view test-data/BrukerBafTest.mzML @ 13:9b61227976d6 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 298cdc1df4609ae9353107dc803af0cf190ded7c"
author galaxyp
date Sat, 25 Jul 2020 18:13:58 -0400
parents 9d5de24e6ef7
children 6153e8ada1ee
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line source

<?xml version="1.0" encoding="utf-8"?>
<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">
  <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="BrukerBafTest" version="1.1.0">
    <cvList count="2">
      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
      <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>
    </cvList>
    <fileDescription>
      <fileContent>
        <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
      </fileContent>
      <sourceFileList count="1">
        <sourceFile id="BrukerBafTest.d_x005c_Analysis.baf" name="Analysis.baf" location="file:///">
          <cvParam cvRef="MS" accession="MS:1000772" name="Bruker BAF nativeID format" value=""/>
          <cvParam cvRef="MS" accession="MS:1000815" name="Bruker BAF format" value=""/>
          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="5e1b8f06983c2e671a4a96714721c327f1e67ee1"/>
        </sourceFile>
      </sourceFileList>
    </fileDescription>
    <referenceableParamGroupList count="1">
      <referenceableParamGroup id="CommonInstrumentParams">
        <cvParam cvRef="MS" accession="MS:1001556" name="Bruker Daltonics apex series" value=""/>
      </referenceableParamGroup>
    </referenceableParamGroupList>
    <softwareList count="3">
      <software id="BAF2SQL" version="2.7.300.20-112">
        <cvParam cvRef="MS" accession="MS:1000692" name="Bruker software" value=""/>
        <userParam name="software name" value="BAF2SQL"/>
      </software>
      <software id="apexControl" version="ApexControl 3.0.0.alpha.35 (development version, April 18, 2008)">
        <cvParam cvRef="MS" accession="MS:1000706" name="apexControl" value=""/>
      </software>
      <software id="pwiz_Reader_Bruker" version="3.0.19044">
        <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
      </software>
    </softwareList>
    <instrumentConfigurationList count="1">
      <instrumentConfiguration id="IC1">
        <referenceableParamGroupRef ref="CommonInstrumentParams"/>
        <componentList count="3">
          <source order="1">
            <cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization" value=""/>
            <cvParam cvRef="MS" accession="MS:1000057" name="electrospray inlet" value=""/>
          </source>
          <analyzer order="2">
            <cvParam cvRef="MS" accession="MS:1000079" name="fourier transform ion cyclotron resonance mass spectrometer" value=""/>
          </analyzer>
          <detector order="3">
            <cvParam cvRef="MS" accession="MS:1000624" name="inductive detector" value=""/>
          </detector>
        </componentList>
        <softwareRef ref="apexControl"/>
      </instrumentConfiguration>
    </instrumentConfigurationList>
    <dataProcessingList count="1">
      <dataProcessing id="pwiz_Reader_Bruker_conversion">
        <processingMethod order="0" softwareRef="pwiz_Reader_Bruker">
          <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
        </processingMethod>
        <processingMethod order="1" softwareRef="pwiz_Reader_Bruker">
          <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
          <userParam name="Bruker/Agilent/CompassXtract peak picking"/>
        </processingMethod>
      </dataProcessing>
    </dataProcessingList>
    <run id="BrukerBafTest" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2008-11-04T10:55:29Z" defaultSourceFileRef="BrukerBafTest.d_x005c_Analysis.baf">
      <spectrumList count="1" defaultDataProcessingRef="pwiz_Reader_Bruker_conversion">
        <spectrum index="0" id="scan=1" defaultArrayLength="71">
          <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
          <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
          <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
          <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="7.81485056e08"/>
          <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="5.704013312e09"/>
          <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
          <scanList count="1">
            <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
            <scan>
              <scanWindowList count="1">
                <scanWindow>
                  <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="347.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                  <cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="2000.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                </scanWindow>
              </scanWindowList>
            </scan>
          </scanList>
          <binaryDataArrayList count="2">
            <binaryDataArray encodedLength="744">
              <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
              <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/>
              <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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            </binaryDataArray>
            <binaryDataArray encodedLength="396">
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            </binaryDataArray>
          </binaryDataArrayList>
        </spectrum>
      </spectrumList>
    </run>
  </mzML>
  <indexList count="2">
    <index name="spectrum">
      <offset idRef="scan=1">4166</offset>
    </index>
    <index name="chromatogram">
    </index>
  </indexList>
  <indexListOffset>7590</indexListOffset>
  <fileChecksum>e6b4d51fdbe306f0823fe1cb583e7ec52629303f</fileChecksum>
</indexedmzML>