Mercurial > repos > galaxyp > peptideshaker

comparison test-data/Identification_Parameters_default_modifications.par @ 55:bb0130ff73ce draft

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"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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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.\nFragment Tolerance: 0.5 Da.\n",
6 "defaultDescription": true,
7 "searchParameters": {
8 "version": "5.0.1",
9 "precursorAccuracyType": "PPM",
10 "fragmentAccuracyType": "DA",
11 "precursorTolerance": 10.0,
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 },
37 "id": 0
38 },
39 "atomChainAdded": {
40 "atomChain": [
41 {
42 "atomSymbol": "C",
43 "isotope": 0,
44 "id": 0
45 },
46 {
47 "atomSymbol": "C",
48 "isotope": 0,
49 "id": 0
50 },
51 {
52 "atomSymbol": "H",
53 "isotope": 0,
54 "id": 0
55 },
56 {
57 "atomSymbol": "H",
58 "isotope": 0,
59 "id": 0
60 },
61 {
62 "atomSymbol": "H",
63 "isotope": 0,
64 "id": 0
65 },
66 {
67 "atomSymbol": "N",
68 "isotope": 0,
69 "id": 0
70 },
71 {
72 "atomSymbol": "O",
73 "isotope": 0,
74 "id": 0
75 }
76 ],
77 "mass": -1.0,
78 "id": 0
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 {
109 "atomSymbol": "C",
110 "isotope": 0,
111 "id": 0
112 },
113 {
114 "atomSymbol": "H",
115 "isotope": 0,
116 "id": 0
117 },
118 {
119 "atomSymbol": "H",
120 "isotope": 0,
121 "id": 0
122 },
123 {
124 "atomSymbol": "H",
125 "isotope": 0,
126 "id": 0
127 },
128 {
129 "atomSymbol": "H",
130 "isotope": 0,
131 "id": 0
132 },
133 {
134 "atomSymbol": "O",
135 "isotope": 0,
136 "id": 0
137 },
138 {
139 "atomSymbol": "S",
140 "isotope": 0,
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": {
154 "length": 0,
155 "residueTargeted": {
156 "0": [
157 "M"
158 ]
159 },
160 "id": 0
161 },
162 "atomChainAdded": {
163 "atomChain": [
164 {
165 "atomSymbol": "O",
166 "isotope": 0,
167 "id": 0
168 }
169 ],
170 "mass": -1.0,
171 "id": 0
172 },
173 "atomChainRemoved": {
174 "atomChain": [],
175 "mass": -1.0,
176 "id": 0
177 },
178 "unimodCvTerm": {
179 "ontology": "UNIMOD",
180 "accession": "UNIMOD:35",
181 "name": "Oxidation",
182 "id": 0
183 },
184 "psiModCvTerm": {
185 "ontology": "MOD",
186 "accession": "MOD:00719",
187 "name": "L-methionine sulfoxide",
188 "id": 0
189 },
190 "category": "Common",
191 "id": 0
192 }
193 },
194 "id": 0
195 },
196 "digestionParameters": {
197 "cleavageParameter": "enzyme",
198 "enzymes": [
199 {
200 "name": "Trypsin",
201 "aminoAcidBefore": [
202 "R",
203 "K"
204 ],
205 "aminoAcidAfter": [],
206 "restrictionBefore": [],
207 "restrictionAfter": [
208 "P"
209 ],
210 "cvTerm": {
211 "ontology": "PSI-MS",
212 "accession": "MS:1001251",
213 "name": "Trypsin",
214 "id": 0
215 },
216 "id": 0
217 }
218 ],
219 "nMissedCleavages": {
220 "Trypsin": 2
221 },
222 "specificity": {
223 "Trypsin": "specific"
224 },
225 "id": 0
226 },
227 "forwardIons": [
228 1
229 ],
230 "rewindIons": [
231 4
232 ],
233 "minChargeSearched": 2,
234 "maxChargeSearched": 4,
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": {
242 "maxEValue": 100.0,
243 "hitListLength": 10,
244 "minimalChargeForMultipleChargedFragments": 3,
245 "minPeptideLength": 8,
246 "maxPeptideLength": 30,
247 "removePrecursor": false,
248 "scalePrecursor": true,
249 "estimateCharge": true,
250 "selectedOutput": "OMX",
251 "memoryMappedSequenceLibraries": false,
252 "neutronThreshold": 1446.94,
253 "lowIntensityCutOff": 0.0,
254 "highIntensityCutOff": 0.2,
255 "intensityCutOffIncrement": 5.0E-4,
256 "singleChargeWindow": 27,
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": false,
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": {
362 "hitListLength": 10,
363 "estimateCharge": true,
364 "correctPrecursorMass": false,
365 "discardLowQualitySpectra": true,
366 "fragmentationModel": "CID_IT_TRYP",
367 "generateQuery": false,
368 "id": 0
369 }
370 },
371 "4": {
372 "type": "com.compomics.util.parameters.identification.tool_specific.AndromedaParameters",
373 "data": {
374 "maxPeptideMass": 4600.0,
375 "maxCombinations": 250,
376 "topPeaks": 8,
377 "topPeaksWindow": 100,
378 "includeWater": true,
379 "includeAmmonia": true,
380 "dependentLosses": true,
381 "fragmentAll": false,
382 "empiricalCorrection": true,
383 "higherCharge": true,
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": {
398 "generateDecoy": false,
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": {
421 "searchDecoyDatabase": false,
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": {
437 "ticCutoffPercentage": 100.0,
438 "maxPeakCount": 100,
439 "numIntensityClasses": 3,
440 "adjustPrecursorMass": false,
441 "minPrecursorAdjustment": -0.5,
442 "maxPrecursorAdjustment": 1.5,
443 "precursorAdjustmentStep": 0.1,
444 "numChargeStates": 3,
445 "outputSuffix": "",
446 "useChargeStateFromMS": true,
447 "duplicateSpectra": true,
448 "deisotopingMode": 0,
449 "isotopeMzTolerance": 0.25,
450 "complementMzTolerance": 0.1,
451 "tagLength": 4,
452 "maxDynamicMods": 2,
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,
469 "removePrecursor": 0,
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": {
491 "type": "com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters",
492 "data": {
493 "minPeptideLength": 8,
494 "maxPeptideLength": 30,
495 "numberOfSpectrumMatches": 10,
496 "ticCutoffPercentage": 0.98,
497 "maxDynamicMods": 2,
498 "minTerminiCleavages": 2,
499 "minPrecursorMass": 600.0,
500 "maxPrecursorMass": 5000.0,
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": {
517 "numberOfPeptides": 10,
518 "lowerPrecursorMass": 300,
519 "upperPrecursorMass": 5000,
520 "acticationType": "HCD",
521 "id": 0
522 }
523 },
524 "28": {
525 "type": "com.compomics.util.parameters.identification.tool_specific.TideParameters",
526 "data": {
527 "fastIndexFolderName": "fasta-index",
528 "maxVariableModificationsPerPeptide": 255,
529 "maxVariableModificationsPerTypePerPeptide": 2,
530 "minPeptideLength": 6,
531 "maxPeptideLength": 30,
532 "minPrecursorMass": 200.0,
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,
542 "digestionType": "full-digest",
543 "computeSpScore": false,
544 "numberOfSpectrumMatches": 10,
545 "computeExactPValues": false,
546 "minSpectrumMz": 0.0,
547 "minSpectrumPeaks": 20,
548 "spectrumCharges": "all",
549 "removePrecursor": false,
550 "removePrecursorTolerance": 1.5,
551 "printProgressIndicatorSize": 1000,
552 "useFlankingPeaks": false,
553 "useNeutralLossPeaks": false,
554 "mzBinWidth": 0.02,
555 "mzBinOffset": 0.0,
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": {
567 "type": "com.compomics.util.parameters.identification.tool_specific.NovorParameters",
568 "data": {
569 "fragmentationMethod": "HCD",
570 "massAnalyzer": "FT",
571 "id": 0
572 }
573 }
574 },
575 "flanking": false,
576 "id": 0
577 },
578 "annotationParameters": {
579 "yAxisZoomExcludesBackgroundPeaks": true,
580 "showAllPeaks": false,
581 "intensityThresholdType": "percentile",
582 "intensityLimit": 0.75,
583 "automaticAnnotation": true,
584 "selectedIonsMap": {
585 "IMMONIUM_ION": [
586 0,
587 1,
588 2,
589 3,
590 4,
591 5,
592 6,
593 7,
594 8,
595 9,
596 10,
597 11,
598 12,
599 13,
600 14,
601 15,
602 16,
603 17,
604 18,
605 19,
606 20
607 ],
608 "PEPTIDE_FRAGMENT_ION": [
609 4,
610 1
611 ],
612 "PRECURSOR_ION": [
613 0
614 ],
615 "TAG_FRAGMENT_ION": [
616 4,
617 1
618 ],
619 "REPORTER_ION": [],
620 "RELATED_ION": [
621 0,
622 1,
623 2,
624 3,
625 4,
626 5,
627 6,
628 7,
629 8,
630 9,
631 10,
632 11,
633 12,
634 13,
635 14,
636 15,
637 16,
638 17,
639 18
640 ]
641 },
642 "neutralLossesList": [
643 {
644 "composition": {
645 "atomChain": [
646 {
647 "atomSymbol": "H",
648 "isotope": 0,
649 "id": 0
650 },
651 {
652 "atomSymbol": "H",
653 "isotope": 0,
654 "id": 0
655 },
656 {
657 "atomSymbol": "O",
658 "isotope": 0,
659 "id": 0
660 }
661 ],
662 "mass": -1.0,
663 "id": 0
664 },
665 "name": "H2O",
666 "fixed": false,
667 "aminoAcids": [
668 "D",
669 "E",
670 "S",
671 "T"
672 ],
673 "id": 0
674 },
675 {
676 "composition": {
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678 {
679 "atomSymbol": "N",
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681 "id": 0
682 },
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686 "id": 0
687 },
688 {
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690 "isotope": 0,
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696 "id": 0
697 }
698 ],
699 "mass": -1.0,
700 "id": 0
701 },
702 "name": "NH3",
703 "fixed": false,
704 "aminoAcids": [
705 "K",
706 "N",
707 "Q",
708 "R"
709 ],
710 "id": 0
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740 {
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750 ],
751 "mass": -1.0,
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754 "name": "CH4OS",
755 "fixed": false,
756 "id": 0
757 }
758 ],
759 "neutralLossesAuto": true,
760 "reporterIons": true,
761 "relatedIons": true,
762 "fragmentIonAccuracy": 10.0,
763 "fragmentIonPpm": false,
764 "showForwardIonDeNovoTags": false,
765 "showRewindIonDeNovoTags": false,
766 "deNovoCharge": 1,
767 "tiesResolution": "mostAccurateMz",
768 "id": 0
769 },
770 "sequenceMatchingParameters": {
771 "sequenceMatchingType": "indistiguishableAminoAcids",
772 "limitX": 0.25,
773 "enzymaticTagsOnly": false,
774 "maxPtmsPerTagPeptide": 3,
775 "minAminoAcidScore": 30,
776 "minTagLength": 3,
777 "id": 0
778 },
779 "peptideVariantsParameters": {
780 "variantType": "NO_VARIANT",
781 "nVariants": 0,
782 "nAaDeletions": 0,
783 "nAaInsertions": 0,
784 "nAaSubstitutions": 0,
785 "nAaSwap": 0,
786 "aaSubstitutionMatrix": {
787 "name": "No Substitution",
788 "description": "No substitution",
789 "substitutions": {},
790 "reverseMap": {},
791 "id": 0
792 },
793 "fixedVariants": {},
794 "id": 0
795 },
796 "geneParameters": {
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798 "useGeneMapping": false,
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800 },
801 "psmScoringParameters": {
802 "spectrumMatchingScores": {
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806 "3": [
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808 ],
809 "27": [
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811 ]
812 },
813 "defaultScores": [
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815 ],
816 "minDecoysInBin": 10,
817 "id": 0
818 },
819 "peptideAssumptionFilter": {
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821 "maxPepLength": 30,
822 "maxMassDeviation": 10.0,
823 "isPpm": true,
824 "unknownModification": true,
825 "minIsotopes": 0,
826 "maxIsotopes": 1,
827 "id": 0
828 },
829 "modificationLocalizationParameters": {
830 "probabilisticScoreCalculation": true,
831 "selectedProbabilisticScore": "PhosphoRS",
832 "dScoreThreshold": 95.0,
833 "probabilisticScoreThreshold": 95.0,
834 "probabilisticScoreNeutralLosses": false,
835 "sequenceMatchingParameters": {
836 "sequenceMatchingType": "aminoAcid",
837 "limitX": 0.25,
838 "enzymaticTagsOnly": false,
839 "maxPtmsPerTagPeptide": 3,
840 "minAminoAcidScore": 30,
841 "minTagLength": 3,
842 "id": 0
843 },
844 "alignNonConfidentModifications": true,
845 "id": 0
846 },
847 "proteinInferenceParameters": {
848 "modificationRefinement": true,
849 "simplifyProteinGroups": true,
850 "simplifyGroupsEvidence": true,
851 "simplifyGroupsConfidence": true,
852 "simplifyGroupsEnzymaticity": true,
853 "simplifyGroupsVariants": true,
854 "confidenceThreshold": 0.05,
855 "id": 0
856 },
857 "idValidationParameters": {
858 "defaultProteinFDR": 1.0,
859 "defaultPeptideFDR": 1.0,
860 "defaultPsmFDR": 1.0,
861 "validationQCPreferences": {
862 "dbSize": false,
863 "firstDecoy": true,
864 "confidenceMargin": 1.0,
865 "id": 0
866 },
867 "id": 0
868 },
869 "fractionParameters": {
870 "proteinConfidenceMwPlots": 95.0,
871 "fractionMolecularWeightRanges": {},
872 "id": 0
873 },
874 "fastaParameters": {
875 "targetDecoy": true,
876 "decoyFlag": "-REVERSED",
877 "decoySuffix": true,
878 "targetDecoyFileNameTag": "_concatenated_target_decoy",
879 "id": 0
880 },
881 "id": 0
882 }