Mercurial > repos > galaxyp > peptideshaker
view test-data/Identification_Parameters_default_modifications.par @ 55:bb0130ff73ce draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
| author | galaxyp |
|---|---|
| date | Fri, 15 Jan 2021 14:06:27 +0000 |
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{ "marshallableParameterType": "identification_parameters", "version": "5.0.1", "name": "IdentificationParametersOutput", "description": "Fixed: Carbamidomethylation of C.\nVariable: Oxidation of M.\nFragment Tolerance: 0.5 Da.\n", "defaultDescription": true, "searchParameters": { "version": "5.0.1", "precursorAccuracyType": "PPM", "fragmentAccuracyType": "DA", "precursorTolerance": 10.0, "fragmentIonMZTolerance": 0.5, "modificationParameters": { "fixedModifications": [ "Carbamidomethylation of C" ], "variableModifications": [ "Oxidation of M" ], "refinementVariableModifications": [], "refinementFixedModifications": [], "colors": {}, "backUp": { "Carbamidomethylation of C": { "modificationType": "modaa", "name": "Carbamidomethylation of C", "shortName": "cmm", "neutralLosses": [], "reporterIons": [], "pattern": { "length": 0, "residueTargeted": { "0": [ "C" ] }, "id": 0 }, "atomChainAdded": { "atomChain": [ { "atomSymbol": "C", "isotope": 0, "id": 0 }, { "atomSymbol": "C", "isotope": 0, "id": 0 }, { "atomSymbol": "H", "isotope": 0, "id": 0 }, { "atomSymbol": "H", "isotope": 0, "id": 0 }, { "atomSymbol": "H", "isotope": 0, "id": 0 }, { "atomSymbol": "N", "isotope": 0, "id": 0 }, { "atomSymbol": "O", "isotope": 0, "id": 0 } ], "mass": -1.0, "id": 0 }, "atomChainRemoved": { "atomChain": [], "mass": -1.0, "id": 0 }, "unimodCvTerm": { "ontology": "UNIMOD", "accession": "UNIMOD:4", "name": "Carbamidomethyl", "id": 0 }, "psiModCvTerm": { "ontology": "MOD", "accession": "MOD:01060", "name": "S-carboxamidomethyl-L-cysteine", "id": 0 }, "category": "Common", "id": 0 }, "Oxidation of M": { "modificationType": "modaa", "name": "Oxidation of M", "shortName": "ox", "neutralLosses": [ { "composition": { "atomChain": [ { "atomSymbol": "C", "isotope": 0, "id": 0 }, { "atomSymbol": "H", "isotope": 0, "id": 0 }, { "atomSymbol": "H", "isotope": 0, "id": 0 }, { "atomSymbol": "H", "isotope": 0, "id": 0 }, { "atomSymbol": "H", "isotope": 0, "id": 0 }, { "atomSymbol": "O", "isotope": 0, "id": 0 }, { "atomSymbol": "S", "isotope": 0, "id": 0 } ], "mass": -1.0, "id": 0 }, "name": "CH4OS", "fixed": false, "id": 0 } ], "reporterIons": [], "pattern": { "length": 0, "residueTargeted": { "0": [ "M" ] }, "id": 0 }, "atomChainAdded": { "atomChain": [ { "atomSymbol": "O", "isotope": 0, "id": 0 } ], "mass": -1.0, "id": 0 }, "atomChainRemoved": { "atomChain": [], "mass": -1.0, "id": 0 }, "unimodCvTerm": { "ontology": "UNIMOD", "accession": "UNIMOD:35", "name": "Oxidation", "id": 0 }, "psiModCvTerm": { "ontology": "MOD", "accession": "MOD:00719", "name": "L-methionine sulfoxide", "id": 0 }, "category": "Common", "id": 0 } }, "id": 0 }, "digestionParameters": { "cleavageParameter": "enzyme", "enzymes": [ { "name": "Trypsin", "aminoAcidBefore": [ "R", "K" ], "aminoAcidAfter": [], "restrictionBefore": [], "restrictionAfter": [ "P" ], "cvTerm": { "ontology": "PSI-MS", "accession": "MS:1001251", "name": "Trypsin", "id": 0 }, "id": 0 } ], "nMissedCleavages": { "Trypsin": 2 }, "specificity": { "Trypsin": "specific" }, "id": 0 }, "forwardIons": [ 1 ], "rewindIons": [ 4 ], "minChargeSearched": 2, "maxChargeSearched": 4, "minIsotopicCorrection": 0, "maxIsotopicCorrection": 1, "refMass": 2000.0, "algorithmParameters": { "1": { "type": "com.compomics.util.parameters.identification.tool_specific.OmssaParameters", "data": { "maxEValue": 100.0, "hitListLength": 10, "minimalChargeForMultipleChargedFragments": 3, "minPeptideLength": 8, "maxPeptideLength": 30, "removePrecursor": false, "scalePrecursor": true, "estimateCharge": true, "selectedOutput": "OMX", "memoryMappedSequenceLibraries": false, "neutronThreshold": 1446.94, "lowIntensityCutOff": 0.0, "highIntensityCutOff": 0.2, "intensityCutOffIncrement": 5.0E-4, "singleChargeWindow": 27, "doubleChargeWindow": 14, "nPeaksInSingleChargeWindow": 2, "nPeaksIndoubleChargeWindow": 2, "maxHitsPerSpectrumPerCharge": 30, "nAnnotatedMostIntensePeaks": 6, "minAnnotatedPeaks": 2, "minPeaks": 4, "cleaveNtermMethionine": true, "maxMzLadders": 128, "maxFragmentCharge": 2, "fractionOfPeaksForChargeEstimation": 0.95, "determineChargePlusOneAlgorithmically": true, "searchPositiveIons": true, "minPrecPerSpectrum": 1, "searchForwardFragmentFirst": false, "searchRewindFragments": true, "maxFragmentPerSeries": 100, "useCorrelationCorrectionScore": true, "consecutiveIonProbability": 0.5, "iterativeSequenceEvalue": 0.0, "iterativeReplaceEvalue": 0.0, "iterativeSpectrumEvalue": 0.01, "noProlineRuleSeries": [], "ptmIndexes": {}, "id": 0 } }, "33": { "type": "com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters", "data": { "minPeptideLength": 8, "maxPeptideLength": 30, "searchType": "Classic", "totalPartitions": 1, "dissociationType": "HCD", "maxModsForPeptide": 2, "initiatorMethionineBehavior": "Variable", "scoreCutoff": 5.0, "useDeltaScore": false, "fragmentationTerminus": "Both", "maxFragmentSize": 30000.0, "massDiffAcceptorType": "OneMM", "writeMzId": true, "writePepXml": false, "useProvidedPrecursorInfo": true, "doPrecursorDeconvolution": true, "deconvolutionIntensityRatio": 3.0, "deconvolutionMassTolerance": 4.0, "deconvolutionMassToleranceType": "PPM", "trimMs1Peaks": false, "trimMsMsPeaks": true, "numberOfPeaksToKeepPerWindow": 200, "minAllowedIntensityRatioToBasePeak": 0.01, "normalizePeaksAcrossAllWindows": false, "modPeptidesAreDifferent": false, "noOneHitWonders": false, "searchTarget": true, "decoyType": "None", "maxModificationIsoforms": 1024, "minVariantDepth": 1, "maxHeterozygousVariants": 4, "runGptm": false, "gPtmCategories": [ "Common_Biological", "Common_Artifact", "Metal" ], "id": 0 } }, "2": { "type": "com.compomics.util.parameters.identification.tool_specific.XtandemParameters", "data": { "maxEValue": 0.01, "outputResults": "all", "dynamicRange": 100.0, "nPeaks": 50, "minPrecursorMass": 500.0, "minFragmentMz": 200.0, "minPeaksPerSpectrum": 5, "proteinQuickAcetyl": true, "quickPyrolidone": true, "refine": true, "refineSemi": false, "refinePointMutations": false, "refineSpectrumSynthesis": true, "refineUnanticipatedCleavages": true, "refineSnaps": true, "maximumExpectationValueRefinement": 0.01, "potentialModificationsForFullRefinment": false, "skylinePath": "", "outputProteins": true, "outputSequences": false, "outputSpectra": true, "outputHistograms": false, "stpBias": false, "useNoiseSuppression": false, "proteinPtmComplexity": 6.0, "parentMonoisotopicMassIsotopeError": true, "id": 0 } }, "3": { "type": "com.compomics.util.parameters.identification.tool_specific.PepnovoParameters", "data": { "hitListLength": 10, "estimateCharge": true, "correctPrecursorMass": false, "discardLowQualitySpectra": true, "fragmentationModel": "CID_IT_TRYP", "generateQuery": false, "id": 0 } }, "4": { "type": "com.compomics.util.parameters.identification.tool_specific.AndromedaParameters", "data": { "maxPeptideMass": 4600.0, "maxCombinations": 250, "topPeaks": 8, "topPeaksWindow": 100, "includeWater": true, "includeAmmonia": true, "dependentLosses": true, "fragmentAll": false, "empiricalCorrection": true, "higherCharge": true, "fragmentationMethod": "CID", "maxNumberOfModifications": 5, "minPeptideLengthNoEnzyme": 8, "maxPeptideLengthNoEnzyme": 30, "equalIL": false, "numberOfCandidates": 10, "ptmIndexes": {}, "decoyMode": "none", "id": 0 } }, "5": { "type": "com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters", "data": { "generateDecoy": false, "reportBothBestHitsForTD": true, "instrumentID": "b, y", "maxRank": 10, "monoisotopic": true, "lowMemoryMode": true, "performDeisotoping": true, "maxModifications": 3, "maxVariableModifications": 4, "maxModificationSites": 6, "maxNeutralLosses": 1, "maxNeutralLossesPerModification": 2, "minPeptideLength": 8, "maxPeptideLength": 30, "maxLoadedProteins": 100000, "maxLoadedSpectra": 2000, "outputFormat": "csv", "id": 0 } }, "7": { "type": "com.compomics.util.parameters.identification.tool_specific.MsgfParameters", "data": { "searchDecoyDatabase": false, "instrumentID": 3, "fragmentationType": 3, "protocol": 0, "minPeptideLength": 8, "maxPeptideLength": 30, "numberOfSpectrumMarches": 10, "additionalOutput": false, "numberTolerableTermini": 2, "numberOfModificationsPerPeptide": 2, "id": 0 } }, "8": { "type": "com.compomics.util.parameters.identification.tool_specific.DirecTagParameters", "data": { "ticCutoffPercentage": 100.0, "maxPeakCount": 100, "numIntensityClasses": 3, "adjustPrecursorMass": false, "minPrecursorAdjustment": -0.5, "maxPrecursorAdjustment": 1.5, "precursorAdjustmentStep": 0.1, "numChargeStates": 3, "outputSuffix": "", "useChargeStateFromMS": true, "duplicateSpectra": true, "deisotopingMode": 0, "isotopeMzTolerance": 0.25, "complementMzTolerance": 0.1, "tagLength": 4, "maxDynamicMods": 2, "maxTagCount": 10, "intensityScoreWeight": 1.0, "mzFidelityScoreWeight": 1.0, "complementScoreWeight": 1.0, "variableModifications": [], "id": 0 } }, "10": { "type": "com.compomics.util.parameters.identification.tool_specific.CometParameters", "data": { "numberOfSpectrumMatches": 10, "maxVariableMods": 10, "requireVariableMods": false, "minPeaks": 10, "minPeakIntensity": 0.0, "removePrecursor": 0, "removePrecursorTolerance": 1.5, "lowerClearMzRange": 0.0, "upperClearMzRange": 0.0, "enzymeType": 2, "isotopeCorrection": 3, "minPrecursorMass": 600.0, "maxPrecursorMass": 5000.0, "maxFragmentCharge": 3, "removeMethionine": false, "batchSize": 0, "theoreticalFragmentIonsSumOnly": false, "fragmentBinOffset": 0.0, "useSparseMatrix": true, "selectedOutputFormat": "PepXML", "printExpectScore": true, "minPeptideLength": 8, "maxPeptideLength": 30, "id": 0 } }, "13": { "type": "com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters", "data": { "minPeptideLength": 8, "maxPeptideLength": 30, "numberOfSpectrumMatches": 10, "ticCutoffPercentage": 0.98, "maxDynamicMods": 2, "minTerminiCleavages": 2, "minPrecursorMass": 600.0, "maxPrecursorMass": 5000.0, "useSmartPlusThreeModel": false, "computeXCorr": false, "numIntensityClasses": 3, "classSizeMultiplier": 2, "numberOfBatches": 50, "lowerIsotopeCorrection": -1, "upperIsotopeCorrection": 2, "fragmentationRule": "CID", "maxPeakCount": 300, "outputFormat": "mzIdentML", "id": 0 } }, "27": { "type": "com.compomics.util.parameters.identification.tool_specific.PNovoParameters", "data": { "numberOfPeptides": 10, "lowerPrecursorMass": 300, "upperPrecursorMass": 5000, "acticationType": "HCD", "id": 0 } }, "28": { "type": "com.compomics.util.parameters.identification.tool_specific.TideParameters", "data": { "fastIndexFolderName": "fasta-index", "maxVariableModificationsPerPeptide": 255, "maxVariableModificationsPerTypePerPeptide": 2, "minPeptideLength": 6, "maxPeptideLength": 30, "minPrecursorMass": 200.0, "maxPrecursorMass": 7200.0, "decoyFormat": "none", "keepTerminalAminoAcids": "NC", "decoySeed": 1, "outputFolderName": "crux-output", "printPeptides": false, "verbosity": 30, "monoisotopicPrecursor": true, "clipNtermMethionine": false, "digestionType": "full-digest", "computeSpScore": false, "numberOfSpectrumMatches": 10, "computeExactPValues": false, "minSpectrumMz": 0.0, "minSpectrumPeaks": 20, "spectrumCharges": "all", "removePrecursor": false, "removePrecursorTolerance": 1.5, "printProgressIndicatorSize": 1000, "useFlankingPeaks": false, "useNeutralLossPeaks": false, "mzBinWidth": 0.02, "mzBinOffset": 0.0, "concatenateTargetDecoy": false, "textOutput": true, "sqtOutput": false, "pepXmlOutput": false, "mzidOutput": false, "pinOutput": false, "removeTempFolders": true, "id": 0 } }, "29": { "type": "com.compomics.util.parameters.identification.tool_specific.NovorParameters", "data": { "fragmentationMethod": "HCD", "massAnalyzer": "FT", "id": 0 } } }, "flanking": false, "id": 0 }, "annotationParameters": { "yAxisZoomExcludesBackgroundPeaks": true, "showAllPeaks": false, "intensityThresholdType": "percentile", "intensityLimit": 0.75, "automaticAnnotation": true, "selectedIonsMap": { "IMMONIUM_ION": [ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 ], "PEPTIDE_FRAGMENT_ION": [ 4, 1 ], "PRECURSOR_ION": [ 0 ], "TAG_FRAGMENT_ION": [ 4, 1 ], "REPORTER_ION": [], "RELATED_ION": [ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18 ] }, "neutralLossesList": [ { "composition": { "atomChain": [ { "atomSymbol": "H", "isotope": 0, "id": 0 }, { "atomSymbol": "H", "isotope": 0, "id": 0 }, { "atomSymbol": "O", "isotope": 0, "id": 0 } ], "mass": -1.0, "id": 0 }, "name": "H2O", "fixed": false, "aminoAcids": [ "D", "E", "S", "T" ], "id": 0 }, { "composition": { "atomChain": [ { "atomSymbol": "N", "isotope": 0, "id": 0 }, { "atomSymbol": "H", "isotope": 0, "id": 0 }, { "atomSymbol": "H", "isotope": 0, "id": 0 }, { "atomSymbol": "H", "isotope": 0, "id": 0 } ], "mass": -1.0, "id": 0 }, "name": "NH3", "fixed": false, "aminoAcids": [ "K", "N", "Q", "R" ], "id": 0 }, { "composition": { "atomChain": [ { "atomSymbol": "C", "isotope": 0, "id": 0 }, { "atomSymbol": "H", "isotope": 0, "id": 0 }, { "atomSymbol": "H", "isotope": 0, "id": 0 }, { "atomSymbol": "H", "isotope": 0, "id": 0 }, { "atomSymbol": "H", "isotope": 0, "id": 0 }, { "atomSymbol": "O", "isotope": 0, "id": 0 }, { "atomSymbol": "S", "isotope": 0, "id": 0 } ], "mass": -1.0, "id": 0 }, "name": "CH4OS", "fixed": false, "id": 0 } ], "neutralLossesAuto": true, "reporterIons": true, "relatedIons": true, "fragmentIonAccuracy": 10.0, "fragmentIonPpm": false, "showForwardIonDeNovoTags": false, "showRewindIonDeNovoTags": false, "deNovoCharge": 1, "tiesResolution": "mostAccurateMz", "id": 0 }, "sequenceMatchingParameters": { "sequenceMatchingType": "indistiguishableAminoAcids", "limitX": 0.25, "enzymaticTagsOnly": false, "maxPtmsPerTagPeptide": 3, "minAminoAcidScore": 30, "minTagLength": 3, "id": 0 }, "peptideVariantsParameters": { "variantType": "NO_VARIANT", "nVariants": 0, "nAaDeletions": 0, "nAaInsertions": 0, "nAaSubstitutions": 0, "nAaSwap": 0, "aaSubstitutionMatrix": { "name": "No Substitution", "description": "No substitution", "substitutions": {}, "reverseMap": {}, "id": 0 }, "fixedVariants": {}, "id": 0 }, "geneParameters": { "autoUpdate": false, "useGeneMapping": false, "id": 0 }, "psmScoringParameters": { "spectrumMatchingScores": { "8": [ 1 ], "3": [ 1 ], "27": [ 1 ] }, "defaultScores": [ -1 ], "minDecoysInBin": 10, "id": 0 }, "peptideAssumptionFilter": { "minPepLength": 8, "maxPepLength": 30, "maxMassDeviation": 10.0, "isPpm": true, "unknownModification": true, "minIsotopes": 0, "maxIsotopes": 1, "id": 0 }, "modificationLocalizationParameters": { "probabilisticScoreCalculation": true, "selectedProbabilisticScore": "PhosphoRS", "dScoreThreshold": 95.0, "probabilisticScoreThreshold": 95.0, "probabilisticScoreNeutralLosses": false, "sequenceMatchingParameters": { "sequenceMatchingType": "aminoAcid", "limitX": 0.25, "enzymaticTagsOnly": false, "maxPtmsPerTagPeptide": 3, "minAminoAcidScore": 30, "minTagLength": 3, "id": 0 }, "alignNonConfidentModifications": true, "id": 0 }, "proteinInferenceParameters": { "modificationRefinement": true, "simplifyProteinGroups": true, "simplifyGroupsEvidence": true, "simplifyGroupsConfidence": true, "simplifyGroupsEnzymaticity": true, "simplifyGroupsVariants": true, "confidenceThreshold": 0.05, "id": 0 }, "idValidationParameters": { "defaultProteinFDR": 1.0, "defaultPeptideFDR": 1.0, "defaultPsmFDR": 1.0, "validationQCPreferences": { "dbSize": false, "firstDecoy": true, "confidenceMargin": 1.0, "id": 0 }, "id": 0 }, "fractionParameters": { "proteinConfidenceMwPlots": 95.0, "fractionMolecularWeightRanges": {}, "id": 0 }, "fastaParameters": { "targetDecoy": true, "decoyFlag": "-REVERSED", "decoySuffix": true, "targetDecoyFileNameTag": "_concatenated_target_decoy", "id": 0 }, "id": 0 }