Mercurial > repos > galaxyp > maxquant

comparison test-data/02/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 f2f79f0be7d1
children 5d013f405259
comparison
equal deleted inserted replaced
10:68d8dcdbddb1 11:057bf124c80e
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <MaxQuantParams> 2 <MaxQuantParams>
3 <fastaFiles> 3 <fastaFiles>
4 <FastaFileInfo> 4 <FastaFileInfo>
5 <fastaFilePath>D:\shared\dglaetzer\maxquant_tool\test1\bsa.fasta</fastaFilePath> 5 <fastaFilePath>/tmp/tmpyzym30dx/files/d/3/1/dataset_d314bbcd-5f08-4e93-b285-2ad6e4739fc9.dat</fastaFilePath>
6 <identifierParseRule>&gt;([^\s]*)</identifierParseRule> 6 <identifierParseRule>&gt;([^\s]*)</identifierParseRule>
7 <descriptionParseRule>&gt;(.*)</descriptionParseRule> 7 <descriptionParseRule>&gt;(.*)</descriptionParseRule>
8 <taxonomyParseRule/> 8 <taxonomyParseRule/>
9 <variationParseRule/> 9 <variationParseRule/>
10 <modificationParseRule/> 10 <modificationParseRule/>
17 </fastaFilesFirstSearch> 17 </fastaFilesFirstSearch>
18 <fixedSearchFolder/> 18 <fixedSearchFolder/>
19 <andromedaCacheSize>350000</andromedaCacheSize> 19 <andromedaCacheSize>350000</andromedaCacheSize>
20 <advancedRatios>True</advancedRatios> 20 <advancedRatios>True</advancedRatios>
21 <pvalThres>0.005</pvalThres> 21 <pvalThres>0.005</pvalThres>
22 <neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification>
23 <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios>
24 <rtShift>False</rtShift> 22 <rtShift>False</rtShift>
25 <separateLfq>False</separateLfq> 23 <separateLfq>False</separateLfq>
26 <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> 24 <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>
27 <lfqRequireMsms>True</lfqRequireMsms> 25 <lfqRequireMsms>True</lfqRequireMsms>
28 <decoyMode>randomize</decoyMode> 26 <decoyMode>randomize</decoyMode>
46 <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns> 44 <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>
47 <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment> 45 <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>
48 <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup> 46 <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>
49 <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions> 47 <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>
50 <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference> 48 <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>
51 <msmsConnection>False</msmsConnection>
52 <ibaq>False</ibaq> 49 <ibaq>False</ibaq>
53 <top3>False</top3> 50 <top3>False</top3>
54 <independentEnzymes>False</independentEnzymes> 51 <independentEnzymes>False</independentEnzymes>
55 <useDeltaScore>False</useDeltaScore> 52 <useDeltaScore>False</useDeltaScore>
56 <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy> 53 <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>
98 </massDifferenceMods> 95 </massDifferenceMods>
99 <mainSearchMaxCombinations>200</mainSearchMaxCombinations> 96 <mainSearchMaxCombinations>200</mainSearchMaxCombinations>
100 <writeMsScansTable>False</writeMsScansTable> 97 <writeMsScansTable>False</writeMsScansTable>
101 <writeMsmsScansTable>True</writeMsmsScansTable> 98 <writeMsmsScansTable>True</writeMsmsScansTable>
102 <writePasefMsmsScansTable>True</writePasefMsmsScansTable> 99 <writePasefMsmsScansTable>True</writePasefMsmsScansTable>
103 <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable> 100 <writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable>
104 <writeMs3ScansTable>True</writeMs3ScansTable> 101 <writeMs3ScansTable>True</writeMs3ScansTable>
105 <writeAllPeptidesTable>True</writeAllPeptidesTable> 102 <writeAllPeptidesTable>True</writeAllPeptidesTable>
106 <writeMzRangeTable>True</writeMzRangeTable> 103 <writeMzRangeTable>True</writeMzRangeTable>
104 <writeDiaFragmentTable>False</writeDiaFragmentTable>
107 <writeMzTab>True</writeMzTab> 105 <writeMzTab>True</writeMzTab>
108 <disableMd5>False</disableMd5> 106 <disableMd5>False</disableMd5>
109 <cacheBinInds>True</cacheBinInds> 107 <cacheBinInds>True</cacheBinInds>
110 <etdIncludeB>False</etdIncludeB> 108 <etdIncludeB>False</etdIncludeB>
111 <ms2PrecursorShift>0</ms2PrecursorShift> 109 <ms2PrecursorShift>0</ms2PrecursorShift>
112 <complementaryIonPpm>20</complementaryIonPpm> 110 <complementaryIonPpm>20</complementaryIonPpm>
113 <variationParseRule/> 111 <variationParseRule/>
114 <variationMode>none</variationMode> 112 <variationMode>none</variationMode>
115 <useSeriesReporters>False</useSeriesReporters> 113 <useSeriesReporters>False</useSeriesReporters>
116 <name>session1</name> 114 <name>templateSession</name>
117 <maxQuantVersion>1.6.10.43</maxQuantVersion> 115 <maxQuantVersion>1.6.17.0</maxQuantVersion>
118 <tempFolder/>
119 <pluginFolder/> 116 <pluginFolder/>
120 <numThreads>1</numThreads> 117 <numThreads>1</numThreads>
118 <batchSize>1</batchSize>
121 <emailAddress/> 119 <emailAddress/>
122 <smtpHost/> 120 <smtpHost/>
123 <emailFromAddress/> 121 <emailFromAddress/>
124 <fixedCombinedFolder/> 122 <fixedCombinedFolder/>
125 <fullMinMz>-1.79589544172745E+308</fullMinMz> 123 <fullMinMz>-1.79769313486232E+308</fullMinMz>
126 <fullMaxMz>1.79589544172745E+308</fullMaxMz> 124 <fullMaxMz>1.79769313486232E+308</fullMaxMz>
127 <sendEmail>False</sendEmail> 125 <sendEmail>False</sendEmail>
128 <ionCountIntensities>False</ionCountIntensities> 126 <ionCountIntensities>False</ionCountIntensities>
129 <verboseColumnHeaders>False</verboseColumnHeaders> 127 <verboseColumnHeaders>False</verboseColumnHeaders>
130 <calcPeakProperties>False</calcPeakProperties> 128 <calcPeakProperties>False</calcPeakProperties>
131 <showCentroidMassDifferences>False</showCentroidMassDifferences> 129 <showCentroidMassDifferences>False</showCentroidMassDifferences>
132 <showIsotopeMassDifferences>False</showIsotopeMassDifferences> 130 <showIsotopeMassDifferences>False</showIsotopeMassDifferences>
133 <useDotNetCore>False</useDotNetCore> 131 <useDotNetCore>True</useDotNetCore>
132 <profilePerformance>False</profilePerformance>
134 <filePaths> 133 <filePaths>
135 <string>D:\shared\dglaetzer\maxquant_tool\test1\BSA_min_23.mzXML</string> 134 <string>/tmp/tmpyzym30dx/job_working_directory/000/7/working/BSA_min_23.mzXML</string>
136 <string>D:\shared\dglaetzer\maxquant_tool\test2\BSA_min_22.mzXML</string> 135 <string>/tmp/tmpyzym30dx/job_working_directory/000/7/working/BSA_min_22.mzxml</string>
137 </filePaths> 136 </filePaths>
138 <experiments> 137 <experiments>
139 <string>BSA_min_23.mzXML</string> 138 <string>BSA_min_23.mzXML</string>
140 <string>BSA_min_22.mzxml</string> 139 <string>BSA_min_22.mzxml</string>
141 </experiments> 140 </experiments>
155 <string/> 154 <string/>
156 <string/> 155 <string/>
157 </referenceChannel> 156 </referenceChannel>
158 <intensPred>False</intensPred> 157 <intensPred>False</intensPred>
159 <intensPredModelReTrain>False</intensPredModelReTrain> 158 <intensPredModelReTrain>False</intensPredModelReTrain>
159 <lfqTopNPeptides>0</lfqTopNPeptides>
160 <parameterGroups> 160 <parameterGroups>
161 <parameterGroup> 161 <parameterGroup>
162 <msInstrument>0</msInstrument> 162 <msInstrument>0</msInstrument>
163 <maxCharge>7</maxCharge> 163 <maxCharge>7</maxCharge>
164 <minPeakLen>2</minPeakLen> 164 <minPeakLen>2</minPeakLen>
165 <diaMinPeakLen>2</diaMinPeakLen> 165 <diaMinPeakLen>1</diaMinPeakLen>
166 <useMs1Centroids>False</useMs1Centroids> 166 <useMs1Centroids>False</useMs1Centroids>
167 <useMs2Centroids>False</useMs2Centroids> 167 <useMs2Centroids>False</useMs2Centroids>
168 <cutPeaks>True</cutPeaks> 168 <cutPeaks>True</cutPeaks>
169 <gapScans>1</gapScans> 169 <gapScans>1</gapScans>
170 <minTime>NaN</minTime> 170 <minTime>NaN</minTime>
176 <centroidHalfWidth>35</centroidHalfWidth> 176 <centroidHalfWidth>35</centroidHalfWidth>
177 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm> 177 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
178 <valleyFactor>1.4</valleyFactor> 178 <valleyFactor>1.4</valleyFactor>
179 <isotopeValleyFactor>1.2</isotopeValleyFactor> 179 <isotopeValleyFactor>1.2</isotopeValleyFactor>
180 <advancedPeakSplitting>False</advancedPeakSplitting> 180 <advancedPeakSplitting>False</advancedPeakSplitting>
181 <intensityThreshold>0</intensityThreshold> 181 <intensityThresholdMs1>0</intensityThresholdMs1>
182 <intensityThresholdMs2>0</intensityThresholdMs2>
182 <labelMods> 183 <labelMods>
183 <string/> 184 <string/>
184 </labelMods> 185 </labelMods>
185 <lcmsRunType>Reporter ion MS2</lcmsRunType> 186 <lcmsRunType>Reporter ion MS2</lcmsRunType>
186 <reQuantify>False</reQuantify> 187 <reQuantify>False</reQuantify>
187 <lfqMode>0</lfqMode> 188 <lfqMode>0</lfqMode>
188 <lfqSkipNorm>False</lfqSkipNorm> 189 <lfqNormClusterSize>80</lfqNormClusterSize>
189 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> 190 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
190 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> 191 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
191 <lfqMaxFeatures>100000</lfqMaxFeatures> 192 <lfqMaxFeatures>100000</lfqMaxFeatures>
192 <neucodeMaxPpm>0</neucodeMaxPpm> 193 <neucodeMaxPpm>0</neucodeMaxPpm>
193 <neucodeResolution>0</neucodeResolution> 194 <neucodeResolution>0</neucodeResolution>
202 <multiplicity>1</multiplicity> 203 <multiplicity>1</multiplicity>
203 <enzymeMode>0</enzymeMode> 204 <enzymeMode>0</enzymeMode>
204 <complementaryReporterType>0</complementaryReporterType> 205 <complementaryReporterType>0</complementaryReporterType>
205 <reporterNormalization>0</reporterNormalization> 206 <reporterNormalization>0</reporterNormalization>
206 <neucodeIntensityMode>0</neucodeIntensityMode> 207 <neucodeIntensityMode>0</neucodeIntensityMode>
207 <fixedModifications> 208 <fixedModifications/>
208 </fixedModifications>
209 <enzymes> 209 <enzymes>
210 <string>Trypsin/P</string> 210 <string>Trypsin/P</string>
211 </enzymes> 211 </enzymes>
212 <enzymesFirstSearch> 212 <enzymesFirstSearch>
213 </enzymesFirstSearch> 213 </enzymesFirstSearch>
276 <timsResolution>0</timsResolution> 276 <timsResolution>0</timsResolution>
277 <timsMinMsmsIntensity>0</timsMinMsmsIntensity> 277 <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
278 <timsRemovePrecursor>True</timsRemovePrecursor> 278 <timsRemovePrecursor>True</timsRemovePrecursor>
279 <timsIsobaricLabels>False</timsIsobaricLabels> 279 <timsIsobaricLabels>False</timsIsobaricLabels>
280 <timsCollapseMsms>True</timsCollapseMsms> 280 <timsCollapseMsms>True</timsCollapseMsms>
281 <crosslinkSearch>False</crosslinkSearch> 281 <crossLinkingType>0</crossLinkingType>
282 <crossLinker/> 282 <crossLinker/>
283 <minMatchXl>0</minMatchXl> 283 <minMatchXl>0</minMatchXl>
284 <minPairedPepLenXl>6</minPairedPepLenXl> 284 <minPairedPepLenXl>6</minPairedPepLenXl>
285 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> 285 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
286 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> 286 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
298 <crosslinkMode/> 298 <crosslinkMode/>
299 <peakRefinement>False</peakRefinement> 299 <peakRefinement>False</peakRefinement>
300 <isobaricSumOverWindow>True</isobaricSumOverWindow> 300 <isobaricSumOverWindow>True</isobaricSumOverWindow>
301 <isobaricWeightExponent>0.75</isobaricWeightExponent> 301 <isobaricWeightExponent>0.75</isobaricWeightExponent>
302 <diaLibraryType>0</diaLibraryType> 302 <diaLibraryType>0</diaLibraryType>
303 <diaLibraryPath/> 303 <diaLibraryPaths>
304 </diaLibraryPaths>
304 <diaPeptidePaths> 305 <diaPeptidePaths>
305 </diaPeptidePaths> 306 </diaPeptidePaths>
306 <diaEvidencePaths> 307 <diaEvidencePaths>
307 </diaEvidencePaths> 308 </diaEvidencePaths>
308 <diaMsmsPaths> 309 <diaMsmsPaths>
311 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm> 312 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
312 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering> 313 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
313 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> 314 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
314 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> 315 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
315 <diaScoreN>7</diaScoreN> 316 <diaScoreN>7</diaScoreN>
316 <diaMinScore>2.99</diaMinScore> 317 <diaMinScore>1.99</diaMinScore>
317 <diaPrecursorQuant>False</diaPrecursorQuant> 318 <diaXgBoostBaseScore>0.4</diaXgBoostBaseScore>
318 <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant> 319 <diaXgBoostSubSample>0.9</diaXgBoostSubSample>
320 <centroidPosition>0</centroidPosition>
321 <diaQuantMethod>7</diaQuantMethod>
322 <diaFeatureQuantMethod>2</diaFeatureQuantMethod>
323 <lfqNormType>1</lfqNormType>
324 <diaTopNForQuant>10</diaTopNForQuant>
325 <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant>
326 <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant>
327 <diaPrecursorFilterType>0</diaPrecursorFilterType>
328 <diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore>
329 <diaMinPrecursorScore>0.5</diaMinPrecursorScore>
330 <diaMinProfileCorrelation>0</diaMinProfileCorrelation>
331 <diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight>
332 <diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth>
333 <diaXgBoostEstimators>580</diaXgBoostEstimators>
334 <diaXgBoostGamma>0.9</diaXgBoostGamma>
335 <diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep>
336 <diaGlobalMl>True</diaGlobalMl>
337 <diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy>
338 <diaMassWindowFactor>3.3</diaMassWindowFactor>
339 <diaRtPrediction>False</diaRtPrediction>
340 <diaRtPredictionSecondRound>False</diaRtPredictionSecondRound>
341 <diaNoMl>False</diaNoMl>
342 <diaPermuteRt>False</diaPermuteRt>
343 <diaPermuteCcs>False</diaPermuteCcs>
344 <diaBackgroundSubtraction>False</diaBackgroundSubtraction>
345 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile>
346 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>
347 <diaLfqWeightedMedian>False</diaLfqWeightedMedian>
319 </parameterGroup> 348 </parameterGroup>
320 <parameterGroup> 349 <parameterGroup>
321 <msInstrument>0</msInstrument> 350 <msInstrument>0</msInstrument>
322 <maxCharge>7</maxCharge> 351 <maxCharge>7</maxCharge>
323 <minPeakLen>2</minPeakLen> 352 <minPeakLen>2</minPeakLen>
324 <diaMinPeakLen>2</diaMinPeakLen> 353 <diaMinPeakLen>1</diaMinPeakLen>
325 <useMs1Centroids>False</useMs1Centroids> 354 <useMs1Centroids>False</useMs1Centroids>
326 <useMs2Centroids>False</useMs2Centroids> 355 <useMs2Centroids>False</useMs2Centroids>
327 <cutPeaks>True</cutPeaks> 356 <cutPeaks>True</cutPeaks>
328 <gapScans>1</gapScans> 357 <gapScans>1</gapScans>
329 <minTime>NaN</minTime> 358 <minTime>NaN</minTime>
335 <centroidHalfWidth>35</centroidHalfWidth> 364 <centroidHalfWidth>35</centroidHalfWidth>
336 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm> 365 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
337 <valleyFactor>1.4</valleyFactor> 366 <valleyFactor>1.4</valleyFactor>
338 <isotopeValleyFactor>1.2</isotopeValleyFactor> 367 <isotopeValleyFactor>1.2</isotopeValleyFactor>
339 <advancedPeakSplitting>False</advancedPeakSplitting> 368 <advancedPeakSplitting>False</advancedPeakSplitting>
340 <intensityThreshold>0</intensityThreshold> 369 <intensityThresholdMs1>0</intensityThresholdMs1>
370 <intensityThresholdMs2>0</intensityThresholdMs2>
341 <labelMods> 371 <labelMods>
342 <string/> 372 <string/>
343 </labelMods> 373 </labelMods>
344 <lcmsRunType>Reporter ion MS2</lcmsRunType> 374 <lcmsRunType>Reporter ion MS2</lcmsRunType>
345 <reQuantify>False</reQuantify> 375 <reQuantify>False</reQuantify>
346 <lfqMode>0</lfqMode> 376 <lfqMode>0</lfqMode>
347 <lfqSkipNorm>False</lfqSkipNorm> 377 <lfqNormClusterSize>80</lfqNormClusterSize>
348 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> 378 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
349 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> 379 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
350 <lfqMaxFeatures>100000</lfqMaxFeatures> 380 <lfqMaxFeatures>100000</lfqMaxFeatures>
351 <neucodeMaxPpm>0</neucodeMaxPpm> 381 <neucodeMaxPpm>0</neucodeMaxPpm>
352 <neucodeResolution>0</neucodeResolution> 382 <neucodeResolution>0</neucodeResolution>
361 <multiplicity>1</multiplicity> 391 <multiplicity>1</multiplicity>
362 <enzymeMode>0</enzymeMode> 392 <enzymeMode>0</enzymeMode>
363 <complementaryReporterType>0</complementaryReporterType> 393 <complementaryReporterType>0</complementaryReporterType>
364 <reporterNormalization>0</reporterNormalization> 394 <reporterNormalization>0</reporterNormalization>
365 <neucodeIntensityMode>0</neucodeIntensityMode> 395 <neucodeIntensityMode>0</neucodeIntensityMode>
366 <fixedModifications> 396 <fixedModifications/>
367 </fixedModifications> 397 <enzymes/>
368 <enzymes>
369 </enzymes>
370 <enzymesFirstSearch> 398 <enzymesFirstSearch>
371 </enzymesFirstSearch> 399 </enzymesFirstSearch>
372 <enzymeModeFirstSearch>0</enzymeModeFirstSearch> 400 <enzymeModeFirstSearch>0</enzymeModeFirstSearch>
373 <useEnzymeFirstSearch>False</useEnzymeFirstSearch> 401 <useEnzymeFirstSearch>False</useEnzymeFirstSearch>
374 <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch> 402 <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
375 <variableModifications> 403 <variableModifications/>
376 </variableModifications>
377 <useMultiModification>False</useMultiModification> 404 <useMultiModification>False</useMultiModification>
378 <multiModifications> 405 <multiModifications>
379 </multiModifications> 406 </multiModifications>
380 <isobaricLabels> 407 <isobaricLabels>
381 <IsobaricLabelInfo> 408 <IsobaricLabelInfo>
451 <timsResolution>0</timsResolution> 478 <timsResolution>0</timsResolution>
452 <timsMinMsmsIntensity>0</timsMinMsmsIntensity> 479 <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
453 <timsRemovePrecursor>True</timsRemovePrecursor> 480 <timsRemovePrecursor>True</timsRemovePrecursor>
454 <timsIsobaricLabels>False</timsIsobaricLabels> 481 <timsIsobaricLabels>False</timsIsobaricLabels>
455 <timsCollapseMsms>True</timsCollapseMsms> 482 <timsCollapseMsms>True</timsCollapseMsms>
456 <crosslinkSearch>False</crosslinkSearch> 483 <crossLinkingType>0</crossLinkingType>
457 <crossLinker/> 484 <crossLinker/>
458 <minMatchXl>0</minMatchXl> 485 <minMatchXl>0</minMatchXl>
459 <minPairedPepLenXl>6</minPairedPepLenXl> 486 <minPairedPepLenXl>6</minPairedPepLenXl>
460 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> 487 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
461 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> 488 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
473 <crosslinkMode/> 500 <crosslinkMode/>
474 <peakRefinement>False</peakRefinement> 501 <peakRefinement>False</peakRefinement>
475 <isobaricSumOverWindow>True</isobaricSumOverWindow> 502 <isobaricSumOverWindow>True</isobaricSumOverWindow>
476 <isobaricWeightExponent>0.75</isobaricWeightExponent> 503 <isobaricWeightExponent>0.75</isobaricWeightExponent>
477 <diaLibraryType>0</diaLibraryType> 504 <diaLibraryType>0</diaLibraryType>
478 <diaLibraryPath/> 505 <diaLibraryPaths>
506 </diaLibraryPaths>
479 <diaPeptidePaths> 507 <diaPeptidePaths>
480 </diaPeptidePaths> 508 </diaPeptidePaths>
481 <diaEvidencePaths> 509 <diaEvidencePaths>
482 </diaEvidencePaths> 510 </diaEvidencePaths>
483 <diaMsmsPaths> 511 <diaMsmsPaths>
486 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm> 514 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
487 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering> 515 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
488 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> 516 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
489 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> 517 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
490 <diaScoreN>7</diaScoreN> 518 <diaScoreN>7</diaScoreN>
491 <diaMinScore>2.99</diaMinScore> 519 <diaMinScore>1.99</diaMinScore>
492 <diaPrecursorQuant>False</diaPrecursorQuant> 520 <diaXgBoostBaseScore>0.4</diaXgBoostBaseScore>
493 <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant> 521 <diaXgBoostSubSample>0.9</diaXgBoostSubSample>
522 <centroidPosition>0</centroidPosition>
523 <diaQuantMethod>7</diaQuantMethod>
524 <diaFeatureQuantMethod>2</diaFeatureQuantMethod>
525 <lfqNormType>1</lfqNormType>
526 <diaTopNForQuant>10</diaTopNForQuant>
527 <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant>
528 <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant>
529 <diaPrecursorFilterType>0</diaPrecursorFilterType>
530 <diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore>
531 <diaMinPrecursorScore>0.5</diaMinPrecursorScore>
532 <diaMinProfileCorrelation>0</diaMinProfileCorrelation>
533 <diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight>
534 <diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth>
535 <diaXgBoostEstimators>580</diaXgBoostEstimators>
536 <diaXgBoostGamma>0.9</diaXgBoostGamma>
537 <diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep>
538 <diaGlobalMl>True</diaGlobalMl>
539 <diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy>
540 <diaMassWindowFactor>3.3</diaMassWindowFactor>
541 <diaRtPrediction>False</diaRtPrediction>
542 <diaRtPredictionSecondRound>False</diaRtPredictionSecondRound>
543 <diaNoMl>False</diaNoMl>
544 <diaPermuteRt>False</diaPermuteRt>
545 <diaPermuteCcs>False</diaPermuteCcs>
546 <diaBackgroundSubtraction>False</diaBackgroundSubtraction>
547 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile>
548 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>
549 <diaLfqWeightedMedian>False</diaLfqWeightedMedian>
494 </parameterGroup> 550 </parameterGroup>
495 </parameterGroups> 551 </parameterGroups>
496 <msmsParamsArray> 552 <msmsParamsArray>
497 <msmsParams> 553 <msmsParams>
498 <Name>FTMS</Name> 554 <Name>FTMS</Name>