Mercurial > repos > jjohnson > peptideshaker
view test-data/Identification_Parameters_specific.par @ 0:8b99cb00e1c4 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
| author | jjohnson |
|---|---|
| date | Tue, 15 May 2018 14:50:35 -0400 |
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{ "marshallableParameterType": "identification_parameters", "name": "SEARCHGUI_IdentificationParameters", "description": "Fixed: Carbamidomethylation of C.\nVariable: Oxidation of M.\nPrecursor Tolerance: 100.0 ppm.\nCharge: 1-3.\nDB: dataset_118.dat.\n", "defaultDescription": true, "searchParameters": { "precursorAccuracyType": "PPM", "fragmentAccuracyType": "DA", "precursorTolerance": 100.0, "precursorToleranceDalton": 0.5, "fragmentIonMZTolerance": 0.5, "ptmSettings": { "fixedModifications": [ "Carbamidomethylation of C" ], "variableModifications": [ "Oxidation of M" ], "refinementVariableModifications": [], "refinementFixedModifications": [], "colors": {}, "backUp": { "Oxidation of M": { "type": 0, "name": "Oxidation of M", "shortName": "ox", "neutralLosses": [ { "composition": { "atomChain": [ { "atomSymbol": "C", "isotope": 0 }, { "atomSymbol": "H", "isotope": 0 }, { "atomSymbol": "H", "isotope": 0 }, { "atomSymbol": "H", "isotope": 0 }, { "atomSymbol": "H", "isotope": 0 }, { "atomSymbol": "O", "isotope": 0 }, { "atomSymbol": "S", "isotope": 0 } ], "mass1": -1.0 }, "name": "CH4OS", "fixed": false } ], "reporterIons": [], "pattern": { "length": 0, "residueTargeted": { "0": [ "M" ] } }, "atomChainAdded": { "atomChain": [ { "atomSymbol": "O", "isotope": 0 } ], "mass1": -1.0 }, "cvTerm": { "ontology": "UNIMOD", "accession": "UNIMOD:35", "name": "Oxidation" } }, "Carbamidomethylation of C": { "type": 0, "name": "Carbamidomethylation of C", "shortName": "cmm", "neutralLosses": [], "reporterIons": [], "pattern": { "length": 0, "residueTargeted": { "0": [ "C" ] } }, "atomChainAdded": { "atomChain": [ { "atomSymbol": "C", "isotope": 0 }, { "atomSymbol": "C", "isotope": 0 }, { "atomSymbol": "H", "isotope": 0 }, { "atomSymbol": "H", "isotope": 0 }, { "atomSymbol": "H", "isotope": 0 }, { "atomSymbol": "N", "isotope": 0 }, { "atomSymbol": "O", "isotope": 0 } ], "mass1": -1.0 }, "cvTerm": { "ontology": "UNIMOD", "accession": "UNIMOD:4", "name": "Carbamidomethyl" } } } }, "nMissedCleavages": 2, "digestionPreferences": { "cleavagePreference": "enzyme", "enzymes": [ { "id": 0, "name": "Trypsin", "aminoAcidBefore": [], "aminoAcidAfter": [], "restrictionBefore": [], "restrictionAfter": [], "aminoAcidBeforeSet": [ "R", "K" ], "aminoAcidAfterSet": [], "restrictionBeforeSet": [], "restrictionAfterSet": [ "P" ], "isSemiSpecific": false, "isWholeProtein": false, "cvTerm": { "ontology": "PSI-MS", "accession": "MS:1001251", "name": "Trypsin" } } ], "nMissedCleavages": { "Trypsin": 2 }, "specificity": { "Trypsin": "specific" } }, "fastaFile": { "path": "./searchgui_tinydb1_concatenated_target_decoy.fasta" }, "parametersFile": {}, "forwardIons": [ 1 ], "rewindIons": [ 4 ], "minChargeSearched": { "sign": 1, "value": 1 }, "maxChargeSearched": { "sign": 1, "value": 3 }, "minIsotopicCorrection": 0, "maxIsotopicCorrection": 1, "refMass": 2000.0, "algorithmParameters": { "1": { "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters", "data": { "maxEValue": 100.0, "hitListLength": 10, "minimalChargeForMultipleChargedFragments": { "sign": 1, "value": 3 }, "minPeptideLength": 8, "maxPeptideLength": 30, "removePrecursor": false, "scalePrecursor": true, "estimateCharge": true, "selectedOutput": "OMX", "memoryMappedSequenceLibraries": false, "numberOfItotopicPeaks": 0, "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": {} } }, "2": { "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters", "data": { "maxEValue": 0.01, "outputResults": "0", "dynamicRange": 100.0, "nPeaks": 50, "minPrecursorMass": 200.0, "minFragmentMz": 200.0, "minPeaksPerSpectrum": 15, "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": true, "proteinPtmComplexity": 6.0 } }, "3": { "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters", "data": { "hitListLength": 10, "estimateCharge": true, "correctPrecursorMass": false, "discardLowQualitySpectra": true, "fragmentationModel": "CID_IT_TRYP", "generateQuery": false } }, "4": { "type": "com.compomics.util.experiment.identification.identification_parameters.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": 25, "equalIL": false, "numberOfCandidates": 10, "ptmIndexes": {}, "decoyMode": "none" } }, "5": { "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters", "data": { "generateDecoy": false, "instrumentID": "b, y", "maxRank": 10, "monoisotopic": true, "lowMemoryMode": true } }, "7": { "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters", "data": { "searchDecoyDatabase": false, "instrumentID": 3, "fragmentationType": 3, "protocol": 0, "minPeptideLength": 8, "maxPeptideLength": 30, "numberOfSpectrumMarches": 10, "additionalOutput": false, "lowerIsotopeErrorRange": -1, "upperIsotopeErrorRange": 2, "numberTolerableTermini": 2, "numberOfPtmsPerPeptide": 2 } }, "8": { "type": "com.compomics.util.experiment.identification.identification_parameters.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, "variablePtms": [] } }, "10": { "type": "com.compomics.util.experiment.identification.identification_parameters.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": 1, "minPrecursorMass": 600.0, "maxPrecursorMass": 5000.0, "maxFragmentCharge": 3, "removeMethionine": false, "batchSize": 0, "theoreticalFragmentIonsSumOnly": false, "fragmentBinOffset": 0.0, "useSparseMatrix": true, "selectedOutputFormat": "PepXML", "printExpectScore": true } }, "27": { "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.PNovoParameters", "data": { "numberOfPeptides": 10, "lowerPrecursorMass": 300, "upperPrecursorMass": 5000, "acticationType": "HCD" } }, "28": { "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters", "data": { "fastIndexFolderName": "fasta-index", "maxVariablePtmsPerTypePerPeptide": 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 } }, "13": { "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters", "data": { "minPeptideLength": 8, "maxPeptideLength": 30, "numberOfSpectrumMatches": 10, "ticCutoffPercentage": 0.98, "maxDynamicMods": 2, "minTerminiCleavages": 2, "minPrecursorMass": 600.0, "maxPrecursorMass": 5000.0, "useSmartPlusThreeModel": true, "computeXCorr": false, "numIntensityClasses": 3, "classSizeMultiplier": 2, "numberOfBatches": 50, "lowerIsotopeCorrection": -1, "upperIsotopeCorrection": 2, "fragmentationRule": "CID", "maxPeakCount": 300, "outputFormat": "mzIdentML" } }, "29": { "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.NovorParameters", "data": { "fragmentationMethod": "HCD", "massAnalyzer": "FT" } } } }, "annotationSettings": { "yAxisZoomExcludesBackgroundPeaks": true, "showAllPeaks": false, "intensityThresholdType": "percentile", "intensityLimit": 0.75, "automaticAnnotation": true, "selectedIonsMap": { "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 ], "PEPTIDE_FRAGMENT_ION": [ 4, 1 ], "PRECURSOR_ION": [ 0 ], "IMMONIUM_ION": [ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 ] }, "neutralLossesList": [ { "composition": { "atomChain": [ { "atomSymbol": "H", "isotope": 0 }, { "atomSymbol": "H", "isotope": 0 }, { "atomSymbol": "O", "isotope": 0 } ], "mass1": -1.0, "stringValue1": "H(2)O" }, "name": "H2O", "fixed": false, "aminoAcids": [ "D", "E", "S", "T" ] }, { "composition": { "atomChain": [ { "atomSymbol": "N", "isotope": 0 }, { "atomSymbol": "H", "isotope": 0 }, { "atomSymbol": "H", "isotope": 0 }, { "atomSymbol": "H", "isotope": 0 } ], "mass1": -1.0, "stringValue1": "H(3)N" }, "name": "NH3", "fixed": false, "aminoAcids": [ "K", "N", "Q", "R" ] }, { "composition": { "atomChain": [ { "atomSymbol": "C", "isotope": 0 }, { "atomSymbol": "H", "isotope": 0 }, { "atomSymbol": "H", "isotope": 0 }, { "atomSymbol": "H", "isotope": 0 }, { "atomSymbol": "H", "isotope": 0 }, { "atomSymbol": "O", "isotope": 0 }, { "atomSymbol": "S", "isotope": 0 } ], "mass1": -1.0 }, "name": "CH4OS", "fixed": false } ], "neutralLossesAuto": true, "reporterIons": true, "relatedIons": true, "fragmentIonAccuracy": 0.5, "fragmentIonPpm": false, "showForwardIonDeNovoTags": false, "showRewindIonDeNovoTags": false, "deNovoCharge": 1, "highResolutionAnnotation": true, "tiesResolution": "mostAccurateMz" }, "sequenceMatchingPreferences": { "sequenceMatchingType": "indistiguishableAminoAcids", "limitX": 0.25, "peptideMapperType": "fm_index" }, "peptideVariantsPreferences": { "useSpecificCount": false, "nVariants": 0, "nAaDeletions": 0, "nAaInsertions": 0, "nAaSubstitutions": 0, "nAaSwap": 0, "aaSubstitutionMatrix": { "name": "No Substitution", "description": "No substitution", "substitutions": {}, "reverseMap": {} } }, "genePreferences": { "autoUpdate": false, "useGeneMapping": false }, "psmScoringPreferences": { "spectrumMatchingScores": { "8": [ 1 ], "3": [ 1 ], "27": [ 1 ] }, "defaultScores": [ -1 ], "minDecoysInBin": 10 }, "peptideAssumptionFilter": { "minPepLength": 8, "maxPepLength": 30, "maxMassDeviation": 10.0, "isPpm": true, "unknownPtm": true, "minIsotopes": 0, "maxIsotopes": 1 }, "ptmScoringPreferences": { "flr": 1.0, "probabilitsticScoreCalculation": true, "selectedProbabilisticScore": "PhosphoRS", "estimateFlr": false, "probabilisticScoreThreshold": 95.0, "probabilisticScoreNeutralLosses": false, "sequenceMatchingPreferences": { "sequenceMatchingType": "aminoAcid", "limitX": 0.25, "peptideMapperType": "fm_index" }, "alignNonConfidentPTMs": true }, "proteinInferencePreferences": { "proteinSequenceDatabase": { "path": "./searchgui_tinydb1_concatenated_target_decoy.fasta" }, "simplifyProteinGroups": true, "simplifyGroupsScore": true, "simplifyGroupsEvidence": true, "simplifyGroupsEnzymaticity": true, "simplifyGroupsUncharacterized": true }, "idValidationPreferences": { "defaultProteinFDR": 1.0, "defaultPeptideFDR": 1.0, "defaultPsmFDR": 1.0, "separatePeptides": true, "separatePsms": true, "mergeSmallSubgroups": true, "validationQCPreferences": { "dbSize": false, "firstDecoy": true, "confidenceMargin": 1.0 } }, "fractionSettings": { "proteinConfidenceMwPlots": 95.0, "fractionMolecularWeightRanges": {} } }