Mercurial > repos > galaxyp > maxquant

comparison test-data/07/mqpar.xml @ 11:d72c96ad9a16 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
author galaxyp
date Tue, 15 Jun 2021 07:55:59 +0000
parents
children 0839f84def5e
comparison
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10:f522c08e900c 11:d72c96ad9a16
1 <?xml version="1.0" ?>
2 <MaxQuantParams>
3 <fastaFiles>
4 <FastaFileInfo>
5 <fastaFilePath>/tmp/tmpfqvn4g0u/files/5/b/8/dataset_5b803772-27b2-44fa-a4cf-8da6ee3cdfb8.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>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>True</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>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/tmpfqvn4g0u/job_working_directory/000/3/working/ptxqc_test3.mzXML</string>
136 </filePaths>
137 <experiments>
138 <string>ptxqc_test3.mzXML</string>
139 </experiments>
140 <fractions>
141 <short>32767</short>
142 </fractions>
143 <ptms>
144 <boolean>False</boolean>
145 </ptms>
146 <paramGroupIndices>
147 <int>0</int>
148 </paramGroupIndices>
149 <referenceChannel>
150 <string/>
151 </referenceChannel>
152 <intensPred>False</intensPred>
153 <intensPredModelReTrain>False</intensPredModelReTrain>
154 <parameterGroups>
155 <parameterGroup>
156 <msInstrument>0</msInstrument>
157 <maxCharge>7</maxCharge>
158 <minPeakLen>2</minPeakLen>
159 <diaMinPeakLen>2</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 <intensityThreshold>0</intensityThreshold>
176 <labelMods>
177 <string/>
178 </labelMods>
179 <lcmsRunType>Reporter ion MS2</lcmsRunType>
180 <reQuantify>False</reQuantify>
181 <lfqMode>0</lfqMode>
182 <lfqSkipNorm>False</lfqSkipNorm>
183 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
184 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
185 <lfqMaxFeatures>100000</lfqMaxFeatures>
186 <neucodeMaxPpm>0</neucodeMaxPpm>
187 <neucodeResolution>0</neucodeResolution>
188 <neucodeResolutionInMda>False</neucodeResolutionInMda>
189 <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
190 <fastLfq>True</fastLfq>
191 <lfqRestrictFeatures>False</lfqRestrictFeatures>
192 <lfqMinRatioCount>2</lfqMinRatioCount>
193 <maxLabeledAa>0</maxLabeledAa>
194 <maxNmods>5</maxNmods>
195 <maxMissedCleavages>2</maxMissedCleavages>
196 <multiplicity>1</multiplicity>
197 <enzymeMode>0</enzymeMode>
198 <complementaryReporterType>0</complementaryReporterType>
199 <reporterNormalization>0</reporterNormalization>
200 <neucodeIntensityMode>0</neucodeIntensityMode>
201 <fixedModifications/>
202 <enzymes>
203 <string>Trypsin/P</string>
204 </enzymes>
205 <enzymesFirstSearch>
206 </enzymesFirstSearch>
207 <enzymeModeFirstSearch>0</enzymeModeFirstSearch>
208 <useEnzymeFirstSearch>False</useEnzymeFirstSearch>
209 <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
210 <variableModifications>
211 <string>Oxidation (M)</string>
212 </variableModifications>
213 <useMultiModification>False</useMultiModification>
214 <multiModifications>
215 </multiModifications>
216 <isobaricLabels>
217 <IsobaricLabelInfo>
218 <internalLabel>TMT10plex-Lys126C</internalLabel>
219 <terminalLabel>TMT10plex-Nter126C</terminalLabel>
220 <correctionFactorM2>0</correctionFactorM2>
221 <correctionFactorM1>0</correctionFactorM1>
222 <correctionFactorP1>0</correctionFactorP1>
223 <correctionFactorP2>0</correctionFactorP2>
224 <tmtLike>True</tmtLike>
225 </IsobaricLabelInfo>
226 <IsobaricLabelInfo>
227 <internalLabel>TMT10plex-Lys127N</internalLabel>
228 <terminalLabel>TMT10plex-Nter127N</terminalLabel>
229 <correctionFactorM2>0</correctionFactorM2>
230 <correctionFactorM1>0</correctionFactorM1>
231 <correctionFactorP1>0</correctionFactorP1>
232 <correctionFactorP2>0</correctionFactorP2>
233 <tmtLike>True</tmtLike>
234 </IsobaricLabelInfo>
235 <IsobaricLabelInfo>
236 <internalLabel>TMT10plex-Lys127C</internalLabel>
237 <terminalLabel>TMT10plex-Nter127C</terminalLabel>
238 <correctionFactorM2>0</correctionFactorM2>
239 <correctionFactorM1>0</correctionFactorM1>
240 <correctionFactorP1>0</correctionFactorP1>
241 <correctionFactorP2>0</correctionFactorP2>
242 <tmtLike>True</tmtLike>
243 </IsobaricLabelInfo>
244 <IsobaricLabelInfo>
245 <internalLabel>TMT10plex-Lys128N</internalLabel>
246 <terminalLabel>TMT10plex-Nter128N</terminalLabel>
247 <correctionFactorM2>0</correctionFactorM2>
248 <correctionFactorM1>0</correctionFactorM1>
249 <correctionFactorP1>0</correctionFactorP1>
250 <correctionFactorP2>0</correctionFactorP2>
251 <tmtLike>True</tmtLike>
252 </IsobaricLabelInfo>
253 <IsobaricLabelInfo>
254 <internalLabel>TMT10plex-Lys128C</internalLabel>
255 <terminalLabel>TMT10plex-Nter128C</terminalLabel>
256 <correctionFactorM2>0</correctionFactorM2>
257 <correctionFactorM1>0</correctionFactorM1>
258 <correctionFactorP1>0</correctionFactorP1>
259 <correctionFactorP2>0</correctionFactorP2>
260 <tmtLike>True</tmtLike>
261 </IsobaricLabelInfo>
262 <IsobaricLabelInfo>
263 <internalLabel>TMT10plex-Lys129N</internalLabel>
264 <terminalLabel>TMT10plex-Nter129N</terminalLabel>
265 <correctionFactorM2>0</correctionFactorM2>
266 <correctionFactorM1>0</correctionFactorM1>
267 <correctionFactorP1>0</correctionFactorP1>
268 <correctionFactorP2>0</correctionFactorP2>
269 <tmtLike>True</tmtLike>
270 </IsobaricLabelInfo>
271 <IsobaricLabelInfo>
272 <internalLabel>TMT10plex-Lys129C</internalLabel>
273 <terminalLabel>TMT10plex-Nter129C</terminalLabel>
274 <correctionFactorM2>0</correctionFactorM2>
275 <correctionFactorM1>0</correctionFactorM1>
276 <correctionFactorP1>0</correctionFactorP1>
277 <correctionFactorP2>0</correctionFactorP2>
278 <tmtLike>True</tmtLike>
279 </IsobaricLabelInfo>
280 <IsobaricLabelInfo>
281 <internalLabel>TMT10plex-Lys130N</internalLabel>
282 <terminalLabel>TMT10plex-Nter130N</terminalLabel>
283 <correctionFactorM2>0</correctionFactorM2>
284 <correctionFactorM1>0</correctionFactorM1>
285 <correctionFactorP1>0</correctionFactorP1>
286 <correctionFactorP2>0</correctionFactorP2>
287 <tmtLike>True</tmtLike>
288 </IsobaricLabelInfo>
289 <IsobaricLabelInfo>
290 <internalLabel>TMT10plex-Lys130C</internalLabel>
291 <terminalLabel>TMT10plex-Nter130C</terminalLabel>
292 <correctionFactorM2>0</correctionFactorM2>
293 <correctionFactorM1>0</correctionFactorM1>
294 <correctionFactorP1>0</correctionFactorP1>
295 <correctionFactorP2>0</correctionFactorP2>
296 <tmtLike>True</tmtLike>
297 </IsobaricLabelInfo>
298 <IsobaricLabelInfo>
299 <internalLabel>TMT10plex-Lys131N</internalLabel>
300 <terminalLabel>TMT10plex-Nter131N</terminalLabel>
301 <correctionFactorM2>0</correctionFactorM2>
302 <correctionFactorM1>0</correctionFactorM1>
303 <correctionFactorP1>0</correctionFactorP1>
304 <correctionFactorP2>0</correctionFactorP2>
305 <tmtLike>True</tmtLike>
306 </IsobaricLabelInfo>
307 </isobaricLabels>
308 <neucodeLabels>
309 </neucodeLabels>
310 <variableModificationsFirstSearch>
311 </variableModificationsFirstSearch>
312 <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
313 <additionalVariableModifications>
314 </additionalVariableModifications>
315 <additionalVariableModificationProteins>
316 </additionalVariableModificationProteins>
317 <doMassFiltering>True</doMassFiltering>
318 <firstSearchTol>20</firstSearchTol>
319 <mainSearchTol>4.5</mainSearchTol>
320 <searchTolInPpm>True</searchTolInPpm>
321 <isotopeMatchTol>2</isotopeMatchTol>
322 <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
323 <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
324 <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
325 <checkMassDeficit>True</checkMassDeficit>
326 <recalibrationInPpm>True</recalibrationInPpm>
327 <intensityDependentCalibration>False</intensityDependentCalibration>
328 <minScoreForCalibration>70</minScoreForCalibration>
329 <matchLibraryFile>False</matchLibraryFile>
330 <libraryFile/>
331 <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
332 <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
333 <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
334 <reporterMassTolerance>0.003</reporterMassTolerance>
335 <reporterPif>0</reporterPif>
336 <filterPif>False</filterPif>
337 <reporterFraction>0</reporterFraction>
338 <reporterBasePeakRatio>0</reporterBasePeakRatio>
339 <timsHalfWidth>0</timsHalfWidth>
340 <timsStep>0</timsStep>
341 <timsResolution>0</timsResolution>
342 <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
343 <timsRemovePrecursor>True</timsRemovePrecursor>
344 <timsIsobaricLabels>False</timsIsobaricLabels>
345 <timsCollapseMsms>True</timsCollapseMsms>
346 <crosslinkSearch>False</crosslinkSearch>
347 <crossLinker/>
348 <minMatchXl>0</minMatchXl>
349 <minPairedPepLenXl>6</minPairedPepLenXl>
350 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
351 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
352 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
353 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
354 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
355 <crosslinkModifications>
356 </crosslinkModifications>
357 <crosslinkFastaFiles>
358 </crosslinkFastaFiles>
359 <crosslinkSites>
360 </crosslinkSites>
361 <crosslinkNetworkFiles>
362 </crosslinkNetworkFiles>
363 <crosslinkMode/>
364 <peakRefinement>False</peakRefinement>
365 <isobaricSumOverWindow>True</isobaricSumOverWindow>
366 <isobaricWeightExponent>0.75</isobaricWeightExponent>
367 <diaLibraryType>0</diaLibraryType>
368 <diaLibraryPath/>
369 <diaPeptidePaths>
370 </diaPeptidePaths>
371 <diaEvidencePaths>
372 </diaEvidencePaths>
373 <diaMsmsPaths>
374 </diaMsmsPaths>
375 <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
376 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
377 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
378 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
379 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
380 <diaScoreN>7</diaScoreN>
381 <diaMinScore>2.99</diaMinScore>
382 <diaPrecursorQuant>False</diaPrecursorQuant>
383 <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>
384 </parameterGroup>
385 </parameterGroups>
386 <msmsParamsArray>
387 <msmsParams>
388 <Name>FTMS</Name>
389 <MatchTolerance>20</MatchTolerance>
390 <MatchToleranceInPpm>True</MatchToleranceInPpm>
391 <DeisotopeTolerance>7</DeisotopeTolerance>
392 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
393 <DeNovoTolerance>10</DeNovoTolerance>
394 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
395 <Deisotope>True</Deisotope>
396 <Topx>12</Topx>
397 <TopxInterval>100</TopxInterval>
398 <HigherCharges>True</HigherCharges>
399 <IncludeWater>True</IncludeWater>
400 <IncludeAmmonia>True</IncludeAmmonia>
401 <DependentLosses>True</DependentLosses>
402 <Recalibration>False</Recalibration>
403 </msmsParams>
404 <msmsParams>
405 <Name>ITMS</Name>
406 <MatchTolerance>0.5</MatchTolerance>
407 <MatchToleranceInPpm>False</MatchToleranceInPpm>
408 <DeisotopeTolerance>0.15</DeisotopeTolerance>
409 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
410 <DeNovoTolerance>0.25</DeNovoTolerance>
411 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
412 <Deisotope>False</Deisotope>
413 <Topx>8</Topx>
414 <TopxInterval>100</TopxInterval>
415 <HigherCharges>True</HigherCharges>
416 <IncludeWater>True</IncludeWater>
417 <IncludeAmmonia>True</IncludeAmmonia>
418 <DependentLosses>True</DependentLosses>
419 <Recalibration>False</Recalibration>
420 </msmsParams>
421 <msmsParams>
422 <Name>TOF</Name>
423 <MatchTolerance>40</MatchTolerance>
424 <MatchToleranceInPpm>True</MatchToleranceInPpm>
425 <DeisotopeTolerance>0.01</DeisotopeTolerance>
426 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
427 <DeNovoTolerance>0.02</DeNovoTolerance>
428 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
429 <Deisotope>True</Deisotope>
430 <Topx>10</Topx>
431 <TopxInterval>100</TopxInterval>
432 <HigherCharges>True</HigherCharges>
433 <IncludeWater>True</IncludeWater>
434 <IncludeAmmonia>True</IncludeAmmonia>
435 <DependentLosses>True</DependentLosses>
436 <Recalibration>False</Recalibration>
437 </msmsParams>
438 <msmsParams>
439 <Name>Unknown</Name>
440 <MatchTolerance>20</MatchTolerance>
441 <MatchToleranceInPpm>True</MatchToleranceInPpm>
442 <DeisotopeTolerance>7</DeisotopeTolerance>
443 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
444 <DeNovoTolerance>10</DeNovoTolerance>
445 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
446 <Deisotope>True</Deisotope>
447 <Topx>12</Topx>
448 <TopxInterval>100</TopxInterval>
449 <HigherCharges>True</HigherCharges>
450 <IncludeWater>True</IncludeWater>
451 <IncludeAmmonia>True</IncludeAmmonia>
452 <DependentLosses>True</DependentLosses>
453 <Recalibration>False</Recalibration>
454 </msmsParams>
455 </msmsParamsArray>
456 <fragmentationParamsArray>
457 <fragmentationParams>
458 <Name>CID</Name>
459 <Connected>False</Connected>
460 <ConnectedScore0>1</ConnectedScore0>
461 <ConnectedScore1>1</ConnectedScore1>
462 <ConnectedScore2>1</ConnectedScore2>
463 <InternalFragments>False</InternalFragments>
464 <InternalFragmentWeight>1</InternalFragmentWeight>
465 <InternalFragmentAas>KRH</InternalFragmentAas>
466 </fragmentationParams>
467 <fragmentationParams>
468 <Name>HCD</Name>
469 <Connected>False</Connected>
470 <ConnectedScore0>1</ConnectedScore0>
471 <ConnectedScore1>1</ConnectedScore1>
472 <ConnectedScore2>1</ConnectedScore2>
473 <InternalFragments>False</InternalFragments>
474 <InternalFragmentWeight>1</InternalFragmentWeight>
475 <InternalFragmentAas>KRH</InternalFragmentAas>
476 </fragmentationParams>
477 <fragmentationParams>
478 <Name>ETD</Name>
479 <Connected>False</Connected>
480 <ConnectedScore0>1</ConnectedScore0>
481 <ConnectedScore1>1</ConnectedScore1>
482 <ConnectedScore2>1</ConnectedScore2>
483 <InternalFragments>False</InternalFragments>
484 <InternalFragmentWeight>1</InternalFragmentWeight>
485 <InternalFragmentAas>KRH</InternalFragmentAas>
486 </fragmentationParams>
487 <fragmentationParams>
488 <Name>PQD</Name>
489 <Connected>False</Connected>
490 <ConnectedScore0>1</ConnectedScore0>
491 <ConnectedScore1>1</ConnectedScore1>
492 <ConnectedScore2>1</ConnectedScore2>
493 <InternalFragments>False</InternalFragments>
494 <InternalFragmentWeight>1</InternalFragmentWeight>
495 <InternalFragmentAas>KRH</InternalFragmentAas>
496 </fragmentationParams>
497 <fragmentationParams>
498 <Name>ETHCD</Name>
499 <Connected>False</Connected>
500 <ConnectedScore0>1</ConnectedScore0>
501 <ConnectedScore1>1</ConnectedScore1>
502 <ConnectedScore2>1</ConnectedScore2>
503 <InternalFragments>False</InternalFragments>
504 <InternalFragmentWeight>1</InternalFragmentWeight>
505 <InternalFragmentAas>KRH</InternalFragmentAas>
506 </fragmentationParams>
507 <fragmentationParams>
508 <Name>ETCID</Name>
509 <Connected>False</Connected>
510 <ConnectedScore0>1</ConnectedScore0>
511 <ConnectedScore1>1</ConnectedScore1>
512 <ConnectedScore2>1</ConnectedScore2>
513 <InternalFragments>False</InternalFragments>
514 <InternalFragmentWeight>1</InternalFragmentWeight>
515 <InternalFragmentAas>KRH</InternalFragmentAas>
516 </fragmentationParams>
517 <fragmentationParams>
518 <Name>UVPD</Name>
519 <Connected>False</Connected>
520 <ConnectedScore0>1</ConnectedScore0>
521 <ConnectedScore1>1</ConnectedScore1>
522 <ConnectedScore2>1</ConnectedScore2>
523 <InternalFragments>False</InternalFragments>
524 <InternalFragmentWeight>1</InternalFragmentWeight>
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538 </MaxQuantParams>
539