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comparison test-data/02/mqpar.xml @ 3:009693badefc draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
author galaxyp
date Sat, 11 Apr 2020 15:48:19 +0000
parents
children 1cdde5989a2d
comparison
equal deleted inserted replaced
2:33c911e66d8e 3:009693badefc
1 <?xml version="1.0" ?>
2 <MaxQuantParams>
3 <fastaFiles>
4 <FastaFileInfo>
5 <fastaFilePath>D:\shared\dglaetzer\maxquant_tool\test1\bsa.fasta</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>revert</decoyMode>
29 <boxCarMode>all</boxCarMode>
30 <includeContaminants>True</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>0.01</peptideFdr>
72 <proteinFdr>0.01</proteinFdr>
73 <siteFdr>0.01</siteFdr>
74 <minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>
75 <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>
76 <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>
77 <minPeptides>1</minPeptides>
78 <minRazorPeptides>1</minRazorPeptides>
79 <minUniquePeptides>0</minUniquePeptides>
80 <useCounterparts>False</useCounterparts>
81 <advancedSiteIntensities>True</advancedSiteIntensities>
82 <customProteinQuantification>False</customProteinQuantification>
83 <customProteinQuantificationFile/>
84 <minRatioCount>2</minRatioCount>
85 <restrictProteinQuantification>True</restrictProteinQuantification>
86 <restrictMods>
87 <string>Oxidation (M)</string>
88 <string>Acetyl (Protein N-term)</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>1</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>session1</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>-1.79589544172745E+308</fullMinMz>
126 <fullMaxMz>1.79589544172745E+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>D:\shared\dglaetzer\maxquant_tool\test1\BSA_min_23.mzXML</string>
136 <string>D:\shared\dglaetzer\maxquant_tool\test2\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 MS2</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 </fixedModifications>
209 <enzymes>
210 <string>Trypsin/P</string>
211 </enzymes>
212 <enzymesFirstSearch>
213 </enzymesFirstSearch>
214 <enzymeModeFirstSearch>0</enzymeModeFirstSearch>
215 <useEnzymeFirstSearch>False</useEnzymeFirstSearch>
216 <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
217 <variableModifications>
218 <string>Oxidation (M)</string>
219 </variableModifications>
220 <useMultiModification>False</useMultiModification>
221 <multiModifications>
222 </multiModifications>
223 <isobaricLabels>
224 <IsobaricLabelInfo>
225 <internalLabel>TMT2plex-Lys126</internalLabel>
226 <terminalLabel>TMT2plex-Nter126</terminalLabel>
227 <correctionFactorM2>0</correctionFactorM2>
228 <correctionFactorM1>0</correctionFactorM1>
229 <correctionFactorP1>6.7</correctionFactorP1>
230 <correctionFactorP2>3</correctionFactorP2>
231 <tmtLike>True</tmtLike>
232 </IsobaricLabelInfo>
233 <IsobaricLabelInfo>
234 <internalLabel>TMT2plex-Lys127</internalLabel>
235 <terminalLabel>TMT2plex-Nter127</terminalLabel>
236 <correctionFactorM2>0</correctionFactorM2>
237 <correctionFactorM1>0</correctionFactorM1>
238 <correctionFactorP1>0</correctionFactorP1>
239 <correctionFactorP2>0</correctionFactorP2>
240 <tmtLike>True</tmtLike>
241 </IsobaricLabelInfo>
242 </isobaricLabels>
243 <neucodeLabels>
244 </neucodeLabels>
245 <variableModificationsFirstSearch>
246 </variableModificationsFirstSearch>
247 <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
248 <additionalVariableModifications>
249 </additionalVariableModifications>
250 <additionalVariableModificationProteins>
251 </additionalVariableModificationProteins>
252 <doMassFiltering>True</doMassFiltering>
253 <firstSearchTol>20</firstSearchTol>
254 <mainSearchTol>4.5</mainSearchTol>
255 <searchTolInPpm>True</searchTolInPpm>
256 <isotopeMatchTol>2</isotopeMatchTol>
257 <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
258 <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
259 <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
260 <checkMassDeficit>True</checkMassDeficit>
261 <recalibrationInPpm>True</recalibrationInPpm>
262 <intensityDependentCalibration>False</intensityDependentCalibration>
263 <minScoreForCalibration>70</minScoreForCalibration>
264 <matchLibraryFile>False</matchLibraryFile>
265 <libraryFile/>
266 <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
267 <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
268 <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
269 <reporterMassTolerance>0.003</reporterMassTolerance>
270 <reporterPif>0</reporterPif>
271 <filterPif>False</filterPif>
272 <reporterFraction>0</reporterFraction>
273 <reporterBasePeakRatio>0</reporterBasePeakRatio>
274 <timsHalfWidth>0</timsHalfWidth>
275 <timsStep>0</timsStep>
276 <timsResolution>0</timsResolution>
277 <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
278 <timsRemovePrecursor>True</timsRemovePrecursor>
279 <timsIsobaricLabels>False</timsIsobaricLabels>
280 <timsCollapseMsms>True</timsCollapseMsms>
281 <crosslinkSearch>False</crosslinkSearch>
282 <crossLinker/>
283 <minMatchXl>0</minMatchXl>
284 <minPairedPepLenXl>6</minPairedPepLenXl>
285 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
286 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
287 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
288 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
289 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
290 <crosslinkModifications>
291 </crosslinkModifications>
292 <crosslinkFastaFiles>
293 </crosslinkFastaFiles>
294 <crosslinkSites>
295 </crosslinkSites>
296 <crosslinkNetworkFiles>
297 </crosslinkNetworkFiles>
298 <crosslinkMode/>
299 <peakRefinement>False</peakRefinement>
300 <isobaricSumOverWindow>True</isobaricSumOverWindow>
301 <isobaricWeightExponent>0.75</isobaricWeightExponent>
302 <diaLibraryType>0</diaLibraryType>
303 <diaLibraryPath/>
304 <diaPeptidePaths>
305 </diaPeptidePaths>
306 <diaEvidencePaths>
307 </diaEvidencePaths>
308 <diaMsmsPaths>
309 </diaMsmsPaths>
310 <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
311 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
312 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
313 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
314 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
315 <diaScoreN>7</diaScoreN>
316 <diaMinScore>2.99</diaMinScore>
317 <diaPrecursorQuant>False</diaPrecursorQuant>
318 <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>
319 </parameterGroup>
320 <parameterGroup>
321 <msInstrument>0</msInstrument>
322 <maxCharge>7</maxCharge>
323 <minPeakLen>2</minPeakLen>
324 <diaMinPeakLen>2</diaMinPeakLen>
325 <useMs1Centroids>False</useMs1Centroids>
326 <useMs2Centroids>False</useMs2Centroids>
327 <cutPeaks>True</cutPeaks>
328 <gapScans>1</gapScans>
329 <minTime>NaN</minTime>
330 <maxTime>NaN</maxTime>
331 <matchType>MatchFromAndTo</matchType>
332 <intensityDetermination>0</intensityDetermination>
333 <centroidMatchTol>8</centroidMatchTol>
334 <centroidMatchTolInPpm>True</centroidMatchTolInPpm>
335 <centroidHalfWidth>35</centroidHalfWidth>
336 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
337 <valleyFactor>1.4</valleyFactor>
338 <isotopeValleyFactor>1.2</isotopeValleyFactor>
339 <advancedPeakSplitting>False</advancedPeakSplitting>
340 <intensityThreshold>0</intensityThreshold>
341 <labelMods>
342 <string/>
343 </labelMods>
344 <lcmsRunType>Reporter ion MS2</lcmsRunType>
345 <reQuantify>False</reQuantify>
346 <lfqMode>0</lfqMode>
347 <lfqSkipNorm>False</lfqSkipNorm>
348 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
349 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
350 <lfqMaxFeatures>100000</lfqMaxFeatures>
351 <neucodeMaxPpm>0</neucodeMaxPpm>
352 <neucodeResolution>0</neucodeResolution>
353 <neucodeResolutionInMda>False</neucodeResolutionInMda>
354 <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
355 <fastLfq>True</fastLfq>
356 <lfqRestrictFeatures>False</lfqRestrictFeatures>
357 <lfqMinRatioCount>2</lfqMinRatioCount>
358 <maxLabeledAa>0</maxLabeledAa>
359 <maxNmods>5</maxNmods>
360 <maxMissedCleavages>2</maxMissedCleavages>
361 <multiplicity>1</multiplicity>
362 <enzymeMode>0</enzymeMode>
363 <complementaryReporterType>0</complementaryReporterType>
364 <reporterNormalization>0</reporterNormalization>
365 <neucodeIntensityMode>0</neucodeIntensityMode>
366 <fixedModifications>
367 </fixedModifications>
368 <enzymes>
369 </enzymes>
370 <enzymesFirstSearch>
371 </enzymesFirstSearch>
372 <enzymeModeFirstSearch>0</enzymeModeFirstSearch>
373 <useEnzymeFirstSearch>False</useEnzymeFirstSearch>
374 <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
375 <variableModifications>
376 </variableModifications>
377 <useMultiModification>False</useMultiModification>
378 <multiModifications>
379 </multiModifications>
380 <isobaricLabels>
381 <IsobaricLabelInfo>
382 <internalLabel>iTRAQ4plex-Lys114</internalLabel>
383 <terminalLabel>iTRAQ4plex-Nter114</terminalLabel>
384 <correctionFactorM2>0</correctionFactorM2>
385 <correctionFactorM1>0</correctionFactorM1>
386 <correctionFactorP1>0</correctionFactorP1>
387 <correctionFactorP2>0</correctionFactorP2>
388 <tmtLike>False</tmtLike>
389 </IsobaricLabelInfo>
390 <IsobaricLabelInfo>
391 <internalLabel>iTRAQ4plex-Lys115</internalLabel>
392 <terminalLabel>iTRAQ4plex-Nter115</terminalLabel>
393 <correctionFactorM2>0</correctionFactorM2>
394 <correctionFactorM1>0</correctionFactorM1>
395 <correctionFactorP1>0</correctionFactorP1>
396 <correctionFactorP2>0</correctionFactorP2>
397 <tmtLike>False</tmtLike>
398 </IsobaricLabelInfo>
399 <IsobaricLabelInfo>
400 <internalLabel>iTRAQ4plex-Lys116</internalLabel>
401 <terminalLabel>iTRAQ4plex-Nter116</terminalLabel>
402 <correctionFactorM2>0</correctionFactorM2>
403 <correctionFactorM1>0</correctionFactorM1>
404 <correctionFactorP1>0</correctionFactorP1>
405 <correctionFactorP2>0</correctionFactorP2>
406 <tmtLike>False</tmtLike>
407 </IsobaricLabelInfo>
408 <IsobaricLabelInfo>
409 <internalLabel>iTRAQ4plex-Lys117</internalLabel>
410 <terminalLabel>iTRAQ4plex-Nter117</terminalLabel>
411 <correctionFactorM2>0</correctionFactorM2>
412 <correctionFactorM1>0</correctionFactorM1>
413 <correctionFactorP1>0</correctionFactorP1>
414 <correctionFactorP2>0</correctionFactorP2>
415 <tmtLike>False</tmtLike>
416 </IsobaricLabelInfo>
417 </isobaricLabels>
418 <neucodeLabels>
419 </neucodeLabels>
420 <variableModificationsFirstSearch>
421 </variableModificationsFirstSearch>
422 <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
423 <additionalVariableModifications>
424 </additionalVariableModifications>
425 <additionalVariableModificationProteins>
426 </additionalVariableModificationProteins>
427 <doMassFiltering>True</doMassFiltering>
428 <firstSearchTol>20</firstSearchTol>
429 <mainSearchTol>4.5</mainSearchTol>
430 <searchTolInPpm>True</searchTolInPpm>
431 <isotopeMatchTol>2</isotopeMatchTol>
432 <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
433 <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
434 <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
435 <checkMassDeficit>True</checkMassDeficit>
436 <recalibrationInPpm>True</recalibrationInPpm>
437 <intensityDependentCalibration>False</intensityDependentCalibration>
438 <minScoreForCalibration>70</minScoreForCalibration>
439 <matchLibraryFile>False</matchLibraryFile>
440 <libraryFile/>
441 <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
442 <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
443 <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
444 <reporterMassTolerance>0.003</reporterMassTolerance>
445 <reporterPif>0</reporterPif>
446 <filterPif>False</filterPif>
447 <reporterFraction>0</reporterFraction>
448 <reporterBasePeakRatio>0</reporterBasePeakRatio>
449 <timsHalfWidth>0</timsHalfWidth>
450 <timsStep>0</timsStep>
451 <timsResolution>0</timsResolution>
452 <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
453 <timsRemovePrecursor>True</timsRemovePrecursor>
454 <timsIsobaricLabels>False</timsIsobaricLabels>
455 <timsCollapseMsms>True</timsCollapseMsms>
456 <crosslinkSearch>False</crosslinkSearch>
457 <crossLinker/>
458 <minMatchXl>0</minMatchXl>
459 <minPairedPepLenXl>6</minPairedPepLenXl>
460 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
461 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
462 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
463 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
464 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
465 <crosslinkModifications>
466 </crosslinkModifications>
467 <crosslinkFastaFiles>
468 </crosslinkFastaFiles>
469 <crosslinkSites>
470 </crosslinkSites>
471 <crosslinkNetworkFiles>
472 </crosslinkNetworkFiles>
473 <crosslinkMode/>
474 <peakRefinement>False</peakRefinement>
475 <isobaricSumOverWindow>True</isobaricSumOverWindow>
476 <isobaricWeightExponent>0.75</isobaricWeightExponent>
477 <diaLibraryType>0</diaLibraryType>
478 <diaLibraryPath/>
479 <diaPeptidePaths>
480 </diaPeptidePaths>
481 <diaEvidencePaths>
482 </diaEvidencePaths>
483 <diaMsmsPaths>
484 </diaMsmsPaths>
485 <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
486 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
487 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
488 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
489 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
490 <diaScoreN>7</diaScoreN>
491 <diaMinScore>2.99</diaMinScore>
492 <diaPrecursorQuant>False</diaPrecursorQuant>
493 <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>
494 </parameterGroup>
495 </parameterGroups>
496 <msmsParamsArray>
497 <msmsParams>
498 <Name>FTMS</Name>
499 <MatchTolerance>20</MatchTolerance>
500 <MatchToleranceInPpm>True</MatchToleranceInPpm>
501 <DeisotopeTolerance>7</DeisotopeTolerance>
502 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
503 <DeNovoTolerance>10</DeNovoTolerance>
504 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
505 <Deisotope>True</Deisotope>
506 <Topx>12</Topx>
507 <TopxInterval>100</TopxInterval>
508 <HigherCharges>True</HigherCharges>
509 <IncludeWater>True</IncludeWater>
510 <IncludeAmmonia>True</IncludeAmmonia>
511 <DependentLosses>True</DependentLosses>
512 <Recalibration>False</Recalibration>
513 </msmsParams>
514 <msmsParams>
515 <Name>ITMS</Name>
516 <MatchTolerance>0.5</MatchTolerance>
517 <MatchToleranceInPpm>False</MatchToleranceInPpm>
518 <DeisotopeTolerance>0.15</DeisotopeTolerance>
519 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
520 <DeNovoTolerance>0.25</DeNovoTolerance>
521 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
522 <Deisotope>False</Deisotope>
523 <Topx>8</Topx>
524 <TopxInterval>100</TopxInterval>
525 <HigherCharges>True</HigherCharges>
526 <IncludeWater>True</IncludeWater>
527 <IncludeAmmonia>True</IncludeAmmonia>
528 <DependentLosses>True</DependentLosses>
529 <Recalibration>False</Recalibration>
530 </msmsParams>
531 <msmsParams>
532 <Name>TOF</Name>
533 <MatchTolerance>40</MatchTolerance>
534 <MatchToleranceInPpm>True</MatchToleranceInPpm>
535 <DeisotopeTolerance>0.01</DeisotopeTolerance>
536 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
537 <DeNovoTolerance>0.02</DeNovoTolerance>
538 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
539 <Deisotope>True</Deisotope>
540 <Topx>10</Topx>
541 <TopxInterval>100</TopxInterval>
542 <HigherCharges>True</HigherCharges>
543 <IncludeWater>True</IncludeWater>
544 <IncludeAmmonia>True</IncludeAmmonia>
545 <DependentLosses>True</DependentLosses>
546 <Recalibration>False</Recalibration>
547 </msmsParams>
548 <msmsParams>
549 <Name>Unknown</Name>
550 <MatchTolerance>20</MatchTolerance>
551 <MatchToleranceInPpm>True</MatchToleranceInPpm>
552 <DeisotopeTolerance>7</DeisotopeTolerance>
553 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
554 <DeNovoTolerance>10</DeNovoTolerance>
555 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
556 <Deisotope>True</Deisotope>
557 <Topx>12</Topx>
558 <TopxInterval>100</TopxInterval>
559 <HigherCharges>True</HigherCharges>
560 <IncludeWater>True</IncludeWater>
561 <IncludeAmmonia>True</IncludeAmmonia>
562 <DependentLosses>True</DependentLosses>
563 <Recalibration>False</Recalibration>
564 </msmsParams>
565 </msmsParamsArray>
566 <fragmentationParamsArray>
567 <fragmentationParams>
568 <Name>CID</Name>
569 <Connected>False</Connected>
570 <ConnectedScore0>1</ConnectedScore0>
571 <ConnectedScore1>1</ConnectedScore1>
572 <ConnectedScore2>1</ConnectedScore2>
573 <InternalFragments>False</InternalFragments>
574 <InternalFragmentWeight>1</InternalFragmentWeight>
575 <InternalFragmentAas>KRH</InternalFragmentAas>
576 </fragmentationParams>
577 <fragmentationParams>
578 <Name>HCD</Name>
579 <Connected>False</Connected>
580 <ConnectedScore0>1</ConnectedScore0>
581 <ConnectedScore1>1</ConnectedScore1>
582 <ConnectedScore2>1</ConnectedScore2>
583 <InternalFragments>False</InternalFragments>
584 <InternalFragmentWeight>1</InternalFragmentWeight>
585 <InternalFragmentAas>KRH</InternalFragmentAas>
586 </fragmentationParams>
587 <fragmentationParams>
588 <Name>ETD</Name>
589 <Connected>False</Connected>
590 <ConnectedScore0>1</ConnectedScore0>
591 <ConnectedScore1>1</ConnectedScore1>
592 <ConnectedScore2>1</ConnectedScore2>
593 <InternalFragments>False</InternalFragments>
594 <InternalFragmentWeight>1</InternalFragmentWeight>
595 <InternalFragmentAas>KRH</InternalFragmentAas>
596 </fragmentationParams>
597 <fragmentationParams>
598 <Name>PQD</Name>
599 <Connected>False</Connected>
600 <ConnectedScore0>1</ConnectedScore0>
601 <ConnectedScore1>1</ConnectedScore1>
602 <ConnectedScore2>1</ConnectedScore2>
603 <InternalFragments>False</InternalFragments>
604 <InternalFragmentWeight>1</InternalFragmentWeight>
605 <InternalFragmentAas>KRH</InternalFragmentAas>
606 </fragmentationParams>
607 <fragmentationParams>
608 <Name>ETHCD</Name>
609 <Connected>False</Connected>
610 <ConnectedScore0>1</ConnectedScore0>
611 <ConnectedScore1>1</ConnectedScore1>
612 <ConnectedScore2>1</ConnectedScore2>
613 <InternalFragments>False</InternalFragments>
614 <InternalFragmentWeight>1</InternalFragmentWeight>
615 <InternalFragmentAas>KRH</InternalFragmentAas>
616 </fragmentationParams>
617 <fragmentationParams>
618 <Name>ETCID</Name>
619 <Connected>False</Connected>
620 <ConnectedScore0>1</ConnectedScore0>
621 <ConnectedScore1>1</ConnectedScore1>
622 <ConnectedScore2>1</ConnectedScore2>
623 <InternalFragments>False</InternalFragments>
624 <InternalFragmentWeight>1</InternalFragmentWeight>
625 <InternalFragmentAas>KRH</InternalFragmentAas>
626 </fragmentationParams>
627 <fragmentationParams>
628 <Name>UVPD</Name>
629 <Connected>False</Connected>
630 <ConnectedScore0>1</ConnectedScore0>
631 <ConnectedScore1>1</ConnectedScore1>
632 <ConnectedScore2>1</ConnectedScore2>
633 <InternalFragments>False</InternalFragments>
634 <InternalFragmentWeight>1</InternalFragmentWeight>
635 <InternalFragmentAas>KRH</InternalFragmentAas>
636 </fragmentationParams>
637 <fragmentationParams>
638 <Name>Unknown</Name>
639 <Connected>False</Connected>
640 <ConnectedScore0>1</ConnectedScore0>
641 <ConnectedScore1>1</ConnectedScore1>
642 <ConnectedScore2>1</ConnectedScore2>
643 <InternalFragments>False</InternalFragments>
644 <InternalFragmentWeight>1</InternalFragmentWeight>
645 <InternalFragmentAas>KRH</InternalFragmentAas>
646 </fragmentationParams>
647 </fragmentationParamsArray>
648 </MaxQuantParams>
649