msmsParams,Deisotope,,False +msmsParamsArray,msmsParams,Topx,,8 +msmsParamsArray,msmsParams,TopxInterval,,100 +msmsParamsArray,msmsParams,HigherCharges,,True +msmsParamsArray,msmsParams,IncludeWater,,True +msmsParamsArray,msmsParams,IncludeAmmonia,,True +msmsParamsArray,msmsParams,IncludeWaterCross,,False +msmsParamsArray,msmsParams,IncludeAmmoniaCross,,False +msmsParamsArray,msmsParams,DependentLosses,,True +msmsParamsArray,msmsParams,Recalibration,,False +msmsParamsArray,msmsParams,Name,,TOF +msmsParamsArray,msmsParams,MatchTolerance,,25 +msmsParamsArray,msmsParams,MatchToleranceInPpm,,True +msmsParamsArray,msmsParams,DeisotopeTolerance,,0.01 +msmsParamsArray,msmsParams,DeisotopeToleranceInPpm,,False +msmsParamsArray,msmsParams,DeNovoTolerance,,25 +msmsParamsArray,msmsParams,DeNovoToleranceInPpm,,True +msmsParamsArray,msmsParams,Deisotope,,True +msmsParamsArray,msmsParams,Topx,,16 +msmsParamsArray,msmsParams,TopxInterval,,100 +msmsParamsArray,msmsParams,HigherCharges,,True +msmsParamsArray,msmsParams,IncludeWater,,True +msmsParamsArray,msmsParams,IncludeAmmonia,,True +msmsParamsArray,msmsParams,IncludeWaterCross,,False +msmsParamsArray,msmsParams,IncludeAmmoniaCross,,False +msmsParamsArray,msmsParams,DependentLosses,,True +msmsParamsArray,msmsParams,Recalibration,,False +msmsParamsArray,msmsParams,Name,,UNKNOWN +msmsParamsArray,msmsParams,MatchTolerance,,20 +msmsParamsArray,msmsParams,MatchToleranceInPpm,,True +msmsParamsArray,msmsParams,DeisotopeTolerance,,7 +msmsParamsArray,msmsParams,DeisotopeToleranceInPpm,,True +msmsParamsArray,msmsParams,DeNovoTolerance,,25 +msmsParamsArray,msmsParams,DeNovoToleranceInPpm,,True +msmsParamsArray,msmsParams,Deisotope,,True +msmsParamsArray,msmsParams,Topx,,12 +msmsParamsArray,msmsParams,TopxInterval,,100 +msmsParamsArray,msmsParams,HigherCharges,,True +msmsParamsArray,msmsParams,IncludeWater,,True +msmsParamsArray,msmsParams,IncludeAmmonia,,True +msmsParamsArray,msmsParams,IncludeWaterCross,,False +msmsParamsArray,msmsParams,IncludeAmmoniaCross,,False +msmsParamsArray,msmsParams,DependentLosses,,True +msmsParamsArray,msmsParams,Recalibration,,False +fragmentationParamsArray,fragmentationParams,Name,,HCD +fragmentationParamsArray,fragmentationParams,UseIntensityPrediction,,False +fragmentationParamsArray,fragmentationParams,UseSequenceBasedModifier,,False +fragmentationParamsArray,fragmentationParams,InternalFragments,,False +fragmentationParamsArray,fragmentationParams,InternalFragmentWeight,,1 +fragmentationParamsArray,fragmentationParams,InternalFragmentAas,,KRH +fragmentationParamsArray,fragmentationParams,Name,,CID +fragmentationParamsArray,fragmentationParams,UseIntensityPrediction,,False +fragmentationParamsArray,fragmentationParams,UseSequenceBasedModifier,,False +fragmentationParamsArray,fragmentationParams,InternalFragments,,False +fragmentationParamsArray,fragmentationParams,InternalFragmentWeight,,1 +fragmentationParamsArray,fragmentationParams,InternalFragmentAas,,KRH +fragmentationParamsArray,fragmentationParams,Name,,ETD +fragmentationParamsArray,fragmentationParams,UseIntensityPrediction,,False +fragmentationParamsArray,fragmentationParams,UseSequenceBasedModifier,,False +fragmentationParamsArray,fragmentationParams,InternalFragments,,False +fragmentationParamsArray,fragmentationParams,InternalFragmentWeight,,1 +fragmentationParamsArray,fragmentationParams,InternalFragmentAas,,KRH +fragmentationParamsArray,fragmentationParams,Name,,PQD +fragmentationParamsArray,fragmentationParams,UseIntensityPrediction,,False +fragmentationParamsArray,fragmentationParams,UseSequenceBasedModifier,,False +fragmentationParamsArray,fragmentationParams,InternalFragments,,False +fragmentationParamsArray,fragmentationParams,InternalFragmentWeight,,1 +fragmentationParamsArray,fragmentationParams,InternalFragmentAas,,KRH +fragmentationParamsArray,fragmentationParams,Name,,ETHCD +fragmentationParamsArray,fragmentationParams,UseIntensityPrediction,,False +fragmentationParamsArray,fragmentationParams,UseSequenceBasedModifier,,False +fragmentationParamsArray,fragmentationParams,InternalFragments,,False +fragmentationParamsArray,fragmentationParams,InternalFragmentWeight,,1 +fragmentationParamsArray,fragmentationParams,InternalFragmentAas,,KRH +fragmentationParamsArray,fragmentationParams,Name,,ETCID +fragmentationParamsArray,fragmentationParams,UseIntensityPrediction,,False +fragmentationParamsArray,fragmentationParams,UseSequenceBasedModifier,,False +fragmentationParamsArray,fragmentationParams,InternalFragments,,False +fragmentationParamsArray,fragmentationParams,InternalFragmentWeight,,1 +fragmentationParamsArray,fragmentationParams,InternalFragmentAas,,KRH +fragmentationParamsArray,fragmentationParams,Name,,UVPD +fragmentationParamsArray,fragmentationParams,UseIntensityPrediction,,False +fragmentationParamsArray,fragmentationParams,UseSequenceBasedModifier,,False +fragmentationParamsArray,fragmentationParams,InternalFragments,,False +fragmentationParamsArray,fragmentationParams,InternalFragmentWeight,,1 +fragmentationParamsArray,fragmentationParams,InternalFragmentAas,,KRH +fragmentationParamsArray,fragmentationParams,Name,,Unknown +fragmentationParamsArray,fragmentationParams,UseIntensityPrediction,,False +fragmentationParamsArray,fragmentationParams,UseSequenceBasedModifier,,False +fragmentationParamsArray,fragmentationParams,InternalFragments,,False +fragmentationParamsArray,fragmentationParams,InternalFragmentWeight,,1 +fragmentationParamsArray,fragmentationParams,InternalFragmentAas,,KRH diff --git a/test/params/mqpar_mq2.6.2.0_1mc_MBR.json b/test/params/mqpar_mq2.6.2.0_1mc_MBR.json new file mode 100644 index 00000000..2100926e --- /dev/null +++ b/test/params/mqpar_mq2.6.2.0_1mc_MBR.json @@ -0,0 +1,1156 @@ +{ + "fastaFiles": { + "FastaFileInfo": [ + { + "fastaFilePath": "\\\\unicph.domain\\users\\abc123\\proteobench_202407\\mq2.6.2.0_1mc_MBR\\ProteoBenchFASTA_DDAQuantification.fasta" + }, + { + "identifierParseRule": ">([^\\s]*)" + }, + { + "descriptionParseRule": ">(.*)" + }, + { + "taxonomyParseRule": null + }, + { + "variationParseRule": null + }, + { + "modificationParseRule": null + }, + { + "taxonomyId": null + } + ] + }, + "fastaFilesProteogenomics": null, + "fastaFilesFirstSearch": null, + "fixedSearchFolder": null, + "andromedaCacheSize": "350000", + "advancedRatios": "True", + "pvalThres": "0.005", + "rtShift": "False", + "separateLfq": "False", + "lfqStabilizeLargeRatios": "True", + "lfqRequireMsms": "True", + "lfqBayesQuant": "False", + "decoyMode": "revert", + "includeContaminants": "False", + "maxPeptideMass": "4600", + "epsilonMutationScore": "True", + "mutatedPeptidesSeparately": "True", + "proteogenomicPeptidesSeparately": "True", + "minDeltaScoreUnmodifiedPeptides": "0", + "minDeltaScoreModifiedPeptides": "6", + "minScoreUnmodifiedPeptides": "0", + "minScoreModifiedPeptides": "40", + "secondPeptide": "True", + "matchBetweenRuns": "True", + "matchUnidentifiedFeatures": "False", + "matchBetweenRunsFdr": "False", + "dependentPeptides": "False", + "dependentPeptideFdr": "0", + "dependentPeptideMassBin": "0", + "dependentPeptidesBetweenRuns": "False", + "dependentPeptidesWithinExperiment": "False", + "dependentPeptidesWithinParameterGroup": "False", + "dependentPeptidesRestrictFractions": "False", + "dependentPeptidesFractionDifference": "0", + "ibaq": "False", + "top3": "False", + "independentEnzymes": "False", + "useDeltaScore": "False", + "splitProteinGroupsByTaxonomy": "True", + "taxonomyLevel": "Species", + "avalon": "False", + "nModColumns": "3", + "ibaqLogFit": "False", + "ibaqChargeNormalization": "False", + "razorProteinFdr": "True", + "deNovoSequencing": "False", + "deNovoVarMods": "False", + "deNovoCompleteSequence": "False", + "deNovoCalibratedMasses": "False", + "deNovoMaxIterations": "0", + "deNovoProteaseReward": "0", + "deNovoProteaseRewardTof": "0", + "deNovoAgPenalty": "0", + "deNovoGgPenalty": "0", + "deNovoUseComplementScore": "True", + "deNovoUseProteaseScore": "True", + "deNovoUseWaterLossScore": "True", + "deNovoUseAmmoniaLossScore": "True", + "deNovoUseA2Score": "True", + "deNovoMassClusterTolDa": "0", + "deNovoScalingFactor": "0", + "massDifferenceSearch": "False", + "isotopeCalc": "False", + "minPeptideLength": "7", + "psmFdrCrosslink": "0.01", + "peptideFdr": "0.01", + "proteinFdr": "0.01", + "siteFdr": "0.01", + "minPeptideLengthForUnspecificSearch": "8", + "maxPeptideLengthForUnspecificSearch": "25", + "useNormRatiosForOccupancy": "True", + "minPeptides": "1", + "minRazorPeptides": "1", + "minUniquePeptides": "0", + "useCounterparts": "False", + "advancedSiteIntensities": "True", + "customProteinQuantification": "False", + "customProteinQuantificationFile": null, + "minRatioCount": "2", + "restrictProteinQuantification": "True", + "restrictMods": [ + { + "string": "Oxidation (M)" + }, + { + "string": "Acetyl (Protein N-term)" + } + ], + "matchingTimeWindow": "0.4", + "matchingIonMobilityWindow": "0.05", + "alignmentTimeWindow": "20", + "alignmentIonMobilityWindow": "1", + "numberOfCandidatesMsms": "15", + "compositionPrediction": "0", + "quantMode": "1", + "massDifferenceMods": null, + "mainSearchMaxCombinations": "200", + "writeMsScansTable": "False", + "writeMsmsScansTable": "True", + "writePasefMsmsScansTable": "True", + "writeAccumulatedMsmsScansTable": "True", + "writeMs3ScansTable": "True", + "writeAllPeptidesTable": "False", + "writeMzRangeTable": "True", + "writeDiaFragmentTable": "False", + "writeDiaFragmentQuantTable": "False", + "writeMzTab": "False", + "writeSdrf": "False", + "disableMd5": "False", + "cacheBinInds": "True", + "etdIncludeB": "False", + "ms2PrecursorShift": "0", + "complementaryIonPpm": "20", + "variationParseRule": null, + "variationMode": "none", + "useSeriesReporters": "False", + "name": "session1", + "maxQuantVersion": "2.6.2.0", + "pluginFolder": null, + "numThreads": "4", + "emailAddress": null, + "smtpHost": null, + "emailFromAddress": null, + "fullMinMz": "-1.7976931348623157E+308", + "fullMaxMz": "1.7976931348623157E+308", + "sendEmail": "False", + "ionCountIntensities": "False", + "verboseColumnHeaders": "False", + "calcPeakProperties": "False", + "showCentroidMassDifferences": "False", + "showIsotopeMassDifferences": "False", + "profilePerformance": "False", + "filePaths": [ + { + "string": "\\\\unicph.domain\\users\\abc123\\proteobench_202407\\mq2.6.2.0_1mc_MBR\\LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.raw" + }, + { + "string": "\\\\unicph.domain\\users\\abc123\\proteobench_202407\\mq2.6.2.0_1mc_MBR\\LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.raw" + }, + { + "string": "\\\\unicph.domain\\users\\abc123\\proteobench_202407\\mq2.6.2.0_1mc_MBR\\LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.raw" + }, + { + "string": "\\\\unicph.domain\\users\\abc123\\proteobench_202407\\mq2.6.2.0_1mc_MBR\\LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.raw" + }, + { + "string": "\\\\unicph.domain\\users\\abc123\\proteobench_202407\\mq2.6.2.0_1mc_MBR\\LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.raw" + }, + { + "string": "\\\\unicph.domain\\users\\abc123\\proteobench_202407\\mq2.6.2.0_1mc_MBR\\LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.raw" + } + ], + "experiments": [ + { + "string": "A_Sample_Alpha_01" + }, + { + "string": "A_Sample_Alpha_02" + }, + { + "string": "A_Sample_Alpha_03" + }, + { + "string": "B_Sample_Alpha_01" + }, + { + "string": "B_Sample_Alpha_02" + }, + { + "string": "B_Sample_Alpha_03" + } + ], + "fractions": [ + { + "short": "32767" + }, + { + "short": "32767" + }, + { + "short": "32767" + }, + { + "short": "32767" + }, + { + "short": "32767" + }, + { + "short": "32767" + } + ], + "ptms": [ + { + "boolean": "False" + }, + { + "boolean": "False" + }, + { + "boolean": "False" + }, + { + "boolean": "False" + }, + { + "boolean": "False" + }, + { + "boolean": "False" + } + ], + "paramGroupIndices": [ + { + "int": "0" + }, + { + "int": "0" + }, + { + "int": "0" + }, + { + "int": "0" + }, + { + "int": "0" + }, + { + "int": "0" + } + ], + "referenceChannel": [ + { + "string": null + }, + { + "string": null + }, + { + "string": null + }, + { + "string": null + }, + { + "string": null + }, + { + "string": null + } + ], + "lfqTopNPeptides": "0", + "diaJoinPrecChargesForLfq": "False", + "diaFragChargesForQuant": "1", + "gridSpacing": "0.7", + "proteinGroupingFile": null, + "simplePepCalculation": "False", + "useAndromeda20": "False", + "useAndromeda20DefaultModel": "False", + "andromeda20AltModelPath": null, + "intensityPredictionFolder": null, + "encoding": "0", + "parameterGroups": { + "parameterGroup": [ + { + "andromeda20AltModelPath": null + }, + { + "andromeda20DefaultModel": "False" + }, + { + "useAndromeda20": "False" + }, + { + "msInstrument": "0" + }, + { + "maxCharge": "7" + }, + { + "minPeakLen": "2" + }, + { + "diaMinPeakLen": "1" + }, + { + "useMs1Centroids": "False" + }, + { + "useMs2Centroids": "False" + }, + { + "cutPeaks": "True" + }, + { + "gapScans": "1" + }, + { + "minTime": "NaN" + }, + { + "maxTime": "NaN" + }, + { + "matchType": "MatchFromAndTo" + }, + { + "intensityDetermination": "0" + }, + { + "centroidMatchTol": "8" + }, + { + "centroidMatchTolInPpm": "True" + }, + { + "centroidHalfWidth": "35" + }, + { + "centroidHalfWidthInPpm": "True" + }, + { + "valleyFactor": "1.4" + }, + { + "isotopeValleyFactor": "1.2" + }, + { + "advancedPeakSplitting": "False" + }, + { + "intensityThresholdMs1Dda": "0" + }, + { + "intensityThresholdMs1Dia": "0" + }, + { + "intensityThresholdMs2": "0" + }, + { + "labelMods": { + "string": null + } + }, + { + "lcmsRunType": "Standard" + }, + { + "reQuantify": "False" + }, + { + "lfqMode": "0" + }, + { + "lfqNormClusterSize": "80" + }, + { + "lfqMinEdgesPerNode": "3" + }, + { + "lfqAvEdgesPerNode": "6" + }, + { + "lfqMaxFeatures": "100000" + }, + { + "neucodeMaxPpm": "0" + }, + { + "neucodeResolution": "0" + }, + { + "neucodeResolutionInMda": "False" + }, + { + "neucodeInSilicoLowRes": "False" + }, + { + "fastLfq": "True" + }, + { + "lfqRestrictFeatures": "False" + }, + { + "lfqMinRatioCount": "2" + }, + { + "lfqMinRatioCountDia": "2" + }, + { + "lfqPrioritizeMs1Dia": "True" + }, + { + "maxLabeledAa": "0" + }, + { + "maxNmods": "5" + }, + { + "maxMissedCleavages": "1" + }, + { + "maxMissedCleavagesDia": "1" + }, + { + "multiplicity": "1" + }, + { + "enzymeMode": "0" + }, + { + "complementaryReporterType": "0" + }, + { + "reporterNormalization": "0" + }, + { + "neucodeIntensityMode": "0" + }, + { + "fixedModifications": { + "string": "Carbamidomethyl (C)" + } + }, + { + "enzymes": { + "string": "Trypsin/P" + } + }, + { + "enzymesFirstSearch": null + }, + { + "enzymeModeFirstSearch": "0" + }, + { + "useEnzymeFirstSearch": "False" + }, + { + "useVariableModificationsFirstSearch": "False" + }, + { + "variableModifications": { + "string": [ + "Oxidation (M)", + "Acetyl (Protein N-term)" + ] + } + }, + { + "useMultiModification": "False" + }, + { + "multiModifications": null + }, + { + "isobaricLabels": null + }, + { + "neucodeLabels": null + }, + { + "variableModificationsFirstSearch": null + }, + { + "hasAdditionalVariableModifications": "False" + }, + { + "additionalVariableModifications": null + }, + { + "additionalVariableModificationProteins": null + }, + { + "doMassFiltering": "True" + }, + { + "firstSearchTol": "20" + }, + { + "mainSearchTol": "4.5" + }, + { + "searchTolInPpm": "True" + }, + { + "isotopeMatchTol": "2" + }, + { + "isotopeMatchTolInPpm": "True" + }, + { + "isotopeTimeCorrelation": "0.6" + }, + { + "theorIsotopeCorrelation": "0.6" + }, + { + "checkMassDeficit": "True" + }, + { + "recalibrationInPpm": "True" + }, + { + "intensityDependentCalibration": "False" + }, + { + "minScoreForCalibration": "70" + }, + { + "matchLibraryFile": "False" + }, + { + "libraryFile": null + }, + { + "matchLibraryMassTolPpm": "0" + }, + { + "matchLibraryTimeTolMin": "0" + }, + { + "matchLabelTimeTolMin": "0" + }, + { + "reporterMassTolerance": "NaN" + }, + { + "reporterPif": "NaN" + }, + { + "filterPif": "False" + }, + { + "reporterFraction": "NaN" + }, + { + "reporterBasePeakRatio": "NaN" + }, + { + "timsHalfWidth": "0" + }, + { + "timsStep": "0" + }, + { + "timsResolution": "0" + }, + { + "timsMinMsmsIntensity": "0" + }, + { + "timsRemovePrecursor": "True" + }, + { + "timsIsobaricLabels": "False" + }, + { + "timsCollapseMsms": "True" + }, + { + "crossLinkingType": "0" + }, + { + "crossLinker": null + }, + { + "minMatchXl": "3" + }, + { + "minPairedPepLenXl": "6" + }, + { + "minScoreDipeptide": "40" + }, + { + "minScoreMonopeptide": "0" + }, + { + "minScorePartialCross": "10" + }, + { + "crosslinkOnlyIntraProtein": "False" + }, + { + "crosslinkIntensityBasedPrecursor": "True" + }, + { + "isHybridPrecDetermination": "False" + }, + { + "topXcross": "3" + }, + { + "doesSeparateInterIntraProteinCross": "False" + }, + { + "crosslinkMaxMonoUnsaturated": "0" + }, + { + "crosslinkMaxMonoSaturated": "0" + }, + { + "crosslinkMaxDiUnsaturated": "0" + }, + { + "crosslinkMaxDiSaturated": "0" + }, + { + "crosslinkModifications": null + }, + { + "crosslinkFastaFiles": null + }, + { + "crosslinkSites": null + }, + { + "crosslinkNetworkFiles": null + }, + { + "crosslinkMode": null + }, + { + "peakRefinement": "False" + }, + { + "peakRefinementCrosslinking": "False" + }, + { + "isobaricSumOverWindow": "True" + }, + { + "isobaricWeightExponent": "0.75" + }, + { + "collapseMsmsOnIsotopePatterns": "False" + }, + { + "diaLibraryType": "0" + }, + { + "diaLibraryPaths": null + }, + { + "diaEvidencePaths": null + }, + { + "diaMsmsPaths": null + }, + { + "diaLabelIndsForLibraryMatch": null + }, + { + "diaInitialPrecMassTolPpm": "20" + }, + { + "diaInitialFragMassTolPpm": "20" + }, + { + "diaCorrThresholdFeatureClustering": "0.85" + }, + { + "diaPrecTolPpmFeatureClustering": "2" + }, + { + "diaFragTolPpmFeatureClustering": "2" + }, + { + "diaScoreN": "12" + }, + { + "diaScoreNAdditional": "5" + }, + { + "diaMinScore": "1.99" + }, + { + "diaXgBoostBaseScore": "0.4" + }, + { + "diaXgBoostSubSample": "0.9" + }, + { + "centroidPosition": "0" + }, + { + "diaQuantMethod": "7" + }, + { + "diaFeatureQuantMethod": "2" + }, + { + "lfqNormType": "1" + }, + { + "diaTopNForQuant": "12" + }, + { + "diaTopNCorrelatingFragmentsForQuant": "7" + }, + { + "diaFragmentCorrelationForQuant": "0.78" + }, + { + "lfqUsePeptideCorrelation": "True" + }, + { + "lfqTopNCorrelatingPeptides": "3" + }, + { + "lfqPeptideCorrelation": "3" + }, + { + "diaMinMsmsIntensityForQuant": "0" + }, + { + "diaTopMsmsIntensityQuantileForQuant": "0.85" + }, + { + "diaMinFragmentOverlapScore": "0" + }, + { + "diaMinPrecursorScore": "0" + }, + { + "diaUseProfileCorrelation": "False" + }, + { + "diaMinPrecProfileCorrelation": "0" + }, + { + "diaMinFragProfileCorrelation": "0" + }, + { + "diaXgBoostMinChildWeight": "9" + }, + { + "diaXgBoostMaximumTreeDepth": "12" + }, + { + "diaXgBoostEstimators": "580" + }, + { + "diaXgBoostGamma": "0.9" + }, + { + "diaXgBoostMaxDeltaStep": "3" + }, + { + "diaGlobalMl": "True" + }, + { + "diaAdaptiveMassAccuracy": "False" + }, + { + "diaMassWindowFactor": "3.3" + }, + { + "diaNoMl": "False" + }, + { + "diaPermuteRt": "False" + }, + { + "diaPermuteCcs": "False" + }, + { + "diaBackgroundSubtraction": "False" + }, + { + "diaBackgroundSubtractionQuantile": "0.5" + }, + { + "diaBackgroundSubtractionFactor": "4" + }, + { + "diaLfqRatioType": "0" + }, + { + "diaTransferQvalue": "0.3" + }, + { + "diaTransferQvalueBetweenLabels": "0.01" + }, + { + "diaTransferQvalueBetweenFractions": "0.01" + }, + { + "diaTransferQvalueBetweenFaims": "0.01" + }, + { + "diaOnlyIsosForRecal": "True" + }, + { + "diaMinPeaks": "5" + }, + { + "diaUseFragIntensForMl": "False" + }, + { + "diaUseFragMassesForMl": "False" + }, + { + "diaMaxTrainInstances": "500000" + }, + { + "diaMaxFragmentCharge": "3" + }, + { + "diaAdaptiveMlScoring": "False" + }, + { + "diaDynamicScoringMaxInstances": "25000" + }, + { + "diaMaxPrecursorMz": "0" + }, + { + "diaHardRtFilter": "True" + }, + { + "diaConvertLibraryCharge2Fragments": "False" + }, + { + "diaChargeNormalizationLibrary": "True" + }, + { + "diaChargeNormalizationSample": "True" + }, + { + "diaDeleteIntermediateResults": "True" + }, + { + "diaScoreWeightScanIndex": "-1" + }, + { + "diaScoreWeightScanValue": "1" + }, + { + "diaNumNonleadingMatches": "0" + }, + { + "diaFragmentModelType": "0" + }, + { + "diaAltFragmentModelPath": null + }, + { + "diaUseDefaultRtModel": "True" + }, + { + "diaAltRtModelPath": null + }, + { + "diaUseDefaultCcsModel": "True" + }, + { + "diaAltCcsModelPath": null + }, + { + "diaBatchProcessing": "True" + }, + { + "diaBatchSize": "25" + }, + { + "diaFirstBatch": "-1" + }, + { + "diaLastBatch": "-1" + }, + { + "diaOnlyPreprocess": "False" + }, + { + "diaMultiplexQuantMethod": "1" + }, + { + "diaOnlyPostprocess": "False" + }, + { + "diaRequirePrecursor": "False" + }, + { + "diaFuturePeptides": "False" + }, + { + "diaOverrideRtWithPrediction": "False" + }, + { + "diaMaxModifications": "0" + }, + { + "diaMaxPositionings": "0" + }, + { + "diaPredictCharges": "False" + }, + { + "diaUseProbScore": "False" + }, + { + "diaProbScoreP": "0.055" + }, + { + "diaProbScoreG": "1.2" + }, + { + "diaProbScoreStep": "0.1" + }, + { + "isM2FragTypeOverride": "False" + }, + { + "ms2FragTypeOverride": "0" + }, + { + "classicLfqForSingleShots": "True" + }, + { + "sequenceBasedModifier": "False" + }, + { + "diaRtFromSamplesForExport": "True" + }, + { + "diaCcsFromSamplesForExport": "True" + }, + { + "diaLibraryExport": "0" + }, + { + "diaUseApexWeightsForPtmLoc": "False" + }, + { + "diaSecondScoreForMultiplex": "True" + }, + { + "diaBestPrecursorChargeForQuant": "False" + }, + { + "diaBestPrecursorMassRangeForQuant": "False" + }, + { + "diaBestPrecursorIntensityForQuant": "False" + }, + { + "diaPtmLocMethod": "0" + }, + { + "diaIndexedSearch": "True" + }, + { + "diaIncreaseSequenceCoverage": "True" + }, + { + "diaSequenceCoverageFdr": "0.03" + } + ] + }, + "msmsParamsArray": [ + { + "msmsParams": { + "Name": "FTMS", + "MatchTolerance": "20", + "MatchToleranceInPpm": "True", + "DeisotopeTolerance": "7", + "DeisotopeToleranceInPpm": "True", + "DeNovoTolerance": "25", + "DeNovoToleranceInPpm": "True", + "Deisotope": "True", + "Topx": "12", + "TopxInterval": "100", + "HigherCharges": "True", + "IncludeWater": "True", + "IncludeAmmonia": "True", + "IncludeWaterCross": "False", + "IncludeAmmoniaCross": "False", + "DependentLosses": "True", + "Recalibration": "False" + } + }, + { + "msmsParams": { + "Name": "ITMS", + "MatchTolerance": "0.5", + "MatchToleranceInPpm": "False", + "DeisotopeTolerance": "0.15", + "DeisotopeToleranceInPpm": "False", + "DeNovoTolerance": "0.5", + "DeNovoToleranceInPpm": "False", + "Deisotope": "False", + "Topx": "8", + "TopxInterval": "100", + "HigherCharges": "True", + "IncludeWater": "True", + "IncludeAmmonia": "True", + "IncludeWaterCross": "False", + "IncludeAmmoniaCross": "False", + "DependentLosses": "True", + "Recalibration": "False" + } + }, + { + "msmsParams": { + "Name": "TOF", + "MatchTolerance": "25", + "MatchToleranceInPpm": "True", + "DeisotopeTolerance": "0.01", + "DeisotopeToleranceInPpm": "False", + "DeNovoTolerance": "25", + "DeNovoToleranceInPpm": "True", + "Deisotope": "True", + "Topx": "16", + "TopxInterval": "100", + "HigherCharges": "True", + "IncludeWater": "True", + "IncludeAmmonia": "True", + "IncludeWaterCross": "False", + "IncludeAmmoniaCross": "False", + "DependentLosses": "True", + "Recalibration": "False" + } + }, + { + "msmsParams": { + "Name": "UNKNOWN", + "MatchTolerance": "20", + "MatchToleranceInPpm": "True", + "DeisotopeTolerance": "7", + "DeisotopeToleranceInPpm": "True", + "DeNovoTolerance": "25", + "DeNovoToleranceInPpm": "True", + "Deisotope": "True", + "Topx": "12", + "TopxInterval": "100", + "HigherCharges": "True", + "IncludeWater": "True", + "IncludeAmmonia": "True", + "IncludeWaterCross": "False", + "IncludeAmmoniaCross": "False", + "DependentLosses": "True", + "Recalibration": "False" + } + } + ], + "fragmentationParamsArray": [ + { + "fragmentationParams": { + "Name": "HCD", + "UseIntensityPrediction": "False", + "UseSequenceBasedModifier": "False", + "InternalFragments": "False", + "InternalFragmentWeight": "1", + "InternalFragmentAas": "KRH" + } + }, + { + "fragmentationParams": { + "Name": "CID", + "UseIntensityPrediction": "False", + "UseSequenceBasedModifier": "False", + "InternalFragments": "False", + "InternalFragmentWeight": "1", + "InternalFragmentAas": "KRH" + } + }, + { + "fragmentationParams": { + "Name": "ETD", + "UseIntensityPrediction": "False", + "UseSequenceBasedModifier": "False", + "InternalFragments": "False", + "InternalFragmentWeight": "1", + "InternalFragmentAas": "KRH" + } + }, + { + "fragmentationParams": { + "Name": "PQD", + "UseIntensityPrediction": "False", + "UseSequenceBasedModifier": "False", + "InternalFragments": "False", + "InternalFragmentWeight": "1", + "InternalFragmentAas": "KRH" + } + }, + { + "fragmentationParams": { + "Name": "ETHCD", + "UseIntensityPrediction": "False", + "UseSequenceBasedModifier": "False", + "InternalFragments": "False", + "InternalFragmentWeight": "1", + "InternalFragmentAas": "KRH" + } + }, + { + "fragmentationParams": { + "Name": "ETCID", + "UseIntensityPrediction": "False", + "UseSequenceBasedModifier": "False", + "InternalFragments": "False", + "InternalFragmentWeight": "1", + "InternalFragmentAas": "KRH" + } + }, + { + "fragmentationParams": { + "Name": "UVPD", + "UseIntensityPrediction": "False", + "UseSequenceBasedModifier": "False", + "InternalFragments": "False", + "InternalFragmentWeight": "1", + "InternalFragmentAas": "KRH" + } + }, + { + "fragmentationParams": { + "Name": "Unknown", + "UseIntensityPrediction": "False", + "UseSequenceBasedModifier": "False", + "InternalFragments": "False", + "InternalFragmentWeight": "1", + "InternalFragmentAas": "KRH" + } + } + ] +} \ No newline at end of file diff --git a/test/params/mqpar_mq2.6.2.0_1mc_MBR.xml b/test/params/mqpar_mq2.6.2.0_1mc_MBR.xml new file mode 100644 index 00000000..746b3473 --- /dev/null +++ b/test/params/mqpar_mq2.6.2.0_1mc_MBR.xml @@ -0,0 +1,603 @@ + + + + + \\unicph.domain\users\abc123\proteobench_202407\mq2.6.2.0_1mc_MBR\ProteoBenchFASTA_DDAQuantification.fasta + >([^\s]*) + >(.*) + + + + + + + + + + + + 350000 + True + 0.005 + False + False + True + True + False + revert + False + 4600 + True + True + True + 0 + 6 + 0 + 40 + True + True + False + False + False + 0 + 0 + False + False + False + False + 0 + False + False + False + False + True + Species + False + 3 + False + False + True + False + False + False + False + 0 + 0 + 0 + 0 + 0 + True + True + True + True + True + 0 + 0 + False + False + 7 + 0.01 + 0.01 + 0.01 + 0.01 + 8 + 25 + True + 1 + 1 + 0 + False + True + False + + 2 + True + + Oxidation (M) + Acetyl (Protein N-term) + + 0.4 + 0.05 + 20 + 1 + 15 + 0 + 1 + + + 200 + False + True + True + True + True + False + True + False + False + False + False + False + True + False + 0 + 20 + + none + False + session1 + 2.6.2.0 + + 4 + + + + -1.7976931348623157E+308 + 1.7976931348623157E+308 + False + False + False + False + False + False + False + + \\unicph.domain\users\abc123\proteobench_202407\mq2.6.2.0_1mc_MBR\LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.raw + \\unicph.domain\users\abc123\proteobench_202407\mq2.6.2.0_1mc_MBR\LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.raw + \\unicph.domain\users\abc123\proteobench_202407\mq2.6.2.0_1mc_MBR\LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.raw + \\unicph.domain\users\abc123\proteobench_202407\mq2.6.2.0_1mc_MBR\LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.raw + \\unicph.domain\users\abc123\proteobench_202407\mq2.6.2.0_1mc_MBR\LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.raw + \\unicph.domain\users\abc123\proteobench_202407\mq2.6.2.0_1mc_MBR\LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.raw + + + A_Sample_Alpha_01 + A_Sample_Alpha_02 + A_Sample_Alpha_03 + B_Sample_Alpha_01 + B_Sample_Alpha_02 + B_Sample_Alpha_03 + + + 32767 + 32767 + 32767 + 32767 + 32767 + 32767 + + + False + False + False + False + False + False + + + 0 + 0 + 0 + 0 + 0 + 0 + + + + + + + + + + 0 + False + 1 + 0.7 + + False + False + False + + + 0 + + + + False + False + 0 + 7 + 2 + 1 + False + False + True + 1 + NaN + NaN + MatchFromAndTo + 0 + 8 + True + 35 + True + 1.4 + 1.2 + False + 0 + 0 + 0 + + + + Standard + False + 0 + 80 + 3 + 6 + 100000 + 0 + 0 + False + False + True + False + 2 + 2 + True + 0 + 5 + 1 + 1 + 1 + 0 + 0 + 0 + 0 + + Carbamidomethyl (C) + + + Trypsin/P + + + + 0 + False + False + + Oxidation (M) + Acetyl (Protein N-term) + + False + + + + + + + + + False + + + + + True + 20 + 4.5 + True + 2 + True + 0.6 + 0.6 + True + True + False + 70 + False + + 0 + 0 + 0 + NaN + NaN + False + NaN + NaN + 0 + 0 + 0 + 0 + True + False + True + 0 + + 3 + 6 + 40 + 0 + 10 + False + True + False + 3 + False + 0 + 0 + 0 + 0 + + + + + + + + + + False + False + True + 0.75 + False + 0 + + + + + + + + + 20 + 20 + 0.85 + 2 + 2 + 12 + 5 + 1.99 + 0.4 + 0.9 + 0 + 7 + 2 + 1 + 12 + 7 + 0.78 + True + 3 + 3 + 0 + 0.85 + 0 + 0 + False + 0 + 0 + 9 + 12 + 580 + 0.9 + 3 + True + False + 3.3 + False + False + False + False + 0.5 + 4 + 0 + 0.3 + 0.01 + 0.01 + 0.01 + True + 5 + False + False + 500000 + 3 + False + 25000 + 0 + True + False + True + True + True + -1 + 1 + 0 + 0 + + True + + True + + True + 25 + -1 + -1 + False + 1 + False + False + False + False + 0 + 0 + False + False + 0.055 + 1.2 + 0.1 + False + 0 + True + False + True + True + 0 + False + True + False + False + False + 0 + True + True + 0.03 + + + + + FTMS + 20 + True + 7 + True + 25 + True + True + 12 + 100 + True + True + True + False + False + True + False + + + ITMS + 0.5 + False + 0.15 + False + 0.5 + False + False + 8 + 100 + True + True + True + False + False + True + False + + + TOF + 25 + True + 0.01 + False + 25 + True + True + 16 + 100 + True + True + True + False + False + True + False + + + UNKNOWN + 20 + True + 7 + True + 25 + True + True + 12 + 100 + True + True + True + False + False + True + False + + + + + HCD + False + False + False + 1 + KRH + + + CID + False + False + False + 1 + KRH + + + ETD + False + False + False + 1 + KRH + + + PQD + False + False + False + 1 + KRH + + + ETHCD + False + False + False + 1 + KRH + + + ETCID + False + False + False + 1 + KRH + + + UVPD + False + False + False + 1 + KRH + + + Unknown + False + False + False + 1 + KRH + + + diff --git a/test/params/mqpar_mq2.6.2.0_1mc_MBR_sel.json b/test/params/mqpar_mq2.6.2.0_1mc_MBR_sel.json new file mode 100644 index 00000000..942531a4 --- /dev/null +++ b/test/params/mqpar_mq2.6.2.0_1mc_MBR_sel.json @@ -0,0 +1,22 @@ +{ + "software_name": null, + "software_version": "2.6.2.0", + "search_engine": "Andromeda", + "search_engine_version": null, + "ident_fdr_psm": null, + "ident_fdr_peptide": "0.01", + "ident_fdr_protein": "0.01", + "enable_match_between_runs": "True", + "precursor_mass_tolerance": "4.5 ppm", + "fragment_mass_tolerance": "20 ppm", + "enzyme": "Trypsin/P", + "allowed_miscleavages": "1", + "min_peptide_length": null, + "max_peptide_length": null, + "fixed_mods": "Carbamidomethyl (C)", + "variable_mods": "Oxidation (M),Acetyl (Protein N-term)", + "max_mods": "5", + "min_precursor_charge": null, + "max_precursor_charge": "7", + "minPeptideLength": "7" +} \ No newline at end of file diff --git a/test/test_parse_params_maxquant.py b/test/test_parse_params_maxquant.py index b60cc22e..fa55278e 100644 --- a/test/test_parse_params_maxquant.py +++ b/test/test_parse_params_maxquant.py @@ -13,6 +13,7 @@ "mqpar_MQ1.6.3.3_MBR.xml", "mqpar_MQ2.1.3.0_noMBR.xml", "mqpar1.5.3.30_MBR.xml", + "mqpar_mq2.6.2.0_1mc_MBR.xml", ] mqpar_fnames = [TESTDATA_DIR / mq_para for mq_para in mqpar_fnames]