comparison test-data/Identification_Parameters_specific.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
parents
children
comparison
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54:7fdd9119cc4f 55:bb0130ff73ce
1 {
2 "marshallableParameterType": "identification_parameters",
3 "version": "5.0.1",
4 "name": "IdentificationParametersOutput",
5 "description": "Fixed: Carbamidomethylation of C.\nVariable: Oxidation of M.\nPrecursor Tolerance: 100.0 ppm.\nFragment Tolerance: 0.5 Da.\nCharge: 1-3.\n",
6 "defaultDescription": true,
7 "searchParameters": {
8 "version": "5.0.1",
9 "precursorAccuracyType": "PPM",
10 "fragmentAccuracyType": "DA",
11 "precursorTolerance": 100.0,
12 "fragmentIonMZTolerance": 0.5,
13 "modificationParameters": {
14 "fixedModifications": [
15 "Carbamidomethylation of C"
16 ],
17 "variableModifications": [
18 "Oxidation of M"
19 ],
20 "refinementVariableModifications": [],
21 "refinementFixedModifications": [],
22 "colors": {},
23 "backUp": {
24 "Carbamidomethylation of C": {
25 "modificationType": "modaa",
26 "name": "Carbamidomethylation of C",
27 "shortName": "cmm",
28 "neutralLosses": [],
29 "reporterIons": [],
30 "pattern": {
31 "length": 0,
32 "residueTargeted": {
33 "0": [
34 "C"
35 ]
36 },
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38 },
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45 },
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49 "id": 0
50 },
51 {
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55 },
56 {
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59 "id": 0
60 },
61 {
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63 "isotope": 0,
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65 },
66 {
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75 }
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77 "mass": -1.0,
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79 },
80 "atomChainRemoved": {
81 "atomChain": [],
82 "mass": -1.0,
83 "id": 0
84 },
85 "unimodCvTerm": {
86 "ontology": "UNIMOD",
87 "accession": "UNIMOD:4",
88 "name": "Carbamidomethyl",
89 "id": 0
90 },
91 "psiModCvTerm": {
92 "ontology": "MOD",
93 "accession": "MOD:01060",
94 "name": "S-carboxamidomethyl-L-cysteine",
95 "id": 0
96 },
97 "category": "Common",
98 "id": 0
99 },
100 "Oxidation of M": {
101 "modificationType": "modaa",
102 "name": "Oxidation of M",
103 "shortName": "ox",
104 "neutralLosses": [
105 {
106 "composition": {
107 "atomChain": [
108 {
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112 },
113 {
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117 },
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122 },
123 {
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127 },
128 {
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132 },
133 {
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137 },
138 {
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141 "id": 0
142 }
143 ],
144 "mass": -1.0,
145 "id": 0
146 },
147 "name": "CH4OS",
148 "fixed": false,
149 "id": 0
150 }
151 ],
152 "reporterIons": [],
153 "pattern": {
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155 "residueTargeted": {
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158 ]
159 },
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161 },
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177 },
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181 "name": "Oxidation",
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183 },
184 "psiModCvTerm": {
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186 "accession": "MOD:00719",
187 "name": "L-methionine sulfoxide",
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189 },
190 "category": "Common",
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192 }
193 },
194 "id": 0
195 },
196 "digestionParameters": {
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198 "enzymes": [
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200 "name": "Trypsin",
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203 "K"
204 ],
205 "aminoAcidAfter": [],
206 "restrictionBefore": [],
207 "restrictionAfter": [
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209 ],
210 "cvTerm": {
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212 "accession": "MS:1001251",
213 "name": "Trypsin",
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215 },
216 "id": 0
217 }
218 ],
219 "nMissedCleavages": {
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221 },
222 "specificity": {
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224 },
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226 },
227 "forwardIons": [
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229 ],
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232 ],
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234 "maxChargeSearched": 3,
235 "minIsotopicCorrection": 0,
236 "maxIsotopicCorrection": 1,
237 "refMass": 2000.0,
238 "algorithmParameters": {
239 "1": {
240 "type": "com.compomics.util.parameters.identification.tool_specific.OmssaParameters",
241 "data": {
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244 "minimalChargeForMultipleChargedFragments": 3,
245 "minPeptideLength": 8,
246 "maxPeptideLength": 30,
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248 "scalePrecursor": true,
249 "estimateCharge": true,
250 "selectedOutput": "OMX",
251 "memoryMappedSequenceLibraries": false,
252 "neutronThreshold": 1446.94,
253 "lowIntensityCutOff": 0.0,
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255 "intensityCutOffIncrement": 5.0E-4,
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257 "doubleChargeWindow": 14,
258 "nPeaksInSingleChargeWindow": 2,
259 "nPeaksIndoubleChargeWindow": 2,
260 "maxHitsPerSpectrumPerCharge": 30,
261 "nAnnotatedMostIntensePeaks": 6,
262 "minAnnotatedPeaks": 2,
263 "minPeaks": 4,
264 "cleaveNtermMethionine": true,
265 "maxMzLadders": 128,
266 "maxFragmentCharge": 2,
267 "fractionOfPeaksForChargeEstimation": 0.95,
268 "determineChargePlusOneAlgorithmically": true,
269 "searchPositiveIons": true,
270 "minPrecPerSpectrum": 1,
271 "searchForwardFragmentFirst": false,
272 "searchRewindFragments": true,
273 "maxFragmentPerSeries": 100,
274 "useCorrelationCorrectionScore": true,
275 "consecutiveIonProbability": 0.5,
276 "iterativeSequenceEvalue": 0.0,
277 "iterativeReplaceEvalue": 0.0,
278 "iterativeSpectrumEvalue": 0.01,
279 "noProlineRuleSeries": [],
280 "ptmIndexes": {},
281 "id": 0
282 }
283 },
284 "33": {
285 "type": "com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters",
286 "data": {
287 "minPeptideLength": 8,
288 "maxPeptideLength": 30,
289 "searchType": "Classic",
290 "totalPartitions": 1,
291 "dissociationType": "HCD",
292 "maxModsForPeptide": 2,
293 "initiatorMethionineBehavior": "Variable",
294 "scoreCutoff": 5.0,
295 "useDeltaScore": false,
296 "fragmentationTerminus": "Both",
297 "maxFragmentSize": 30000.0,
298 "massDiffAcceptorType": "OneMM",
299 "writeMzId": true,
300 "writePepXml": false,
301 "useProvidedPrecursorInfo": true,
302 "doPrecursorDeconvolution": true,
303 "deconvolutionIntensityRatio": 3.0,
304 "deconvolutionMassTolerance": 4.0,
305 "deconvolutionMassToleranceType": "PPM",
306 "trimMs1Peaks": false,
307 "trimMsMsPeaks": true,
308 "numberOfPeaksToKeepPerWindow": 200,
309 "minAllowedIntensityRatioToBasePeak": 0.01,
310 "normalizePeaksAcrossAllWindows": false,
311 "modPeptidesAreDifferent": false,
312 "noOneHitWonders": false,
313 "searchTarget": true,
314 "decoyType": "None",
315 "maxModificationIsoforms": 1024,
316 "minVariantDepth": 1,
317 "maxHeterozygousVariants": 4,
318 "runGptm": false,
319 "gPtmCategories": [
320 "Common_Biological",
321 "Common_Artifact",
322 "Metal"
323 ],
324 "id": 0
325 }
326 },
327 "2": {
328 "type": "com.compomics.util.parameters.identification.tool_specific.XtandemParameters",
329 "data": {
330 "maxEValue": 0.01,
331 "outputResults": "all",
332 "dynamicRange": 100.0,
333 "nPeaks": 50,
334 "minPrecursorMass": 500.0,
335 "minFragmentMz": 200.0,
336 "minPeaksPerSpectrum": 5,
337 "proteinQuickAcetyl": true,
338 "quickPyrolidone": true,
339 "refine": true,
340 "refineSemi": false,
341 "refinePointMutations": false,
342 "refineSpectrumSynthesis": true,
343 "refineUnanticipatedCleavages": true,
344 "refineSnaps": true,
345 "maximumExpectationValueRefinement": 0.01,
346 "potentialModificationsForFullRefinment": true,
347 "skylinePath": "",
348 "outputProteins": true,
349 "outputSequences": false,
350 "outputSpectra": true,
351 "outputHistograms": false,
352 "stpBias": false,
353 "useNoiseSuppression": false,
354 "proteinPtmComplexity": 6.0,
355 "parentMonoisotopicMassIsotopeError": true,
356 "id": 0
357 }
358 },
359 "3": {
360 "type": "com.compomics.util.parameters.identification.tool_specific.PepnovoParameters",
361 "data": {
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364 "correctPrecursorMass": false,
365 "discardLowQualitySpectra": true,
366 "fragmentationModel": "CID_IT_TRYP",
367 "generateQuery": false,
368 "id": 0
369 }
370 },
371 "4": {
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373 "data": {
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375 "maxCombinations": 250,
376 "topPeaks": 8,
377 "topPeaksWindow": 100,
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379 "includeAmmonia": true,
380 "dependentLosses": true,
381 "fragmentAll": false,
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384 "fragmentationMethod": "CID",
385 "maxNumberOfModifications": 5,
386 "minPeptideLengthNoEnzyme": 8,
387 "maxPeptideLengthNoEnzyme": 30,
388 "equalIL": false,
389 "numberOfCandidates": 10,
390 "ptmIndexes": {},
391 "decoyMode": "none",
392 "id": 0
393 }
394 },
395 "5": {
396 "type": "com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters",
397 "data": {
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399 "reportBothBestHitsForTD": true,
400 "instrumentID": "b, y",
401 "maxRank": 10,
402 "monoisotopic": true,
403 "lowMemoryMode": true,
404 "performDeisotoping": true,
405 "maxModifications": 3,
406 "maxVariableModifications": 4,
407 "maxModificationSites": 6,
408 "maxNeutralLosses": 1,
409 "maxNeutralLossesPerModification": 2,
410 "minPeptideLength": 8,
411 "maxPeptideLength": 30,
412 "maxLoadedProteins": 100000,
413 "maxLoadedSpectra": 2000,
414 "outputFormat": "csv",
415 "id": 0
416 }
417 },
418 "7": {
419 "type": "com.compomics.util.parameters.identification.tool_specific.MsgfParameters",
420 "data": {
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422 "instrumentID": 3,
423 "fragmentationType": 3,
424 "protocol": 0,
425 "minPeptideLength": 8,
426 "maxPeptideLength": 30,
427 "numberOfSpectrumMarches": 10,
428 "additionalOutput": false,
429 "numberTolerableTermini": 2,
430 "numberOfModificationsPerPeptide": 2,
431 "id": 0
432 }
433 },
434 "8": {
435 "type": "com.compomics.util.parameters.identification.tool_specific.DirecTagParameters",
436 "data": {
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438 "maxPeakCount": 100,
439 "numIntensityClasses": 3,
440 "adjustPrecursorMass": false,
441 "minPrecursorAdjustment": -0.5,
442 "maxPrecursorAdjustment": 1.5,
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446 "useChargeStateFromMS": true,
447 "duplicateSpectra": true,
448 "deisotopingMode": 0,
449 "isotopeMzTolerance": 0.25,
450 "complementMzTolerance": 0.1,
451 "tagLength": 4,
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453 "maxTagCount": 10,
454 "intensityScoreWeight": 1.0,
455 "mzFidelityScoreWeight": 1.0,
456 "complementScoreWeight": 1.0,
457 "variableModifications": [],
458 "id": 0
459 }
460 },
461 "10": {
462 "type": "com.compomics.util.parameters.identification.tool_specific.CometParameters",
463 "data": {
464 "numberOfSpectrumMatches": 10,
465 "maxVariableMods": 10,
466 "requireVariableMods": false,
467 "minPeaks": 10,
468 "minPeakIntensity": 0.0,
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470 "removePrecursorTolerance": 1.5,
471 "lowerClearMzRange": 0.0,
472 "upperClearMzRange": 0.0,
473 "enzymeType": 2,
474 "isotopeCorrection": 3,
475 "minPrecursorMass": 600.0,
476 "maxPrecursorMass": 5000.0,
477 "maxFragmentCharge": 3,
478 "removeMethionine": false,
479 "batchSize": 0,
480 "theoreticalFragmentIonsSumOnly": false,
481 "fragmentBinOffset": 0.0,
482 "useSparseMatrix": true,
483 "selectedOutputFormat": "PepXML",
484 "printExpectScore": true,
485 "minPeptideLength": 8,
486 "maxPeptideLength": 30,
487 "id": 0
488 }
489 },
490 "13": {
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492 "data": {
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494 "maxPeptideLength": 30,
495 "numberOfSpectrumMatches": 10,
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497 "maxDynamicMods": 2,
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501 "useSmartPlusThreeModel": false,
502 "computeXCorr": false,
503 "numIntensityClasses": 3,
504 "classSizeMultiplier": 2,
505 "numberOfBatches": 50,
506 "lowerIsotopeCorrection": -1,
507 "upperIsotopeCorrection": 2,
508 "fragmentationRule": "CID",
509 "maxPeakCount": 300,
510 "outputFormat": "mzIdentML",
511 "id": 0
512 }
513 },
514 "27": {
515 "type": "com.compomics.util.parameters.identification.tool_specific.PNovoParameters",
516 "data": {
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518 "lowerPrecursorMass": 300,
519 "upperPrecursorMass": 5000,
520 "acticationType": "HCD",
521 "id": 0
522 }
523 },
524 "28": {
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528 "maxVariableModificationsPerPeptide": 255,
529 "maxVariableModificationsPerTypePerPeptide": 2,
530 "minPeptideLength": 6,
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533 "maxPrecursorMass": 7200.0,
534 "decoyFormat": "none",
535 "keepTerminalAminoAcids": "NC",
536 "decoySeed": 1,
537 "outputFolderName": "crux-output",
538 "printPeptides": false,
539 "verbosity": 30,
540 "monoisotopicPrecursor": true,
541 "clipNtermMethionine": false,
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546 "minSpectrumMz": 0.0,
547 "minSpectrumPeaks": 20,
548 "spectrumCharges": "all",
549 "removePrecursor": false,
550 "removePrecursorTolerance": 1.5,
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552 "useFlankingPeaks": false,
553 "useNeutralLossPeaks": false,
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556 "concatenateTargetDecoy": false,
557 "textOutput": true,
558 "sqtOutput": false,
559 "pepXmlOutput": false,
560 "mzidOutput": false,
561 "pinOutput": false,
562 "removeTempFolders": true,
563 "id": 0
564 }
565 },
566 "29": {
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568 "data": {
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570 "massAnalyzer": "FT",
571 "id": 0
572 }
573 }
574 },
575 "flanking": false,
576 "id": 0
577 },
578 "annotationParameters": {
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580 "showAllPeaks": false,
581 "intensityThresholdType": "percentile",
582 "intensityLimit": 0.75,
583 "automaticAnnotation": true,
584 "selectedIonsMap": {
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607 ],
608 "PEPTIDE_FRAGMENT_ION": [
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610 1
611 ],
612 "PRECURSOR_ION": [
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614 ],
615 "TAG_FRAGMENT_ION": [
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618 ],
619 "REPORTER_ION": [],
620 "RELATED_ION": [
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640 ]
641 },
642 "neutralLossesList": [
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761 "relatedIons": true,
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793 "fixedVariants": {},
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825 "minIsotopes": 0,
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829 "modificationLocalizationParameters": {
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831 "selectedProbabilisticScore": "PhosphoRS",
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833 "probabilisticScoreThreshold": 95.0,
834 "probabilisticScoreNeutralLosses": false,
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843 },
844 "alignNonConfidentModifications": true,
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847 "proteinInferenceParameters": {
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849 "simplifyProteinGroups": true,
850 "simplifyGroupsEvidence": true,
851 "simplifyGroupsConfidence": true,
852 "simplifyGroupsEnzymaticity": true,
853 "simplifyGroupsVariants": true,
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857 "idValidationParameters": {
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859 "defaultPeptideFDR": 1.0,
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861 "validationQCPreferences": {
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863 "firstDecoy": true,
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871 "fractionMolecularWeightRanges": {},
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873 },
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876 "decoyFlag": "-REVERSED",
877 "decoySuffix": true,
878 "targetDecoyFileNameTag": "_concatenated_target_decoy",
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881 "id": 0
882 }