Mercurial > repos > galaxyp > maxquant

comparison test-data/06/mqpar.xml @ 9:fe479bf15bd3 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
author galaxyp
date Fri, 12 Mar 2021 08:39:34 +0000
parents
children 057bf124c80e
comparison
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8:55f8e3f91e0b 9:fe479bf15bd3
1 <?xml version="1.0" ?>
2 <MaxQuantParams>
3 <fastaFiles>
4 <FastaFileInfo>
5 <fastaFilePath>/tmp/tmp0wswhy4o/files/e/e/e/dataset_eee05aed-87d2-4635-87b0-dd7930cc43dc.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 <neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification>
23 <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios>
24 <rtShift>False</rtShift>
25 <separateLfq>False</separateLfq>
26 <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>
27 <lfqRequireMsms>True</lfqRequireMsms>
28 <decoyMode>randomize</decoyMode>
29 <boxCarMode>all</boxCarMode>
30 <includeContaminants>False</includeContaminants>
31 <maxPeptideMass>4600</maxPeptideMass>
32 <epsilonMutationScore>True</epsilonMutationScore>
33 <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>
34 <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>
35 <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>
36 <minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>
37 <minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>
38 <minScoreModifiedPeptides>40</minScoreModifiedPeptides>
39 <secondPeptide>True</secondPeptide>
40 <matchBetweenRuns>False</matchBetweenRuns>
41 <matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>
42 <matchBetweenRunsFdr>False</matchBetweenRunsFdr>
43 <dependentPeptides>False</dependentPeptides>
44 <dependentPeptideFdr>0</dependentPeptideFdr>
45 <dependentPeptideMassBin>0</dependentPeptideMassBin>
46 <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>
47 <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>
48 <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>
49 <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>
50 <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>
51 <msmsConnection>False</msmsConnection>
52 <ibaq>False</ibaq>
53 <top3>False</top3>
54 <independentEnzymes>False</independentEnzymes>
55 <useDeltaScore>False</useDeltaScore>
56 <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>
57 <taxonomyLevel>Species</taxonomyLevel>
58 <avalon>False</avalon>
59 <nModColumns>3</nModColumns>
60 <ibaqLogFit>False</ibaqLogFit>
61 <razorProteinFdr>True</razorProteinFdr>
62 <deNovoSequencing>False</deNovoSequencing>
63 <deNovoVarMods>True</deNovoVarMods>
64 <massDifferenceSearch>False</massDifferenceSearch>
65 <isotopeCalc>False</isotopeCalc>
66 <writePeptidesForSpectrumFile/>
67 <intensityPredictionsFile>
68 </intensityPredictionsFile>
69 <minPepLen>7</minPepLen>
70 <psmFdrCrosslink>0.01</psmFdrCrosslink>
71 <peptideFdr>0.5</peptideFdr>
72 <proteinFdr>0.4</proteinFdr>
73 <siteFdr>0.01</siteFdr>
74 <minPeptideLengthForUnspecificSearch>7</minPeptideLengthForUnspecificSearch>
75 <maxPeptideLengthForUnspecificSearch>24</maxPeptideLengthForUnspecificSearch>
76 <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>
77 <minPeptides>1</minPeptides>
78 <minRazorPeptides>1</minRazorPeptides>
79 <minUniquePeptides>0</minUniquePeptides>
80 <useCounterparts>True</useCounterparts>
81 <advancedSiteIntensities>True</advancedSiteIntensities>
82 <customProteinQuantification>False</customProteinQuantification>
83 <customProteinQuantificationFile/>
84 <minRatioCount>2</minRatioCount>
85 <restrictProteinQuantification>True</restrictProteinQuantification>
86 <restrictMods>
87 <string>Pro5</string>
88 <string>Pro6</string>
89 </restrictMods>
90 <matchingTimeWindow>0</matchingTimeWindow>
91 <matchingIonMobilityWindow>0</matchingIonMobilityWindow>
92 <alignmentTimeWindow>0</alignmentTimeWindow>
93 <alignmentIonMobilityWindow>0</alignmentIonMobilityWindow>
94 <numberOfCandidatesMsms>15</numberOfCandidatesMsms>
95 <compositionPrediction>0</compositionPrediction>
96 <quantMode>0</quantMode>
97 <massDifferenceMods>
98 </massDifferenceMods>
99 <mainSearchMaxCombinations>200</mainSearchMaxCombinations>
100 <writeMsScansTable>False</writeMsScansTable>
101 <writeMsmsScansTable>True</writeMsmsScansTable>
102 <writePasefMsmsScansTable>True</writePasefMsmsScansTable>
103 <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable>
104 <writeMs3ScansTable>True</writeMs3ScansTable>
105 <writeAllPeptidesTable>True</writeAllPeptidesTable>
106 <writeMzRangeTable>True</writeMzRangeTable>
107 <writeMzTab>True</writeMzTab>
108 <disableMd5>False</disableMd5>
109 <cacheBinInds>True</cacheBinInds>
110 <etdIncludeB>False</etdIncludeB>
111 <ms2PrecursorShift>0</ms2PrecursorShift>
112 <complementaryIonPpm>20</complementaryIonPpm>
113 <variationParseRule/>
114 <variationMode>none</variationMode>
115 <useSeriesReporters>False</useSeriesReporters>
116 <name>templateSession</name>
117 <maxQuantVersion>1.6.10.43</maxQuantVersion>
118 <tempFolder/>
119 <pluginFolder/>
120 <numThreads>1</numThreads>
121 <emailAddress/>
122 <smtpHost/>
123 <emailFromAddress/>
124 <fixedCombinedFolder/>
125 <fullMinMz>-1.79769313486232E+308</fullMinMz>
126 <fullMaxMz>1.79769313486232E+308</fullMaxMz>
127 <sendEmail>False</sendEmail>
128 <ionCountIntensities>False</ionCountIntensities>
129 <verboseColumnHeaders>False</verboseColumnHeaders>
130 <calcPeakProperties>False</calcPeakProperties>
131 <showCentroidMassDifferences>False</showCentroidMassDifferences>
132 <showIsotopeMassDifferences>False</showIsotopeMassDifferences>
133 <useDotNetCore>False</useDotNetCore>
134 <filePaths>
135 <string>/tmp/tmp0wswhy4o/job_working_directory/000/4/working/BSA_min_23.mzXML</string>
136 <string>/tmp/tmp0wswhy4o/job_working_directory/000/4/working/BSA_min_22.mzxml</string>
137 </filePaths>
138 <experiments>
139 <string>BSA_min_23.mzXML</string>
140 <string>BSA_min_22.mzxml</string>
141 </experiments>
142 <fractions>
143 <short>32767</short>
144 <short>32767</short>
145 </fractions>
146 <ptms>
147 <boolean>False</boolean>
148 <boolean>False</boolean>
149 </ptms>
150 <paramGroupIndices>
151 <int>0</int>
152 <int>1</int>
153 </paramGroupIndices>
154 <referenceChannel>
155 <string/>
156 <string/>
157 </referenceChannel>
158 <intensPred>False</intensPred>
159 <intensPredModelReTrain>False</intensPredModelReTrain>
160 <parameterGroups>
161 <parameterGroup>
162 <msInstrument>0</msInstrument>
163 <maxCharge>7</maxCharge>
164 <minPeakLen>2</minPeakLen>
165 <diaMinPeakLen>2</diaMinPeakLen>
166 <useMs1Centroids>False</useMs1Centroids>
167 <useMs2Centroids>False</useMs2Centroids>
168 <cutPeaks>True</cutPeaks>
169 <gapScans>1</gapScans>
170 <minTime>NaN</minTime>
171 <maxTime>NaN</maxTime>
172 <matchType>MatchFromAndTo</matchType>
173 <intensityDetermination>0</intensityDetermination>
174 <centroidMatchTol>8</centroidMatchTol>
175 <centroidMatchTolInPpm>True</centroidMatchTolInPpm>
176 <centroidHalfWidth>35</centroidHalfWidth>
177 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
178 <valleyFactor>1.4</valleyFactor>
179 <isotopeValleyFactor>1.2</isotopeValleyFactor>
180 <advancedPeakSplitting>False</advancedPeakSplitting>
181 <intensityThreshold>0</intensityThreshold>
182 <labelMods>
183 <string/>
184 </labelMods>
185 <lcmsRunType>Reporter ion MS3</lcmsRunType>
186 <reQuantify>False</reQuantify>
187 <lfqMode>0</lfqMode>
188 <lfqSkipNorm>False</lfqSkipNorm>
189 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
190 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
191 <lfqMaxFeatures>100000</lfqMaxFeatures>
192 <neucodeMaxPpm>0</neucodeMaxPpm>
193 <neucodeResolution>0</neucodeResolution>
194 <neucodeResolutionInMda>False</neucodeResolutionInMda>
195 <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
196 <fastLfq>True</fastLfq>
197 <lfqRestrictFeatures>False</lfqRestrictFeatures>
198 <lfqMinRatioCount>2</lfqMinRatioCount>
199 <maxLabeledAa>0</maxLabeledAa>
200 <maxNmods>5</maxNmods>
201 <maxMissedCleavages>2</maxMissedCleavages>
202 <multiplicity>1</multiplicity>
203 <enzymeMode>0</enzymeMode>
204 <complementaryReporterType>0</complementaryReporterType>
205 <reporterNormalization>0</reporterNormalization>
206 <neucodeIntensityMode>0</neucodeIntensityMode>
207 <fixedModifications/>
208 <enzymes>
209 <string>Trypsin/P</string>
210 </enzymes>
211 <enzymesFirstSearch>
212 </enzymesFirstSearch>
213 <enzymeModeFirstSearch>0</enzymeModeFirstSearch>
214 <useEnzymeFirstSearch>False</useEnzymeFirstSearch>
215 <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
216 <variableModifications>
217 <string>Oxidation (M)</string>
218 </variableModifications>
219 <useMultiModification>False</useMultiModification>
220 <multiModifications>
221 </multiModifications>
222 <isobaricLabels>
223 <IsobaricLabelInfo>
224 <internalLabel>TMT2plex-Lys126</internalLabel>
225 <terminalLabel>TMT2plex-Nter126</terminalLabel>
226 <correctionFactorM2>0</correctionFactorM2>
227 <correctionFactorM1>0</correctionFactorM1>
228 <correctionFactorP1>6.7</correctionFactorP1>
229 <correctionFactorP2>3</correctionFactorP2>
230 <tmtLike>True</tmtLike>
231 </IsobaricLabelInfo>
232 <IsobaricLabelInfo>
233 <internalLabel>TMT2plex-Lys127</internalLabel>
234 <terminalLabel>TMT2plex-Nter127</terminalLabel>
235 <correctionFactorM2>0</correctionFactorM2>
236 <correctionFactorM1>0</correctionFactorM1>
237 <correctionFactorP1>0</correctionFactorP1>
238 <correctionFactorP2>0</correctionFactorP2>
239 <tmtLike>True</tmtLike>
240 </IsobaricLabelInfo>
241 </isobaricLabels>
242 <neucodeLabels>
243 </neucodeLabels>
244 <variableModificationsFirstSearch>
245 </variableModificationsFirstSearch>
246 <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
247 <additionalVariableModifications>
248 </additionalVariableModifications>
249 <additionalVariableModificationProteins>
250 </additionalVariableModificationProteins>
251 <doMassFiltering>True</doMassFiltering>
252 <firstSearchTol>20</firstSearchTol>
253 <mainSearchTol>4.5</mainSearchTol>
254 <searchTolInPpm>True</searchTolInPpm>
255 <isotopeMatchTol>2</isotopeMatchTol>
256 <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
257 <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
258 <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
259 <checkMassDeficit>True</checkMassDeficit>
260 <recalibrationInPpm>True</recalibrationInPpm>
261 <intensityDependentCalibration>False</intensityDependentCalibration>
262 <minScoreForCalibration>70</minScoreForCalibration>
263 <matchLibraryFile>False</matchLibraryFile>
264 <libraryFile/>
265 <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
266 <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
267 <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
268 <reporterMassTolerance>0.003</reporterMassTolerance>
269 <reporterPif>0</reporterPif>
270 <filterPif>False</filterPif>
271 <reporterFraction>0</reporterFraction>
272 <reporterBasePeakRatio>0</reporterBasePeakRatio>
273 <timsHalfWidth>0</timsHalfWidth>
274 <timsStep>0</timsStep>
275 <timsResolution>0</timsResolution>
276 <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
277 <timsRemovePrecursor>True</timsRemovePrecursor>
278 <timsIsobaricLabels>False</timsIsobaricLabels>
279 <timsCollapseMsms>True</timsCollapseMsms>
280 <crosslinkSearch>False</crosslinkSearch>
281 <crossLinker/>
282 <minMatchXl>0</minMatchXl>
283 <minPairedPepLenXl>6</minPairedPepLenXl>
284 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
285 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
286 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
287 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
288 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
289 <crosslinkModifications>
290 </crosslinkModifications>
291 <crosslinkFastaFiles>
292 </crosslinkFastaFiles>
293 <crosslinkSites>
294 </crosslinkSites>
295 <crosslinkNetworkFiles>
296 </crosslinkNetworkFiles>
297 <crosslinkMode/>
298 <peakRefinement>False</peakRefinement>
299 <isobaricSumOverWindow>True</isobaricSumOverWindow>
300 <isobaricWeightExponent>0.75</isobaricWeightExponent>
301 <diaLibraryType>0</diaLibraryType>
302 <diaLibraryPath/>
303 <diaPeptidePaths>
304 </diaPeptidePaths>
305 <diaEvidencePaths>
306 </diaEvidencePaths>
307 <diaMsmsPaths>
308 </diaMsmsPaths>
309 <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
310 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
311 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
312 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
313 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
314 <diaScoreN>7</diaScoreN>
315 <diaMinScore>2.99</diaMinScore>
316 <diaPrecursorQuant>False</diaPrecursorQuant>
317 <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>
318 </parameterGroup>
319 <parameterGroup>
320 <msInstrument>0</msInstrument>
321 <maxCharge>7</maxCharge>
322 <minPeakLen>2</minPeakLen>
323 <diaMinPeakLen>2</diaMinPeakLen>
324 <useMs1Centroids>False</useMs1Centroids>
325 <useMs2Centroids>False</useMs2Centroids>
326 <cutPeaks>True</cutPeaks>
327 <gapScans>1</gapScans>
328 <minTime>NaN</minTime>
329 <maxTime>NaN</maxTime>
330 <matchType>MatchFromAndTo</matchType>
331 <intensityDetermination>0</intensityDetermination>
332 <centroidMatchTol>8</centroidMatchTol>
333 <centroidMatchTolInPpm>True</centroidMatchTolInPpm>
334 <centroidHalfWidth>35</centroidHalfWidth>
335 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
336 <valleyFactor>1.4</valleyFactor>
337 <isotopeValleyFactor>1.2</isotopeValleyFactor>
338 <advancedPeakSplitting>False</advancedPeakSplitting>
339 <intensityThreshold>0</intensityThreshold>
340 <labelMods>
341 <string/>
342 </labelMods>
343 <lcmsRunType>Reporter ion MS3</lcmsRunType>
344 <reQuantify>False</reQuantify>
345 <lfqMode>0</lfqMode>
346 <lfqSkipNorm>False</lfqSkipNorm>
347 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
348 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
349 <lfqMaxFeatures>100000</lfqMaxFeatures>
350 <neucodeMaxPpm>0</neucodeMaxPpm>
351 <neucodeResolution>0</neucodeResolution>
352 <neucodeResolutionInMda>False</neucodeResolutionInMda>
353 <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
354 <fastLfq>True</fastLfq>
355 <lfqRestrictFeatures>False</lfqRestrictFeatures>
356 <lfqMinRatioCount>2</lfqMinRatioCount>
357 <maxLabeledAa>0</maxLabeledAa>
358 <maxNmods>5</maxNmods>
359 <maxMissedCleavages>2</maxMissedCleavages>
360 <multiplicity>1</multiplicity>
361 <enzymeMode>0</enzymeMode>
362 <complementaryReporterType>0</complementaryReporterType>
363 <reporterNormalization>0</reporterNormalization>
364 <neucodeIntensityMode>0</neucodeIntensityMode>
365 <fixedModifications/>
366 <enzymes/>
367 <enzymesFirstSearch>
368 </enzymesFirstSearch>
369 <enzymeModeFirstSearch>0</enzymeModeFirstSearch>
370 <useEnzymeFirstSearch>False</useEnzymeFirstSearch>
371 <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
372 <variableModifications/>
373 <useMultiModification>False</useMultiModification>
374 <multiModifications>
375 </multiModifications>
376 <isobaricLabels>
377 <IsobaricLabelInfo>
378 <internalLabel>iTRAQ4plex-Lys114</internalLabel>
379 <terminalLabel>iTRAQ4plex-Nter114</terminalLabel>
380 <correctionFactorM2>0</correctionFactorM2>
381 <correctionFactorM1>0</correctionFactorM1>
382 <correctionFactorP1>0</correctionFactorP1>
383 <correctionFactorP2>0</correctionFactorP2>
384 <tmtLike>False</tmtLike>
385 </IsobaricLabelInfo>
386 <IsobaricLabelInfo>
387 <internalLabel>iTRAQ4plex-Lys115</internalLabel>
388 <terminalLabel>iTRAQ4plex-Nter115</terminalLabel>
389 <correctionFactorM2>0</correctionFactorM2>
390 <correctionFactorM1>0</correctionFactorM1>
391 <correctionFactorP1>0</correctionFactorP1>
392 <correctionFactorP2>0</correctionFactorP2>
393 <tmtLike>False</tmtLike>
394 </IsobaricLabelInfo>
395 <IsobaricLabelInfo>
396 <internalLabel>iTRAQ4plex-Lys116</internalLabel>
397 <terminalLabel>iTRAQ4plex-Nter116</terminalLabel>
398 <correctionFactorM2>0</correctionFactorM2>
399 <correctionFactorM1>0</correctionFactorM1>
400 <correctionFactorP1>0</correctionFactorP1>
401 <correctionFactorP2>0</correctionFactorP2>
402 <tmtLike>False</tmtLike>
403 </IsobaricLabelInfo>
404 <IsobaricLabelInfo>
405 <internalLabel>iTRAQ4plex-Lys117</internalLabel>
406 <terminalLabel>iTRAQ4plex-Nter117</terminalLabel>
407 <correctionFactorM2>0</correctionFactorM2>
408 <correctionFactorM1>0</correctionFactorM1>
409 <correctionFactorP1>0</correctionFactorP1>
410 <correctionFactorP2>0</correctionFactorP2>
411 <tmtLike>False</tmtLike>
412 </IsobaricLabelInfo>
413 </isobaricLabels>
414 <neucodeLabels>
415 </neucodeLabels>
416 <variableModificationsFirstSearch>
417 </variableModificationsFirstSearch>
418 <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
419 <additionalVariableModifications>
420 </additionalVariableModifications>
421 <additionalVariableModificationProteins>
422 </additionalVariableModificationProteins>
423 <doMassFiltering>True</doMassFiltering>
424 <firstSearchTol>20</firstSearchTol>
425 <mainSearchTol>4.5</mainSearchTol>
426 <searchTolInPpm>True</searchTolInPpm>
427 <isotopeMatchTol>2</isotopeMatchTol>
428 <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
429 <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
430 <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
431 <checkMassDeficit>True</checkMassDeficit>
432 <recalibrationInPpm>True</recalibrationInPpm>
433 <intensityDependentCalibration>False</intensityDependentCalibration>
434 <minScoreForCalibration>70</minScoreForCalibration>
435 <matchLibraryFile>False</matchLibraryFile>
436 <libraryFile/>
437 <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
438 <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
439 <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
440 <reporterMassTolerance>0.003</reporterMassTolerance>
441 <reporterPif>0.8</reporterPif>
442 <filterPif>True</filterPif>
443 <reporterFraction>0</reporterFraction>
444 <reporterBasePeakRatio>0</reporterBasePeakRatio>
445 <timsHalfWidth>0</timsHalfWidth>
446 <timsStep>0</timsStep>
447 <timsResolution>0</timsResolution>
448 <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
449 <timsRemovePrecursor>True</timsRemovePrecursor>
450 <timsIsobaricLabels>False</timsIsobaricLabels>
451 <timsCollapseMsms>True</timsCollapseMsms>
452 <crosslinkSearch>False</crosslinkSearch>
453 <crossLinker/>
454 <minMatchXl>0</minMatchXl>
455 <minPairedPepLenXl>6</minPairedPepLenXl>
456 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
457 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
458 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
459 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
460 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
461 <crosslinkModifications>
462 </crosslinkModifications>
463 <crosslinkFastaFiles>
464 </crosslinkFastaFiles>
465 <crosslinkSites>
466 </crosslinkSites>
467 <crosslinkNetworkFiles>
468 </crosslinkNetworkFiles>
469 <crosslinkMode/>
470 <peakRefinement>False</peakRefinement>
471 <isobaricSumOverWindow>True</isobaricSumOverWindow>
472 <isobaricWeightExponent>0.75</isobaricWeightExponent>
473 <diaLibraryType>0</diaLibraryType>
474 <diaLibraryPath/>
475 <diaPeptidePaths>
476 </diaPeptidePaths>
477 <diaEvidencePaths>
478 </diaEvidencePaths>
479 <diaMsmsPaths>
480 </diaMsmsPaths>
481 <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
482 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
483 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
484 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
485 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
486 <diaScoreN>7</diaScoreN>
487 <diaMinScore>2.99</diaMinScore>
488 <diaPrecursorQuant>False</diaPrecursorQuant>
489 <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>
490 </parameterGroup>
491 </parameterGroups>
492 <msmsParamsArray>
493 <msmsParams>
494 <Name>FTMS</Name>
495 <MatchTolerance>20</MatchTolerance>
496 <MatchToleranceInPpm>True</MatchToleranceInPpm>
497 <DeisotopeTolerance>7</DeisotopeTolerance>
498 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
499 <DeNovoTolerance>10</DeNovoTolerance>
500 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
501 <Deisotope>True</Deisotope>
502 <Topx>12</Topx>
503 <TopxInterval>100</TopxInterval>
504 <HigherCharges>True</HigherCharges>
505 <IncludeWater>True</IncludeWater>
506 <IncludeAmmonia>True</IncludeAmmonia>
507 <DependentLosses>True</DependentLosses>
508 <Recalibration>False</Recalibration>
509 </msmsParams>
510 <msmsParams>
511 <Name>ITMS</Name>
512 <MatchTolerance>0.5</MatchTolerance>
513 <MatchToleranceInPpm>False</MatchToleranceInPpm>
514 <DeisotopeTolerance>0.15</DeisotopeTolerance>
515 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
516 <DeNovoTolerance>0.25</DeNovoTolerance>
517 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
518 <Deisotope>False</Deisotope>
519 <Topx>8</Topx>
520 <TopxInterval>100</TopxInterval>
521 <HigherCharges>True</HigherCharges>
522 <IncludeWater>True</IncludeWater>
523 <IncludeAmmonia>True</IncludeAmmonia>
524 <DependentLosses>True</DependentLosses>
525 <Recalibration>False</Recalibration>
526 </msmsParams>
527 <msmsParams>
528 <Name>TOF</Name>
529 <MatchTolerance>40</MatchTolerance>
530 <MatchToleranceInPpm>True</MatchToleranceInPpm>
531 <DeisotopeTolerance>0.01</DeisotopeTolerance>
532 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
533 <DeNovoTolerance>0.02</DeNovoTolerance>
534 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
535 <Deisotope>True</Deisotope>
536 <Topx>10</Topx>
537 <TopxInterval>100</TopxInterval>
538 <HigherCharges>True</HigherCharges>
539 <IncludeWater>True</IncludeWater>
540 <IncludeAmmonia>True</IncludeAmmonia>
541 <DependentLosses>True</DependentLosses>
542 <Recalibration>False</Recalibration>
543 </msmsParams>
544 <msmsParams>
545 <Name>Unknown</Name>
546 <MatchTolerance>20</MatchTolerance>
547 <MatchToleranceInPpm>True</MatchToleranceInPpm>
548 <DeisotopeTolerance>7</DeisotopeTolerance>
549 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
550 <DeNovoTolerance>10</DeNovoTolerance>
551 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
552 <Deisotope>True</Deisotope>
553 <Topx>12</Topx>
554 <TopxInterval>100</TopxInterval>
555 <HigherCharges>True</HigherCharges>
556 <IncludeWater>True</IncludeWater>
557 <IncludeAmmonia>True</IncludeAmmonia>
558 <DependentLosses>True</DependentLosses>
559 <Recalibration>False</Recalibration>
560 </msmsParams>
561 </msmsParamsArray>
562 <fragmentationParamsArray>
563 <fragmentationParams>
564 <Name>CID</Name>
565 <Connected>False</Connected>
566 <ConnectedScore0>1</ConnectedScore0>
567 <ConnectedScore1>1</ConnectedScore1>
568 <ConnectedScore2>1</ConnectedScore2>
569 <InternalFragments>False</InternalFragments>
570 <InternalFragmentWeight>1</InternalFragmentWeight>
571 <InternalFragmentAas>KRH</InternalFragmentAas>
572 </fragmentationParams>
573 <fragmentationParams>
574 <Name>HCD</Name>
575 <Connected>False</Connected>
576 <ConnectedScore0>1</ConnectedScore0>
577 <ConnectedScore1>1</ConnectedScore1>
578 <ConnectedScore2>1</ConnectedScore2>
579 <InternalFragments>False</InternalFragments>
580 <InternalFragmentWeight>1</InternalFragmentWeight>
581 <InternalFragmentAas>KRH</InternalFragmentAas>
582 </fragmentationParams>
583 <fragmentationParams>
584 <Name>ETD</Name>
585 <Connected>False</Connected>
586 <ConnectedScore0>1</ConnectedScore0>
587 <ConnectedScore1>1</ConnectedScore1>
588 <ConnectedScore2>1</ConnectedScore2>
589 <InternalFragments>False</InternalFragments>
590 <InternalFragmentWeight>1</InternalFragmentWeight>
591 <InternalFragmentAas>KRH</InternalFragmentAas>
592 </fragmentationParams>
593 <fragmentationParams>
594 <Name>PQD</Name>
595 <Connected>False</Connected>
596 <ConnectedScore0>1</ConnectedScore0>
597 <ConnectedScore1>1</ConnectedScore1>
598 <ConnectedScore2>1</ConnectedScore2>
599 <InternalFragments>False</InternalFragments>
600 <InternalFragmentWeight>1</InternalFragmentWeight>
601 <InternalFragmentAas>KRH</InternalFragmentAas>
602 </fragmentationParams>
603 <fragmentationParams>
604 <Name>ETHCD</Name>
605 <Connected>False</Connected>
606 <ConnectedScore0>1</ConnectedScore0>
607 <ConnectedScore1>1</ConnectedScore1>
608 <ConnectedScore2>1</ConnectedScore2>
609 <InternalFragments>False</InternalFragments>
610 <InternalFragmentWeight>1</InternalFragmentWeight>
611 <InternalFragmentAas>KRH</InternalFragmentAas>
612 </fragmentationParams>
613 <fragmentationParams>
614 <Name>ETCID</Name>
615 <Connected>False</Connected>
616 <ConnectedScore0>1</ConnectedScore0>
617 <ConnectedScore1>1</ConnectedScore1>
618 <ConnectedScore2>1</ConnectedScore2>
619 <InternalFragments>False</InternalFragments>
620 <InternalFragmentWeight>1</InternalFragmentWeight>
621 <InternalFragmentAas>KRH</InternalFragmentAas>
622 </fragmentationParams>
623 <fragmentationParams>
624 <Name>UVPD</Name>
625 <Connected>False</Connected>
626 <ConnectedScore0>1</ConnectedScore0>
627 <ConnectedScore1>1</ConnectedScore1>
628 <ConnectedScore2>1</ConnectedScore2>
629 <InternalFragments>False</InternalFragments>
630 <InternalFragmentWeight>1</InternalFragmentWeight>
631 <InternalFragmentAas>KRH</InternalFragmentAas>
632 </fragmentationParams>
633 <fragmentationParams>
634 <Name>Unknown</Name>
635 <Connected>False</Connected>
636 <ConnectedScore0>1</ConnectedScore0>
637 <ConnectedScore1>1</ConnectedScore1>
638 <ConnectedScore2>1</ConnectedScore2>
639 <InternalFragments>False</InternalFragments>
640 <InternalFragmentWeight>1</InternalFragmentWeight>
641 <InternalFragmentAas>KRH</InternalFragmentAas>
642 </fragmentationParams>
643 </fragmentationParamsArray>
644 </MaxQuantParams>
645