Mercurial > repos > galaxyp > msconvert_nix

annotate test-data/small-threshold.mzML @ 1:7016f1f10f42 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
author galaxyp
date Tue, 14 Mar 2017 16:45:30 -0400
parents baa6c072fccc
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">
1
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5 <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
0
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6 <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/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:///C:\pwiz-src\trunk\pwiz\example_data">
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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:///">
1
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23 <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2d5cdd239d18de37386cf9409e30693767b16f82"/>
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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>
1
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40 <software id="pwiz_3.0.9987" version="3.0.9987">
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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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parents:
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1942 <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="1.6495375e07"/>
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1943 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="200.00018816645" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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1944 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="2000.009946620377" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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diff changeset
1945 <scanList count="1">
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1946 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
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1947 <scan>
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1948 <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="0.358558333333" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
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1949 <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="FTMS + p ESI Full ms [200.00-2000.00]"/>
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1950 <cvParam cvRef="MS" accession="MS:1000616" name="preset scan configuration" value="1"/>
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1951 <cvParam cvRef="MS" accession="MS:1000927" name="ion injection time" value="66.962379455566" unitCvRef="UO" unitAccession="UO:0000028" unitName="millisecond"/>
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1952 <scanWindowList count="1">
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1953 <scanWindow>
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1954 <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="200.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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1955 <cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="2000.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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1956 </scanWindow>
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1957 </scanWindowList>
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1958 </scan>
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1959 </scanList>
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1960 <binaryDataArrayList count="2">
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1961 <binaryDataArray encodedLength="512">
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1962 <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>
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1963 <cvParam cvRef="MS" accession="MS:1002312" name="MS-Numpress linear prediction compression" value=""/>
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1964 <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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1965 <binary>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</binary>
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1966 </binaryDataArray>
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1967 <binaryDataArray encodedLength="356">
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1968 <cvParam cvRef="MS" accession="MS:1000519" name="32-bit integer" value=""/>
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1969 <cvParam cvRef="MS" accession="MS:1002313" name="MS-Numpress positive integer compression" value=""/>
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1970 <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
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parents:
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1971 <binary>S7+EZNxP9OQHVko95BfXR0ZUETtAhlQu2kyxdBqrOf5RMPlRRvWksLlIo0SgB07ZRGMaMjLBRV6DtNMj5kIUUvVHa4SSZkQHU90zI4lWFEvWTF3U66ZOIJRdVj+SYjvlwUL3xBz8T/WkFPZHWpROikDSpPBGI/aKEvt7UTdcOjXVokcdhFCWQ6FULX9MceSHtUC9tJF5R9lDL8LTbwDD6TdTEA4U+uZHXkTphUTtxBd5STxESlRFxkS1FUhkY1J0E0YWFB35TUZDVzxzaaM0XBtA05S1BUhnZLRlSTZD01Qj0sAUBlZDQVQ1CUajhJfFQ1hE3SZHrmOOUiPdCBRAyjSsoTSeQU4iwA==</binary>
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1972 </binaryDataArray>
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1973 </binaryDataArrayList>
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1974 </spectrum>
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1975 <spectrum index="35" id="controllerType=0 controllerNumber=1 scan=36" defaultArrayLength="100" dataProcessingRef="pwiz_Reader_conversion">
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1976 <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
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1977 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
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1978 <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
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parents:
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1979 <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
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parents:
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1980 <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="810.545532226563" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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parents:
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1981 <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="1.057720703125e05" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
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parents:
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1982 <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="6.5487065e06"/>
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parents:
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1983 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="200.090909093618" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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parents:
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1984 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="2000.00005364418" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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parents:
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1985 <scanList count="1">
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1986 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
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parents:
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1987 <scan instrumentConfigurationRef="IC2">
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parents:
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1988 <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="0.361428333333" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
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parents:
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1989 <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="ITMS + p ESI Full ms [200.00-2000.00]"/>
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1990 <cvParam cvRef="MS" accession="MS:1000616" name="preset scan configuration" value="2"/>
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1991 <cvParam cvRef="MS" accession="MS:1000927" name="ion injection time" value="1.416100502014" unitCvRef="UO" unitAccession="UO:0000028" unitName="millisecond"/>
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parents:
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1992 <scanWindowList count="1">
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1993 <scanWindow>
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1994 <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="200.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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1995 <cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="2000.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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1996 </scanWindow>
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1997 </scanWindowList>
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1998 </scan>
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1999 </scanList>
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2000 <binaryDataArrayList count="2">
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2001 <binaryDataArray encodedLength="532">
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2002 <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>
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2003 <cvParam cvRef="MS" accession="MS:1002312" name="MS-Numpress linear prediction compression" value=""/>
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2004 <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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diff changeset
2006 </binaryDataArray>
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2007 <binaryDataArray encodedLength="296">
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2008 <cvParam cvRef="MS" accession="MS:1000519" name="32-bit integer" value=""/>
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diff changeset
2009 <cvParam cvRef="MS" accession="MS:1002313" name="MS-Numpress positive integer compression" value=""/>
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diff changeset
2010 <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
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2011 <binary>VP1U2FI5XshZyURVFEhhUg1PsxXetdqE1oJdilB5XdtV2FS9VTtV/Fj4WIhVOVq8VlxaDEUvJbS1cKTkEVhdXJlZmEoRJLACXH9TqE9uFFXBVahSWEmhFUGkYhFeXFsLVo9d/kvCFcfEg+NBTSShEUlAFdeEUBFLWSTuMk8yFPYBV9he+V5ZQutEApFHaBVotTvVdNW+lTa1faTDQTwtkTLsMUihFHvxQZMUZdpAPKSwQlpPXttJAhVPhR3UWqFeq0qhNIvRVNtXLFG4QcEVzIXahQyU3iFaq0RGFLMB</binary>
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diff changeset
2012 </binaryDataArray>
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diff changeset
2013 </binaryDataArrayList>
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2014 </spectrum>
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2015 <spectrum index="36" id="controllerType=0 controllerNumber=1 scan=37" defaultArrayLength="100" dataProcessingRef="pwiz_Reader_conversion">
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2016 <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
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2017 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2"/>
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2018 <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
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2019 <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
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2025 <scanList count="1">
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2027 <scan instrumentConfigurationRef="IC2">
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2030 <cvParam cvRef="MS" accession="MS:1000616" name="preset scan configuration" value="3"/>
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2032 <userParam name="[Thermo Trailer Extra]Monoisotopic M/Z:" value="0" type="xsd:float"/>
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2034 <scanWindow>
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2037 </scanWindow>
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2038 </scanWindowList>
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2039 </scan>
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2040 </scanList>
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2041 <precursorList count="1">
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2042 <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=36">
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2043 <isolationWindow>
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2047 </isolationWindow>
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2048 <selectedIonList count="1">
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2049 <selectedIon>
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2052 </selectedIon>
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2053 </selectedIonList>
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2057 </activation>
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2058 </precursor>
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2059 </precursorList>
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7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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