Mercurial > repos > galaxyp > maxquant

comparison test-data/08/mqpar.xml @ 11:057bf124c80e draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
author galaxyp
date Sun, 20 Jun 2021 16:36:56 +0000
parents
children 5d013f405259
comparison
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10:68d8dcdbddb1 11:057bf124c80e
1 <?xml version="1.0" ?>
2 <MaxQuantParams>
3 <fastaFiles>
4 <FastaFileInfo>
5 <fastaFilePath>/tmp/tmpd7w978vs/files/0/f/c/dataset_0fc77a17-694f-4046-a911-98d071f76050.dat</fastaFilePath>
6 <identifierParseRule>&gt;([^\s]*)</identifierParseRule>
7 <descriptionParseRule>&gt;(.*)</descriptionParseRule>
8 <taxonomyParseRule/>
9 <variationParseRule/>
10 <modificationParseRule/>
11 <taxonomyId/>
12 </FastaFileInfo>
13 </fastaFiles>
14 <fastaFilesProteogenomics>
15 </fastaFilesProteogenomics>
16 <fastaFilesFirstSearch>
17 </fastaFilesFirstSearch>
18 <fixedSearchFolder/>
19 <andromedaCacheSize>350000</andromedaCacheSize>
20 <advancedRatios>True</advancedRatios>
21 <pvalThres>0.005</pvalThres>
22 <rtShift>False</rtShift>
23 <separateLfq>False</separateLfq>
24 <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>
25 <lfqRequireMsms>True</lfqRequireMsms>
26 <decoyMode>revert</decoyMode>
27 <boxCarMode>all</boxCarMode>
28 <includeContaminants>True</includeContaminants>
29 <maxPeptideMass>4600</maxPeptideMass>
30 <epsilonMutationScore>True</epsilonMutationScore>
31 <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>
32 <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>
33 <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>
34 <minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>
35 <minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>
36 <minScoreModifiedPeptides>40</minScoreModifiedPeptides>
37 <secondPeptide>True</secondPeptide>
38 <matchBetweenRuns>False</matchBetweenRuns>
39 <matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>
40 <matchBetweenRunsFdr>False</matchBetweenRunsFdr>
41 <dependentPeptides>False</dependentPeptides>
42 <dependentPeptideFdr>0</dependentPeptideFdr>
43 <dependentPeptideMassBin>0</dependentPeptideMassBin>
44 <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>
45 <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>
46 <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>
47 <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>
48 <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>
49 <ibaq>False</ibaq>
50 <top3>False</top3>
51 <independentEnzymes>False</independentEnzymes>
52 <useDeltaScore>False</useDeltaScore>
53 <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>
54 <taxonomyLevel>Species</taxonomyLevel>
55 <avalon>False</avalon>
56 <nModColumns>3</nModColumns>
57 <ibaqLogFit>False</ibaqLogFit>
58 <razorProteinFdr>True</razorProteinFdr>
59 <deNovoSequencing>False</deNovoSequencing>
60 <deNovoVarMods>True</deNovoVarMods>
61 <massDifferenceSearch>False</massDifferenceSearch>
62 <isotopeCalc>False</isotopeCalc>
63 <writePeptidesForSpectrumFile/>
64 <intensityPredictionsFile>
65 </intensityPredictionsFile>
66 <minPepLen>7</minPepLen>
67 <psmFdrCrosslink>0.01</psmFdrCrosslink>
68 <peptideFdr>0.01</peptideFdr>
69 <proteinFdr>0.01</proteinFdr>
70 <siteFdr>0.01</siteFdr>
71 <minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>
72 <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>
73 <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>
74 <minPeptides>1</minPeptides>
75 <minRazorPeptides>1</minRazorPeptides>
76 <minUniquePeptides>0</minUniquePeptides>
77 <useCounterparts>True</useCounterparts>
78 <advancedSiteIntensities>True</advancedSiteIntensities>
79 <customProteinQuantification>False</customProteinQuantification>
80 <customProteinQuantificationFile/>
81 <minRatioCount>2</minRatioCount>
82 <restrictProteinQuantification>True</restrictProteinQuantification>
83 <restrictMods>
84 <string>Oxidation (M)</string>
85 <string>Acetyl (Protein N-term)</string>
86 </restrictMods>
87 <matchingTimeWindow>0</matchingTimeWindow>
88 <matchingIonMobilityWindow>0</matchingIonMobilityWindow>
89 <alignmentTimeWindow>0</alignmentTimeWindow>
90 <alignmentIonMobilityWindow>0</alignmentIonMobilityWindow>
91 <numberOfCandidatesMsms>15</numberOfCandidatesMsms>
92 <compositionPrediction>0</compositionPrediction>
93 <quantMode>1</quantMode>
94 <massDifferenceMods>
95 </massDifferenceMods>
96 <mainSearchMaxCombinations>200</mainSearchMaxCombinations>
97 <writeMsScansTable>False</writeMsScansTable>
98 <writeMsmsScansTable>True</writeMsmsScansTable>
99 <writePasefMsmsScansTable>True</writePasefMsmsScansTable>
100 <writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable>
101 <writeMs3ScansTable>True</writeMs3ScansTable>
102 <writeAllPeptidesTable>True</writeAllPeptidesTable>
103 <writeMzRangeTable>True</writeMzRangeTable>
104 <writeDiaFragmentTable>False</writeDiaFragmentTable>
105 <writeMzTab>False</writeMzTab>
106 <disableMd5>False</disableMd5>
107 <cacheBinInds>True</cacheBinInds>
108 <etdIncludeB>False</etdIncludeB>
109 <ms2PrecursorShift>0</ms2PrecursorShift>
110 <complementaryIonPpm>20</complementaryIonPpm>
111 <variationParseRule/>
112 <variationMode>none</variationMode>
113 <useSeriesReporters>False</useSeriesReporters>
114 <name>templateSession</name>
115 <maxQuantVersion>1.6.17.0</maxQuantVersion>
116 <pluginFolder/>
117 <numThreads>1</numThreads>
118 <batchSize>1</batchSize>
119 <emailAddress/>
120 <smtpHost/>
121 <emailFromAddress/>
122 <fixedCombinedFolder/>
123 <fullMinMz>-1.79769313486232E+308</fullMinMz>
124 <fullMaxMz>1.79769313486232E+308</fullMaxMz>
125 <sendEmail>False</sendEmail>
126 <ionCountIntensities>False</ionCountIntensities>
127 <verboseColumnHeaders>False</verboseColumnHeaders>
128 <calcPeakProperties>False</calcPeakProperties>
129 <showCentroidMassDifferences>False</showCentroidMassDifferences>
130 <showIsotopeMassDifferences>False</showIsotopeMassDifferences>
131 <useDotNetCore>True</useDotNetCore>
132 <profilePerformance>False</profilePerformance>
133 <filePaths>
134 <string>/tmp/tmpd7w978vs/job_working_directory/000/3/working/tmt16_ori.mzXML</string>
135 </filePaths>
136 <experiments>
137 <string>tmt16_ori.mzXML</string>
138 </experiments>
139 <fractions>
140 <short>32767</short>
141 </fractions>
142 <ptms>
143 <boolean>False</boolean>
144 </ptms>
145 <paramGroupIndices>
146 <int>0</int>
147 </paramGroupIndices>
148 <referenceChannel>
149 <string/>
150 </referenceChannel>
151 <intensPred>False</intensPred>
152 <intensPredModelReTrain>False</intensPredModelReTrain>
153 <lfqTopNPeptides>0</lfqTopNPeptides>
154 <parameterGroups>
155 <parameterGroup>
156 <msInstrument>0</msInstrument>
157 <maxCharge>7</maxCharge>
158 <minPeakLen>2</minPeakLen>
159 <diaMinPeakLen>1</diaMinPeakLen>
160 <useMs1Centroids>False</useMs1Centroids>
161 <useMs2Centroids>False</useMs2Centroids>
162 <cutPeaks>True</cutPeaks>
163 <gapScans>1</gapScans>
164 <minTime>NaN</minTime>
165 <maxTime>NaN</maxTime>
166 <matchType>MatchFromAndTo</matchType>
167 <intensityDetermination>0</intensityDetermination>
168 <centroidMatchTol>8</centroidMatchTol>
169 <centroidMatchTolInPpm>True</centroidMatchTolInPpm>
170 <centroidHalfWidth>35</centroidHalfWidth>
171 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
172 <valleyFactor>1.4</valleyFactor>
173 <isotopeValleyFactor>1.2</isotopeValleyFactor>
174 <advancedPeakSplitting>False</advancedPeakSplitting>
175 <intensityThresholdMs1>0</intensityThresholdMs1>
176 <intensityThresholdMs2>0</intensityThresholdMs2>
177 <labelMods>
178 <string/>
179 </labelMods>
180 <lcmsRunType>Reporter ion MS2</lcmsRunType>
181 <reQuantify>False</reQuantify>
182 <lfqMode>0</lfqMode>
183 <lfqNormClusterSize>80</lfqNormClusterSize>
184 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
185 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
186 <lfqMaxFeatures>100000</lfqMaxFeatures>
187 <neucodeMaxPpm>0</neucodeMaxPpm>
188 <neucodeResolution>0</neucodeResolution>
189 <neucodeResolutionInMda>False</neucodeResolutionInMda>
190 <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
191 <fastLfq>True</fastLfq>
192 <lfqRestrictFeatures>False</lfqRestrictFeatures>
193 <lfqMinRatioCount>2</lfqMinRatioCount>
194 <maxLabeledAa>0</maxLabeledAa>
195 <maxNmods>5</maxNmods>
196 <maxMissedCleavages>2</maxMissedCleavages>
197 <multiplicity>1</multiplicity>
198 <enzymeMode>0</enzymeMode>
199 <complementaryReporterType>0</complementaryReporterType>
200 <reporterNormalization>0</reporterNormalization>
201 <neucodeIntensityMode>0</neucodeIntensityMode>
202 <fixedModifications/>
203 <enzymes>
204 <string>Trypsin/P</string>
205 </enzymes>
206 <enzymesFirstSearch>
207 </enzymesFirstSearch>
208 <enzymeModeFirstSearch>0</enzymeModeFirstSearch>
209 <useEnzymeFirstSearch>False</useEnzymeFirstSearch>
210 <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
211 <variableModifications>
212 <string>Oxidation (M)</string>
213 </variableModifications>
214 <useMultiModification>False</useMultiModification>
215 <multiModifications>
216 </multiModifications>
217 <isobaricLabels>
218 <IsobaricLabelInfo>
219 <internalLabel>TMTpro16plex-Lys127N</internalLabel>
220 <terminalLabel>TMTpro16plex-Nter127N</terminalLabel>
221 <correctionFactorM2>0</correctionFactorM2>
222 <correctionFactorM1>0</correctionFactorM1>
223 <correctionFactorP1>0</correctionFactorP1>
224 <correctionFactorP2>0</correctionFactorP2>
225 <tmtLike>True</tmtLike>
226 </IsobaricLabelInfo>
227 <IsobaricLabelInfo>
228 <internalLabel>TMTpro16plex-Lys127C</internalLabel>
229 <terminalLabel>TMTpro16plex-Nter127C</terminalLabel>
230 <correctionFactorM2>0</correctionFactorM2>
231 <correctionFactorM1>0</correctionFactorM1>
232 <correctionFactorP1>0</correctionFactorP1>
233 <correctionFactorP2>0</correctionFactorP2>
234 <tmtLike>True</tmtLike>
235 </IsobaricLabelInfo>
236 <IsobaricLabelInfo>
237 <internalLabel>TMTpro16plex-Lys128N</internalLabel>
238 <terminalLabel>TMTpro16plex-Nter128N</terminalLabel>
239 <correctionFactorM2>0</correctionFactorM2>
240 <correctionFactorM1>0</correctionFactorM1>
241 <correctionFactorP1>0</correctionFactorP1>
242 <correctionFactorP2>0</correctionFactorP2>
243 <tmtLike>True</tmtLike>
244 </IsobaricLabelInfo>
245 <IsobaricLabelInfo>
246 <internalLabel>TMTpro16plex-Lys128C</internalLabel>
247 <terminalLabel>TMTpro16plex-Nter128C</terminalLabel>
248 <correctionFactorM2>0</correctionFactorM2>
249 <correctionFactorM1>0</correctionFactorM1>
250 <correctionFactorP1>0</correctionFactorP1>
251 <correctionFactorP2>0</correctionFactorP2>
252 <tmtLike>True</tmtLike>
253 </IsobaricLabelInfo>
254 <IsobaricLabelInfo>
255 <internalLabel>TMTpro16plex-Lys129N</internalLabel>
256 <terminalLabel>TMTpro16plex-Nter129N</terminalLabel>
257 <correctionFactorM2>0</correctionFactorM2>
258 <correctionFactorM1>0</correctionFactorM1>
259 <correctionFactorP1>0</correctionFactorP1>
260 <correctionFactorP2>0</correctionFactorP2>
261 <tmtLike>True</tmtLike>
262 </IsobaricLabelInfo>
263 <IsobaricLabelInfo>
264 <internalLabel>TMTpro16plex-Lys129C</internalLabel>
265 <terminalLabel>TMTpro16plex-Nter129C</terminalLabel>
266 <correctionFactorM2>0</correctionFactorM2>
267 <correctionFactorM1>0</correctionFactorM1>
268 <correctionFactorP1>0</correctionFactorP1>
269 <correctionFactorP2>0</correctionFactorP2>
270 <tmtLike>True</tmtLike>
271 </IsobaricLabelInfo>
272 <IsobaricLabelInfo>
273 <internalLabel>TMTpro16plex-Lys130N</internalLabel>
274 <terminalLabel>TMTpro16plex-Nter130N</terminalLabel>
275 <correctionFactorM2>0</correctionFactorM2>
276 <correctionFactorM1>0</correctionFactorM1>
277 <correctionFactorP1>0</correctionFactorP1>
278 <correctionFactorP2>0</correctionFactorP2>
279 <tmtLike>True</tmtLike>
280 </IsobaricLabelInfo>
281 <IsobaricLabelInfo>
282 <internalLabel>TMTpro16plex-Lys130C</internalLabel>
283 <terminalLabel>TMTpro16plex-Nter130C</terminalLabel>
284 <correctionFactorM2>0</correctionFactorM2>
285 <correctionFactorM1>0</correctionFactorM1>
286 <correctionFactorP1>0</correctionFactorP1>
287 <correctionFactorP2>0</correctionFactorP2>
288 <tmtLike>True</tmtLike>
289 </IsobaricLabelInfo>
290 <IsobaricLabelInfo>
291 <internalLabel>TMTpro16plex-Lys131N</internalLabel>
292 <terminalLabel>TMTpro16plex-Nter131N</terminalLabel>
293 <correctionFactorM2>0</correctionFactorM2>
294 <correctionFactorM1>0</correctionFactorM1>
295 <correctionFactorP1>0</correctionFactorP1>
296 <correctionFactorP2>0</correctionFactorP2>
297 <tmtLike>True</tmtLike>
298 </IsobaricLabelInfo>
299 <IsobaricLabelInfo>
300 <internalLabel>TMTpro16plex-Lys131C</internalLabel>
301 <terminalLabel>TMTpro16plex-Nter131C</terminalLabel>
302 <correctionFactorM2>0</correctionFactorM2>
303 <correctionFactorM1>0</correctionFactorM1>
304 <correctionFactorP1>0</correctionFactorP1>
305 <correctionFactorP2>0</correctionFactorP2>
306 <tmtLike>True</tmtLike>
307 </IsobaricLabelInfo>
308 <IsobaricLabelInfo>
309 <internalLabel>TMTpro16plex-Lys132N</internalLabel>
310 <terminalLabel>TMTpro16plex-Nter132N</terminalLabel>
311 <correctionFactorM2>0</correctionFactorM2>
312 <correctionFactorM1>0</correctionFactorM1>
313 <correctionFactorP1>0</correctionFactorP1>
314 <correctionFactorP2>0</correctionFactorP2>
315 <tmtLike>True</tmtLike>
316 </IsobaricLabelInfo>
317 <IsobaricLabelInfo>
318 <internalLabel>TMTpro16plex-Lys132C</internalLabel>
319 <terminalLabel>TMTpro16plex-Nter132C</terminalLabel>
320 <correctionFactorM2>0</correctionFactorM2>
321 <correctionFactorM1>0</correctionFactorM1>
322 <correctionFactorP1>0</correctionFactorP1>
323 <correctionFactorP2>0</correctionFactorP2>
324 <tmtLike>True</tmtLike>
325 </IsobaricLabelInfo>
326 <IsobaricLabelInfo>
327 <internalLabel>TMTpro16plex-Lys133N</internalLabel>
328 <terminalLabel>TMTpro16plex-Nter133N</terminalLabel>
329 <correctionFactorM2>0</correctionFactorM2>
330 <correctionFactorM1>0</correctionFactorM1>
331 <correctionFactorP1>0</correctionFactorP1>
332 <correctionFactorP2>0</correctionFactorP2>
333 <tmtLike>True</tmtLike>
334 </IsobaricLabelInfo>
335 <IsobaricLabelInfo>
336 <internalLabel>TMTpro16plex-Lys133C</internalLabel>
337 <terminalLabel>TMTpro16plex-Nter133C</terminalLabel>
338 <correctionFactorM2>0</correctionFactorM2>
339 <correctionFactorM1>0</correctionFactorM1>
340 <correctionFactorP1>0</correctionFactorP1>
341 <correctionFactorP2>0</correctionFactorP2>
342 <tmtLike>True</tmtLike>
343 </IsobaricLabelInfo>
344 <IsobaricLabelInfo>
345 <internalLabel>TMTpro16plex-Lys134N</internalLabel>
346 <terminalLabel>TMTpro16plex-Nter134N</terminalLabel>
347 <correctionFactorM2>0</correctionFactorM2>
348 <correctionFactorM1>0</correctionFactorM1>
349 <correctionFactorP1>0</correctionFactorP1>
350 <correctionFactorP2>0</correctionFactorP2>
351 <tmtLike>True</tmtLike>
352 </IsobaricLabelInfo>
353 <IsobaricLabelInfo>
354 <internalLabel>TMTpro16plex-Lys126C</internalLabel>
355 <terminalLabel>TMTpro16plex-Nter126C</terminalLabel>
356 <correctionFactorM2>0</correctionFactorM2>
357 <correctionFactorM1>0</correctionFactorM1>
358 <correctionFactorP1>0</correctionFactorP1>
359 <correctionFactorP2>0</correctionFactorP2>
360 <tmtLike>True</tmtLike>
361 </IsobaricLabelInfo>
362 </isobaricLabels>
363 <neucodeLabels>
364 </neucodeLabels>
365 <variableModificationsFirstSearch>
366 </variableModificationsFirstSearch>
367 <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
368 <additionalVariableModifications>
369 </additionalVariableModifications>
370 <additionalVariableModificationProteins>
371 </additionalVariableModificationProteins>
372 <doMassFiltering>True</doMassFiltering>
373 <firstSearchTol>20</firstSearchTol>
374 <mainSearchTol>4.5</mainSearchTol>
375 <searchTolInPpm>True</searchTolInPpm>
376 <isotopeMatchTol>2</isotopeMatchTol>
377 <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
378 <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
379 <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
380 <checkMassDeficit>True</checkMassDeficit>
381 <recalibrationInPpm>True</recalibrationInPpm>
382 <intensityDependentCalibration>False</intensityDependentCalibration>
383 <minScoreForCalibration>70</minScoreForCalibration>
384 <matchLibraryFile>False</matchLibraryFile>
385 <libraryFile/>
386 <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
387 <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
388 <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
389 <reporterMassTolerance>0.003</reporterMassTolerance>
390 <reporterPif>0</reporterPif>
391 <filterPif>False</filterPif>
392 <reporterFraction>0</reporterFraction>
393 <reporterBasePeakRatio>0</reporterBasePeakRatio>
394 <timsHalfWidth>0</timsHalfWidth>
395 <timsStep>0</timsStep>
396 <timsResolution>0</timsResolution>
397 <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
398 <timsRemovePrecursor>True</timsRemovePrecursor>
399 <timsIsobaricLabels>False</timsIsobaricLabels>
400 <timsCollapseMsms>True</timsCollapseMsms>
401 <crossLinkingType>0</crossLinkingType>
402 <crossLinker/>
403 <minMatchXl>0</minMatchXl>
404 <minPairedPepLenXl>6</minPairedPepLenXl>
405 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
406 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
407 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
408 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
409 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
410 <crosslinkModifications>
411 </crosslinkModifications>
412 <crosslinkFastaFiles>
413 </crosslinkFastaFiles>
414 <crosslinkSites>
415 </crosslinkSites>
416 <crosslinkNetworkFiles>
417 </crosslinkNetworkFiles>
418 <crosslinkMode/>
419 <peakRefinement>False</peakRefinement>
420 <isobaricSumOverWindow>True</isobaricSumOverWindow>
421 <isobaricWeightExponent>0.75</isobaricWeightExponent>
422 <diaLibraryType>0</diaLibraryType>
423 <diaLibraryPaths>
424 </diaLibraryPaths>
425 <diaPeptidePaths>
426 </diaPeptidePaths>
427 <diaEvidencePaths>
428 </diaEvidencePaths>
429 <diaMsmsPaths>
430 </diaMsmsPaths>
431 <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
432 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
433 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
434 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
435 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
436 <diaScoreN>7</diaScoreN>
437 <diaMinScore>1.99</diaMinScore>
438 <diaXgBoostBaseScore>0.4</diaXgBoostBaseScore>
439 <diaXgBoostSubSample>0.9</diaXgBoostSubSample>
440 <centroidPosition>0</centroidPosition>
441 <diaQuantMethod>7</diaQuantMethod>
442 <diaFeatureQuantMethod>2</diaFeatureQuantMethod>
443 <lfqNormType>1</lfqNormType>
444 <diaTopNForQuant>10</diaTopNForQuant>
445 <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant>
446 <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant>
447 <diaPrecursorFilterType>0</diaPrecursorFilterType>
448 <diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore>
449 <diaMinPrecursorScore>0.5</diaMinPrecursorScore>
450 <diaMinProfileCorrelation>0</diaMinProfileCorrelation>
451 <diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight>
452 <diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth>
453 <diaXgBoostEstimators>580</diaXgBoostEstimators>
454 <diaXgBoostGamma>0.9</diaXgBoostGamma>
455 <diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep>
456 <diaGlobalMl>True</diaGlobalMl>
457 <diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy>
458 <diaMassWindowFactor>3.3</diaMassWindowFactor>
459 <diaRtPrediction>False</diaRtPrediction>
460 <diaRtPredictionSecondRound>False</diaRtPredictionSecondRound>
461 <diaNoMl>False</diaNoMl>
462 <diaPermuteRt>False</diaPermuteRt>
463 <diaPermuteCcs>False</diaPermuteCcs>
464 <diaBackgroundSubtraction>False</diaBackgroundSubtraction>
465 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile>
466 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>
467 <diaLfqWeightedMedian>False</diaLfqWeightedMedian>
468 </parameterGroup>
469 </parameterGroups>
470 <msmsParamsArray>
471 <msmsParams>
472 <Name>FTMS</Name>
473 <MatchTolerance>20</MatchTolerance>
474 <MatchToleranceInPpm>True</MatchToleranceInPpm>
475 <DeisotopeTolerance>7</DeisotopeTolerance>
476 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
477 <DeNovoTolerance>10</DeNovoTolerance>
478 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
479 <Deisotope>True</Deisotope>
480 <Topx>12</Topx>
481 <TopxInterval>100</TopxInterval>
482 <HigherCharges>True</HigherCharges>
483 <IncludeWater>True</IncludeWater>
484 <IncludeAmmonia>True</IncludeAmmonia>
485 <DependentLosses>True</DependentLosses>
486 <Recalibration>False</Recalibration>
487 </msmsParams>
488 <msmsParams>
489 <Name>ITMS</Name>
490 <MatchTolerance>0.5</MatchTolerance>
491 <MatchToleranceInPpm>False</MatchToleranceInPpm>
492 <DeisotopeTolerance>0.15</DeisotopeTolerance>
493 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
494 <DeNovoTolerance>0.25</DeNovoTolerance>
495 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
496 <Deisotope>False</Deisotope>
497 <Topx>8</Topx>
498 <TopxInterval>100</TopxInterval>
499 <HigherCharges>True</HigherCharges>
500 <IncludeWater>True</IncludeWater>
501 <IncludeAmmonia>True</IncludeAmmonia>
502 <DependentLosses>True</DependentLosses>
503 <Recalibration>False</Recalibration>
504 </msmsParams>
505 <msmsParams>
506 <Name>TOF</Name>
507 <MatchTolerance>40</MatchTolerance>
508 <MatchToleranceInPpm>True</MatchToleranceInPpm>
509 <DeisotopeTolerance>0.01</DeisotopeTolerance>
510 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
511 <DeNovoTolerance>0.02</DeNovoTolerance>
512 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
513 <Deisotope>True</Deisotope>
514 <Topx>10</Topx>
515 <TopxInterval>100</TopxInterval>
516 <HigherCharges>True</HigherCharges>
517 <IncludeWater>True</IncludeWater>
518 <IncludeAmmonia>True</IncludeAmmonia>
519 <DependentLosses>True</DependentLosses>
520 <Recalibration>False</Recalibration>
521 </msmsParams>
522 <msmsParams>
523 <Name>Unknown</Name>
524 <MatchTolerance>20</MatchTolerance>
525 <MatchToleranceInPpm>True</MatchToleranceInPpm>
526 <DeisotopeTolerance>7</DeisotopeTolerance>
527 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
528 <DeNovoTolerance>10</DeNovoTolerance>
529 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
530 <Deisotope>True</Deisotope>
531 <Topx>12</Topx>
532 <TopxInterval>100</TopxInterval>
533 <HigherCharges>True</HigherCharges>
534 <IncludeWater>True</IncludeWater>
535 <IncludeAmmonia>True</IncludeAmmonia>
536 <DependentLosses>True</DependentLosses>
537 <Recalibration>False</Recalibration>
538 </msmsParams>
539 </msmsParamsArray>
540 <fragmentationParamsArray>
541 <fragmentationParams>
542 <Name>CID</Name>
543 <Connected>False</Connected>
544 <ConnectedScore0>1</ConnectedScore0>
545 <ConnectedScore1>1</ConnectedScore1>
546 <ConnectedScore2>1</ConnectedScore2>
547 <InternalFragments>False</InternalFragments>
548 <InternalFragmentWeight>1</InternalFragmentWeight>
549 <InternalFragmentAas>KRH</InternalFragmentAas>
550 </fragmentationParams>
551 <fragmentationParams>
552 <Name>HCD</Name>
553 <Connected>False</Connected>
554 <ConnectedScore0>1</ConnectedScore0>
555 <ConnectedScore1>1</ConnectedScore1>
556 <ConnectedScore2>1</ConnectedScore2>
557 <InternalFragments>False</InternalFragments>
558 <InternalFragmentWeight>1</InternalFragmentWeight>
559 <InternalFragmentAas>KRH</InternalFragmentAas>
560 </fragmentationParams>
561 <fragmentationParams>
562 <Name>ETD</Name>
563 <Connected>False</Connected>
564 <ConnectedScore0>1</ConnectedScore0>
565 <ConnectedScore1>1</ConnectedScore1>
566 <ConnectedScore2>1</ConnectedScore2>
567 <InternalFragments>False</InternalFragments>
568 <InternalFragmentWeight>1</InternalFragmentWeight>
569 <InternalFragmentAas>KRH</InternalFragmentAas>
570 </fragmentationParams>
571 <fragmentationParams>
572 <Name>PQD</Name>
573 <Connected>False</Connected>
574 <ConnectedScore0>1</ConnectedScore0>
575 <ConnectedScore1>1</ConnectedScore1>
576 <ConnectedScore2>1</ConnectedScore2>
577 <InternalFragments>False</InternalFragments>
578 <InternalFragmentWeight>1</InternalFragmentWeight>
579 <InternalFragmentAas>KRH</InternalFragmentAas>
580 </fragmentationParams>
581 <fragmentationParams>
582 <Name>ETHCD</Name>
583 <Connected>False</Connected>
584 <ConnectedScore0>1</ConnectedScore0>
585 <ConnectedScore1>1</ConnectedScore1>
586 <ConnectedScore2>1</ConnectedScore2>
587 <InternalFragments>False</InternalFragments>
588 <InternalFragmentWeight>1</InternalFragmentWeight>
589 <InternalFragmentAas>KRH</InternalFragmentAas>
590 </fragmentationParams>
591 <fragmentationParams>
592 <Name>ETCID</Name>
593 <Connected>False</Connected>
594 <ConnectedScore0>1</ConnectedScore0>
595 <ConnectedScore1>1</ConnectedScore1>
596 <ConnectedScore2>1</ConnectedScore2>
597 <InternalFragments>False</InternalFragments>
598 <InternalFragmentWeight>1</InternalFragmentWeight>
599 <InternalFragmentAas>KRH</InternalFragmentAas>
600 </fragmentationParams>
601 <fragmentationParams>
602 <Name>UVPD</Name>
603 <Connected>False</Connected>
604 <ConnectedScore0>1</ConnectedScore0>
605 <ConnectedScore1>1</ConnectedScore1>
606 <ConnectedScore2>1</ConnectedScore2>
607 <InternalFragments>False</InternalFragments>
608 <InternalFragmentWeight>1</InternalFragmentWeight>
609 <InternalFragmentAas>KRH</InternalFragmentAas>
610 </fragmentationParams>
611 <fragmentationParams>
612 <Name>Unknown</Name>
613 <Connected>False</Connected>
614 <ConnectedScore0>1</ConnectedScore0>
615 <ConnectedScore1>1</ConnectedScore1>
616 <ConnectedScore2>1</ConnectedScore2>
617 <InternalFragments>False</InternalFragments>
618 <InternalFragmentWeight>1</InternalFragmentWeight>
619 <InternalFragmentAas>KRH</InternalFragmentAas>
620 </fragmentationParams>
621 </fragmentationParamsArray>
622 </MaxQuantParams>
623