annotate test-data/small-index-filter.mzML @ 17:ab6c14374bc0 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit e3d24f3dc7a9812f8fa4447c9391e5bd3b5d4dc6
author galaxyp
date Thu, 15 Aug 2024 16:19:28 +0000
parents 6153e8ada1ee
children
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd">
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3 <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="small" version="1.1.0">
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4 <cvList count="2">
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5 <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
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6 <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>
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7 </cvList>
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8 <fileDescription>
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9 <fileContent>
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10 <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
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11 <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
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12 </fileContent>
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13 <sourceFileList count="3">
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14 <sourceFile id="RAW1" name="small.RAW" location="file:///">
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15 <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>
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16 <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/>
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17 <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="b43e9286b40e8b5dbc0dfa2e428495769ca96a96"/>
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18 </sourceFile>
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19 <sourceFile id="small.mzML" name="small.mzML" location="file:///">
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20 <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>
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21 </sourceFile>
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22 <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">
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23 <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>
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24 </sourceFile>
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25 </sourceFileList>
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26 </fileDescription>
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27 <referenceableParamGroupList count="1">
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28 <referenceableParamGroup id="CommonInstrumentParams">
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29 <cvParam cvRef="MS" accession="MS:1000448" name="LTQ FT" value=""/>
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30 <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/>
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31 </referenceableParamGroup>
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32 </referenceableParamGroupList>
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33 <softwareList count="3">
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34 <software id="Xcalibur" version="1.1 Beta 7">
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35 <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>
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36 </software>
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37 <software id="pwiz" version="3.0.8981">
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38 <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
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39 </software>
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40 <software id="pwiz_3.0.20287" version="3.0.20287">
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41 <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
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42 </software>
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43 </softwareList>
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44 <instrumentConfigurationList count="2">
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45 <instrumentConfiguration id="IC1">
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46 <referenceableParamGroupRef ref="CommonInstrumentParams"/>
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47 <componentList count="3">
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48 <source order="1">
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49 <cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization" value=""/>
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50 <cvParam cvRef="MS" accession="MS:1000057" name="electrospray inlet" value=""/>
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51 </source>
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52 <analyzer order="2">
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53 <cvParam cvRef="MS" accession="MS:1000079" name="fourier transform ion cyclotron resonance mass spectrometer" value=""/>
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54 </analyzer>
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55 <detector order="3">
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56 <cvParam cvRef="MS" accession="MS:1000624" name="inductive detector" value=""/>
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57 </detector>
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58 </componentList>
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59 <softwareRef ref="Xcalibur"/>
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60 </instrumentConfiguration>
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61 <instrumentConfiguration id="IC2">
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62 <referenceableParamGroupRef ref="CommonInstrumentParams"/>
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63 <componentList count="3">
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64 <source order="1">
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65 <cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization" value=""/>
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66 <cvParam cvRef="MS" accession="MS:1000057" name="electrospray inlet" value=""/>
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67 </source>
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68 <analyzer order="2">
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69 <cvParam cvRef="MS" accession="MS:1000083" name="radial ejection linear ion trap" value=""/>
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70 </analyzer>
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71 <detector order="3">
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72 <cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier" value=""/>
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73 </detector>
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74 </componentList>
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75 <softwareRef ref="Xcalibur"/>
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76 </instrumentConfiguration>
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77 </instrumentConfigurationList>
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78 <dataProcessingList count="2">
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79 <dataProcessing id="pwiz_Reader_Thermo_conversion">
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80 <processingMethod order="0" softwareRef="pwiz">
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81 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
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82 </processingMethod>
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83 </dataProcessing>
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84 <dataProcessing id="pwiz_Reader_conversion">
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85 <processingMethod order="0" softwareRef="pwiz_3.0.20287">
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86 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
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87 </processingMethod>
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88 <processingMethod order="1" softwareRef="pwiz_3.0.20287">
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89 <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
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90 <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
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91 </processingMethod>
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92 </dataProcessing>
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93 </dataProcessingList>
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94 <run id="small" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2005-07-20T14:44:22Z" defaultSourceFileRef="RAW1">
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95 <spectrumList count="7" defaultDataProcessingRef="pwiz_Reader_conversion">
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96 <spectrum index="0" id="controllerType=0 controllerNumber=1 scan=3" defaultArrayLength="485">
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97 <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
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98 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2"/>
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99 <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
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100 <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
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101 <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="736.637084960938" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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102 <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="1.61140859375e05" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
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103 <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="5.86279e05"/>
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104 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="231.38883972168" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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115 <scanWindow>
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119 </scanWindowList>
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120 </scan>
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121 </scanList>
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128 </isolationWindow>
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133 </selectedIon>
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134 </selectedIonList>
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135 <activation>
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138 </activation>
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139 </precursor>
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140 </precursorList>
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145 <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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199 </precursor>
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215 </spectrum>
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216 <spectrum index="2" id="controllerType=0 controllerNumber=1 scan=5" defaultArrayLength="837">
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217 <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
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218 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2"/>
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219 <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
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220 <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
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221 <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="578.985595703125" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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222 <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="8601.798828125" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
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223 <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="1.14331703125e05"/>
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224 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="203.22233581543" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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225 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="1412.570434570313" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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226 <scanList count="1">
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227 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
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228 <scan instrumentConfigurationRef="IC2">
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229 <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="0.034925" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
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230 <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="ITMS + c ESI d Full ms2 725.36@cid35.00 [185.00-1465.00]"/>
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231 <cvParam cvRef="MS" accession="MS:1000616" name="preset scan configuration" value="5"/>
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232 <cvParam cvRef="MS" accession="MS:1000927" name="ion injection time" value="57.43083190918" unitCvRef="UO" unitAccession="UO:0000028" unitName="millisecond"/>
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233 <userParam name="[Thermo Trailer Extra]Monoisotopic M/Z:" value="0" type="xsd:float"/>
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234 <scanWindowList count="1">
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235 <scanWindow>
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236 <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="185.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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237 <cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="1465.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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238 </scanWindow>
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239 </scanWindowList>
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240 </scan>
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241 </scanList>
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242 <precursorList count="1">
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243 <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=2">
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244 <isolationWindow>
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245 <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="725.36" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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246 <cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="1.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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247 <cvParam cvRef="MS" accession="MS:1000829" name="isolation window upper offset" value="1.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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248 </isolationWindow>
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249 <selectedIonList count="1">
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250 <selectedIon>
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251 <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="725.36" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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252 <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="28425.76953125" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
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253 </selectedIon>
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254 </selectedIonList>
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255 <activation>
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256 <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
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257 <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="35.0" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
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258 </activation>
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259 </precursor>
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260 </precursorList>
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261 <binaryDataArrayList count="2">
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262 <binaryDataArray encodedLength="3864">
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263 <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>
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264 <cvParam cvRef="MS" accession="MS:1002312" name="MS-Numpress linear prediction compression" value=""/>
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265 <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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267 </binaryDataArray>
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269 <cvParam cvRef="MS" accession="MS:1000519" name="32-bit integer" value=""/>
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270 <cvParam cvRef="MS" accession="MS:1002313" name="MS-Numpress positive integer compression" value=""/>
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271 <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
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298 </scanWindow>
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299 </scanWindowList>
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300 </scan>
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308 </isolationWindow>
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313 </selectedIon>
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314 </selectedIonList>
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315 <activation>
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316 <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
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318 </activation>
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319 </precursor>
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320 </precursorList>
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325 <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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378 </activation>
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379 </precursor>
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380 </precursorList>
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391 <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
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457 </scanWindow>
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458 </scanWindowList>
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459 </scan>
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470 <cvParam cvRef="MS" accession="MS:1002313" name="MS-Numpress positive integer compression" value=""/>
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471 <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
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474 </binaryDataArrayList>
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475 </spectrum>
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476 </spectrumList>
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490 <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
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495 </chromatogramList>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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496 </run>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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497 </mzML>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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498 <indexList count="2">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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499 <index name="spectrum">
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6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
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6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
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6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
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6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
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6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
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6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
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6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
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dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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507 </index>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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508 <index name="chromatogram">
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6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
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dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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510 </index>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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511 </indexList>
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6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
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6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
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dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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514 </indexedmzML>