Mercurial > repos > galaxyp > maxquant

comparison test-data/mqpar/mqpar.xml @ 15:97a7f34fcb6a draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
author galaxyp
date Wed, 11 Aug 2021 09:24:23 +0000
parents
children 8934bc76bb52
comparison
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14:e42225f8a659 15:97a7f34fcb6a
1 <?xml version="1.0" ?>
2 <MaxQuantParams>
3 <fastaFiles>
4 <FastaFileInfo>
5 <fastaFilePath>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 <rtShift>False</rtShift>
23 <separateLfq>False</separateLfq>
24 <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>
25 <lfqRequireMsms>True</lfqRequireMsms>
26 <decoyMode>revert</decoyMode>
27 <boxCarMode>all</boxCarMode>
28 <includeContaminants>True</includeContaminants>
29 <maxPeptideMass>4600</maxPeptideMass>
30 <epsilonMutationScore>True</epsilonMutationScore>
31 <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>
32 <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>
33 <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>
34 <minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>
35 <minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>
36 <minScoreModifiedPeptides>40</minScoreModifiedPeptides>
37 <secondPeptide>True</secondPeptide>
38 <matchBetweenRuns>False</matchBetweenRuns>
39 <matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>
40 <matchBetweenRunsFdr>False</matchBetweenRunsFdr>
41 <dependentPeptides>False</dependentPeptides>
42 <dependentPeptideFdr>0</dependentPeptideFdr>
43 <dependentPeptideMassBin>0</dependentPeptideMassBin>
44 <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>
45 <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>
46 <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>
47 <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>
48 <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>
49 <ibaq>False</ibaq>
50 <top3>False</top3>
51 <independentEnzymes>False</independentEnzymes>
52 <useDeltaScore>False</useDeltaScore>
53 <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>
54 <taxonomyLevel>Species</taxonomyLevel>
55 <avalon>False</avalon>
56 <nModColumns>3</nModColumns>
57 <ibaqLogFit>False</ibaqLogFit>
58 <razorProteinFdr>True</razorProteinFdr>
59 <deNovoSequencing>False</deNovoSequencing>
60 <deNovoVarMods>True</deNovoVarMods>
61 <massDifferenceSearch>False</massDifferenceSearch>
62 <isotopeCalc>False</isotopeCalc>
63 <writePeptidesForSpectrumFile/>
64 <intensityPredictionsFile>
65 </intensityPredictionsFile>
66 <minPepLen>7</minPepLen>
67 <psmFdrCrosslink>0.01</psmFdrCrosslink>
68 <peptideFdr>0.01</peptideFdr>
69 <proteinFdr>0.01</proteinFdr>
70 <siteFdr>0.01</siteFdr>
71 <minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>
72 <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>
73 <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>
74 <minPeptides>1</minPeptides>
75 <minRazorPeptides>1</minRazorPeptides>
76 <minUniquePeptides>0</minUniquePeptides>
77 <useCounterparts>False</useCounterparts>
78 <advancedSiteIntensities>True</advancedSiteIntensities>
79 <customProteinQuantification>False</customProteinQuantification>
80 <customProteinQuantificationFile/>
81 <minRatioCount>2</minRatioCount>
82 <restrictProteinQuantification>True</restrictProteinQuantification>
83 <restrictMods>
84 <string>Oxidation (M)</string>
85 <string>Acetyl (Protein N-term)</string>
86 </restrictMods>
87 <matchingTimeWindow>0</matchingTimeWindow>
88 <matchingIonMobilityWindow>0</matchingIonMobilityWindow>
89 <alignmentTimeWindow>0</alignmentTimeWindow>
90 <alignmentIonMobilityWindow>0</alignmentIonMobilityWindow>
91 <numberOfCandidatesMsms>15</numberOfCandidatesMsms>
92 <compositionPrediction>0</compositionPrediction>
93 <quantMode>1</quantMode>
94 <massDifferenceMods>
95 </massDifferenceMods>
96 <mainSearchMaxCombinations>200</mainSearchMaxCombinations>
97 <writeMsScansTable>False</writeMsScansTable>
98 <writeMsmsScansTable>True</writeMsmsScansTable>
99 <writePasefMsmsScansTable>True</writePasefMsmsScansTable>
100 <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable>
101 <writeMs3ScansTable>True</writeMs3ScansTable>
102 <writeAllPeptidesTable>True</writeAllPeptidesTable>
103 <writeMzRangeTable>True</writeMzRangeTable>
104 <writeDiaFragmentTable>False</writeDiaFragmentTable>
105 <writeMzTab>False</writeMzTab>
106 <disableMd5>False</disableMd5>
107 <cacheBinInds>True</cacheBinInds>
108 <etdIncludeB>False</etdIncludeB>
109 <ms2PrecursorShift>0</ms2PrecursorShift>
110 <complementaryIonPpm>20</complementaryIonPpm>
111 <variationParseRule/>
112 <variationMode>none</variationMode>
113 <useSeriesReporters>False</useSeriesReporters>
114 <name>session1</name>
115 <maxQuantVersion>1.6.17.0</maxQuantVersion>
116 <pluginFolder/>
117 <numThreads>1</numThreads>
118 <batchSize>1</batchSize>
119 <emailAddress/>
120 <smtpHost/>
121 <emailFromAddress/>
122 <fixedCombinedFolder/>
123 <fullMinMz>-1.79769313486232E+308</fullMinMz>
124 <fullMaxMz>1.79769313486232E+308</fullMaxMz>
125 <sendEmail>False</sendEmail>
126 <ionCountIntensities>False</ionCountIntensities>
127 <verboseColumnHeaders>False</verboseColumnHeaders>
128 <calcPeakProperties>False</calcPeakProperties>
129 <showCentroidMassDifferences>False</showCentroidMassDifferences>
130 <showIsotopeMassDifferences>False</showIsotopeMassDifferences>
131 <useDotNetCore>True</useDotNetCore>
132 <profilePerformance>False</profilePerformance>
133 <filePaths>
134 <string>BSA_min_21.mzXML</string>
135 <string>BSA_min_22.mzxml</string>
136 </filePaths>
137 <experiments>
138 <string/>
139 <string/>
140 </experiments>
141 <fractions>
142 <short>32767</short>
143 <short>32767</short>
144 </fractions>
145 <ptms>
146 <boolean>False</boolean>
147 <boolean>False</boolean>
148 </ptms>
149 <paramGroupIndices>
150 <int>0</int>
151 <int>0</int>
152 </paramGroupIndices>
153 <referenceChannel>
154 <string/>
155 <string/>
156 </referenceChannel>
157 <intensPred>False</intensPred>
158 <intensPredModelReTrain>False</intensPredModelReTrain>
159 <parameterGroups>
160 <parameterGroup>
161 <msInstrument>0</msInstrument>
162 <maxCharge>7</maxCharge>
163 <minPeakLen>2</minPeakLen>
164 <diaMinPeakLen>2</diaMinPeakLen>
165 <useMs1Centroids>False</useMs1Centroids>
166 <useMs2Centroids>False</useMs2Centroids>
167 <cutPeaks>True</cutPeaks>
168 <gapScans>1</gapScans>
169 <minTime>NaN</minTime>
170 <maxTime>NaN</maxTime>
171 <matchType>MatchFromAndTo</matchType>
172 <intensityDetermination>0</intensityDetermination>
173 <centroidMatchTol>8</centroidMatchTol>
174 <centroidMatchTolInPpm>True</centroidMatchTolInPpm>
175 <centroidHalfWidth>35</centroidHalfWidth>
176 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
177 <valleyFactor>1.4</valleyFactor>
178 <isotopeValleyFactor>1.2</isotopeValleyFactor>
179 <advancedPeakSplitting>False</advancedPeakSplitting>
180 <intensityThresholdMs1>0</intensityThresholdMs1>
181 <intensityThresholdMs2>0</intensityThresholdMs2>
182 <labelMods>
183 <string/>
184 </labelMods>
185 <lcmsRunType>Standard</lcmsRunType>
186 <reQuantify>False</reQuantify>
187 <lfqMode>0</lfqMode>
188 <lfqSkipNorm>False</lfqSkipNorm>
189 <lfqNormClusterSize>80</lfqNormClusterSize>
190 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
191 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
192 <lfqMaxFeatures>100000</lfqMaxFeatures>
193 <neucodeMaxPpm>0</neucodeMaxPpm>
194 <neucodeResolution>0</neucodeResolution>
195 <neucodeResolutionInMda>False</neucodeResolutionInMda>
196 <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
197 <fastLfq>True</fastLfq>
198 <lfqRestrictFeatures>False</lfqRestrictFeatures>
199 <lfqMinRatioCount>2</lfqMinRatioCount>
200 <maxLabeledAa>0</maxLabeledAa>
201 <maxNmods>5</maxNmods>
202 <maxMissedCleavages>0</maxMissedCleavages>
203 <multiplicity>1</multiplicity>
204 <enzymeMode>0</enzymeMode>
205 <complementaryReporterType>0</complementaryReporterType>
206 <reporterNormalization>0</reporterNormalization>
207 <neucodeIntensityMode>0</neucodeIntensityMode>
208 <fixedModifications>
209 <string>Carbamidomethyl (C)</string>
210 </fixedModifications>
211 <enzymes>
212 <string>Trypsin/P</string>
213 </enzymes>
214 <enzymesFirstSearch>
215 </enzymesFirstSearch>
216 <enzymeModeFirstSearch>0</enzymeModeFirstSearch>
217 <useEnzymeFirstSearch>False</useEnzymeFirstSearch>
218 <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
219 <variableModifications>
220 <string>Oxidation (M)</string>
221 <string>Acetyl (Protein N-term)</string>
222 </variableModifications>
223 <useMultiModification>False</useMultiModification>
224 <multiModifications>
225 </multiModifications>
226 <isobaricLabels>
227 </isobaricLabels>
228 <neucodeLabels>
229 </neucodeLabels>
230 <variableModificationsFirstSearch>
231 </variableModificationsFirstSearch>
232 <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
233 <additionalVariableModifications>
234 </additionalVariableModifications>
235 <additionalVariableModificationProteins>
236 </additionalVariableModificationProteins>
237 <doMassFiltering>True</doMassFiltering>
238 <firstSearchTol>20</firstSearchTol>
239 <mainSearchTol>4.5</mainSearchTol>
240 <searchTolInPpm>True</searchTolInPpm>
241 <isotopeMatchTol>2</isotopeMatchTol>
242 <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
243 <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
244 <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
245 <checkMassDeficit>True</checkMassDeficit>
246 <recalibrationInPpm>True</recalibrationInPpm>
247 <intensityDependentCalibration>False</intensityDependentCalibration>
248 <minScoreForCalibration>70</minScoreForCalibration>
249 <matchLibraryFile>False</matchLibraryFile>
250 <libraryFile/>
251 <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
252 <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
253 <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
254 <reporterMassTolerance>NaN</reporterMassTolerance>
255 <reporterPif>NaN</reporterPif>
256 <filterPif>False</filterPif>
257 <reporterFraction>NaN</reporterFraction>
258 <reporterBasePeakRatio>NaN</reporterBasePeakRatio>
259 <timsHalfWidth>0</timsHalfWidth>
260 <timsStep>0</timsStep>
261 <timsResolution>0</timsResolution>
262 <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
263 <timsRemovePrecursor>True</timsRemovePrecursor>
264 <timsIsobaricLabels>False</timsIsobaricLabels>
265 <timsCollapseMsms>True</timsCollapseMsms>
266 <crossLinkingType>0</crossLinkingType>
267 <crossLinker/>
268 <minMatchXl>0</minMatchXl>
269 <minPairedPepLenXl>6</minPairedPepLenXl>
270 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
271 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
272 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
273 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
274 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
275 <crosslinkModifications>
276 </crosslinkModifications>
277 <crosslinkFastaFiles>
278 </crosslinkFastaFiles>
279 <crosslinkSites>
280 </crosslinkSites>
281 <crosslinkNetworkFiles>
282 </crosslinkNetworkFiles>
283 <crosslinkMode/>
284 <peakRefinement>False</peakRefinement>
285 <isobaricSumOverWindow>True</isobaricSumOverWindow>
286 <isobaricWeightExponent>0.75</isobaricWeightExponent>
287 <diaLibraryType>0</diaLibraryType>
288 <diaLibraryPath/>
289 <diaPeptidePaths>
290 </diaPeptidePaths>
291 <diaEvidencePaths>
292 </diaEvidencePaths>
293 <diaMsmsPaths>
294 </diaMsmsPaths>
295 <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
296 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
297 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
298 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
299 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
300 <diaScoreN>7</diaScoreN>
301 <diaMinScore>2.99</diaMinScore>
302 <diaXgBoostBaseScore>0.4</diaXgBoostBaseScore>
303 <diaXgBoostSubSample>0.9</diaXgBoostSubSample>
304 <centroidPosition>0</centroidPosition>
305 <diaQuantMethod>7</diaQuantMethod>
306 <diaFeatureQuantMethod>2</diaFeatureQuantMethod>
307 <lfqNormType>1</lfqNormType>
308 <diaTopNForQuant>10</diaTopNForQuant>
309 <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant>
310 <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant>
311 <diaPrecursorFilterType>0</diaPrecursorFilterType>
312 <diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore>
313 <diaMinPrecursorScore>0.5</diaMinPrecursorScore>
314 <diaMinProfileCorrelation>0</diaMinProfileCorrelation>
315 <diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight>
316 <diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth>
317 <diaXgBoostEstimators>580</diaXgBoostEstimators>
318 <diaXgBoostGamma>0.9</diaXgBoostGamma>
319 <diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep>
320 <diaGlobalMl>True</diaGlobalMl>
321 <diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy>
322 <diaMassWindowFactor>3.3</diaMassWindowFactor>
323 <diaRtPrediction>False</diaRtPrediction>
324 <diaRtPredictionSecondRound>False</diaRtPredictionSecondRound>
325 <diaNoMl>False</diaNoMl>
326 <diaPermuteRt>False</diaPermuteRt>
327 <diaPermuteCcs>False</diaPermuteCcs>
328 <diaBackgroundSubtraction>False</diaBackgroundSubtraction>
329 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile>
330 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>
331 <diaLfqWeightedMedian>False</diaLfqWeightedMedian>
332 </parameterGroup>
333 </parameterGroups>
334 <msmsParamsArray>
335 <msmsParams>
336 <Name>FTMS</Name>
337 <MatchTolerance>20</MatchTolerance>
338 <MatchToleranceInPpm>True</MatchToleranceInPpm>
339 <DeisotopeTolerance>7</DeisotopeTolerance>
340 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
341 <DeNovoTolerance>10</DeNovoTolerance>
342 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
343 <Deisotope>True</Deisotope>
344 <Topx>12</Topx>
345 <TopxInterval>100</TopxInterval>
346 <HigherCharges>True</HigherCharges>
347 <IncludeWater>True</IncludeWater>
348 <IncludeAmmonia>True</IncludeAmmonia>
349 <DependentLosses>True</DependentLosses>
350 <Recalibration>False</Recalibration>
351 </msmsParams>
352 <msmsParams>
353 <Name>ITMS</Name>
354 <MatchTolerance>0.5</MatchTolerance>
355 <MatchToleranceInPpm>False</MatchToleranceInPpm>
356 <DeisotopeTolerance>0.15</DeisotopeTolerance>
357 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
358 <DeNovoTolerance>0.25</DeNovoTolerance>
359 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
360 <Deisotope>False</Deisotope>
361 <Topx>8</Topx>
362 <TopxInterval>100</TopxInterval>
363 <HigherCharges>True</HigherCharges>
364 <IncludeWater>True</IncludeWater>
365 <IncludeAmmonia>True</IncludeAmmonia>
366 <DependentLosses>True</DependentLosses>
367 <Recalibration>False</Recalibration>
368 </msmsParams>
369 <msmsParams>
370 <Name>TOF</Name>
371 <MatchTolerance>40</MatchTolerance>
372 <MatchToleranceInPpm>True</MatchToleranceInPpm>
373 <DeisotopeTolerance>0.01</DeisotopeTolerance>
374 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
375 <DeNovoTolerance>0.02</DeNovoTolerance>
376 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
377 <Deisotope>True</Deisotope>
378 <Topx>10</Topx>
379 <TopxInterval>100</TopxInterval>
380 <HigherCharges>True</HigherCharges>
381 <IncludeWater>True</IncludeWater>
382 <IncludeAmmonia>True</IncludeAmmonia>
383 <DependentLosses>True</DependentLosses>
384 <Recalibration>False</Recalibration>
385 </msmsParams>
386 <msmsParams>
387 <Name>Unknown</Name>
388 <MatchTolerance>20</MatchTolerance>
389 <MatchToleranceInPpm>True</MatchToleranceInPpm>
390 <DeisotopeTolerance>7</DeisotopeTolerance>
391 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
392 <DeNovoTolerance>10</DeNovoTolerance>
393 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
394 <Deisotope>True</Deisotope>
395 <Topx>12</Topx>
396 <TopxInterval>100</TopxInterval>
397 <HigherCharges>True</HigherCharges>
398 <IncludeWater>True</IncludeWater>
399 <IncludeAmmonia>True</IncludeAmmonia>
400 <DependentLosses>True</DependentLosses>
401 <Recalibration>False</Recalibration>
402 </msmsParams>
403 </msmsParamsArray>
404 <fragmentationParamsArray>
405 <fragmentationParams>
406 <Name>CID</Name>
407 <Connected>False</Connected>
408 <ConnectedScore0>1</ConnectedScore0>
409 <ConnectedScore1>1</ConnectedScore1>
410 <ConnectedScore2>1</ConnectedScore2>
411 <InternalFragments>False</InternalFragments>
412 <InternalFragmentWeight>1</InternalFragmentWeight>
413 <InternalFragmentAas>KRH</InternalFragmentAas>
414 </fragmentationParams>
415 <fragmentationParams>
416 <Name>HCD</Name>
417 <Connected>False</Connected>
418 <ConnectedScore0>1</ConnectedScore0>
419 <ConnectedScore1>1</ConnectedScore1>
420 <ConnectedScore2>1</ConnectedScore2>
421 <InternalFragments>False</InternalFragments>
422 <InternalFragmentWeight>1</InternalFragmentWeight>
423 <InternalFragmentAas>KRH</InternalFragmentAas>
424 </fragmentationParams>
425 <fragmentationParams>
426 <Name>ETD</Name>
427 <Connected>False</Connected>
428 <ConnectedScore0>1</ConnectedScore0>
429 <ConnectedScore1>1</ConnectedScore1>
430 <ConnectedScore2>1</ConnectedScore2>
431 <InternalFragments>False</InternalFragments>
432 <InternalFragmentWeight>1</InternalFragmentWeight>
433 <InternalFragmentAas>KRH</InternalFragmentAas>
434 </fragmentationParams>
435 <fragmentationParams>
436 <Name>PQD</Name>
437 <Connected>False</Connected>
438 <ConnectedScore0>1</ConnectedScore0>
439 <ConnectedScore1>1</ConnectedScore1>
440 <ConnectedScore2>1</ConnectedScore2>
441 <InternalFragments>False</InternalFragments>
442 <InternalFragmentWeight>1</InternalFragmentWeight>
443 <InternalFragmentAas>KRH</InternalFragmentAas>
444 </fragmentationParams>
445 <fragmentationParams>
446 <Name>ETHCD</Name>
447 <Connected>False</Connected>
448 <ConnectedScore0>1</ConnectedScore0>
449 <ConnectedScore1>1</ConnectedScore1>
450 <ConnectedScore2>1</ConnectedScore2>
451 <InternalFragments>False</InternalFragments>
452 <InternalFragmentWeight>1</InternalFragmentWeight>
453 <InternalFragmentAas>KRH</InternalFragmentAas>
454 </fragmentationParams>
455 <fragmentationParams>
456 <Name>ETCID</Name>
457 <Connected>False</Connected>
458 <ConnectedScore0>1</ConnectedScore0>
459 <ConnectedScore1>1</ConnectedScore1>
460 <ConnectedScore2>1</ConnectedScore2>
461 <InternalFragments>False</InternalFragments>
462 <InternalFragmentWeight>1</InternalFragmentWeight>
463 <InternalFragmentAas>KRH</InternalFragmentAas>
464 </fragmentationParams>
465 <fragmentationParams>
466 <Name>UVPD</Name>
467 <Connected>False</Connected>
468 <ConnectedScore0>1</ConnectedScore0>
469 <ConnectedScore1>1</ConnectedScore1>
470 <ConnectedScore2>1</ConnectedScore2>
471 <InternalFragments>False</InternalFragments>
472 <InternalFragmentWeight>1</InternalFragmentWeight>
473 <InternalFragmentAas>KRH</InternalFragmentAas>
474 </fragmentationParams>
475 <fragmentationParams>
476 <Name>Unknown</Name>
477 <Connected>False</Connected>
478 <ConnectedScore0>1</ConnectedScore0>
479 <ConnectedScore1>1</ConnectedScore1>
480 <ConnectedScore2>1</ConnectedScore2>
481 <InternalFragments>False</InternalFragments>
482 <InternalFragmentWeight>1</InternalFragmentWeight>
483 <InternalFragmentAas>KRH</InternalFragmentAas>
484 </fragmentationParams>
485 </fragmentationParamsArray>
486 </MaxQuantParams>
487