view test-data/peak_detection2.imzml @ 3:36d38d2cf88c draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
author galaxyp
date Fri, 15 Feb 2019 10:26:45 -0500
parents
children 160538a890a6
line wrap: on
line source

<?xml version="1.0" encoding="utf-8"?>
<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="out" version="1.1.0">
 <cvList count="2">
  <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.44.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
  <cv id="UO" fullName="Unit Ontology" version="12:10:2012" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
  <cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo"/>
 </cvList>
 <fileDescription>
  <fileContent>
   <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>
   <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{cc20fc46-860b-42cc-91a3-69e42329f338}"/>
   <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="64664d4479a6efec0398b19c652ffa2688d95d92"/>
   <cvParam cvRef="IMS" accession="IMS:1000031" name="processed"/>
   <userParam name="MALDIquantForeign" value="MALDIquant object(s) exported to mzML"/>
  </fileContent>
 </fileDescription>
 <softwareList count="1">
  <software id="MALDIquantForeign" version="0.11.5"/>
 </softwareList>
 <referenceableParamGroupList count="2">
  <referenceableParamGroup id="mzArray">
   <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
   <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
   <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
   <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
  </referenceableParamGroup>
  <referenceableParamGroup id="intensityArray">
   <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>
   <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
   <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
   <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
  </referenceableParamGroup>
 </referenceableParamGroupList>
 <scanSettingsList count="1">
  <scanSettings id="scansetting1">
   <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3"/>
   <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3"/>
   <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
   <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
   <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="100" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
   <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="100" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
  </scanSettings>
 </scanSettingsList>
 <instrumentConfigurationList count="1">
  <instrumentConfiguration id="IC0"/>
 </instrumentConfigurationList>
 <dataProcessingList count="1">
  <dataProcessing id="export">
   <processingMethod order="1" softwareRef="MALDIquantForeign">
    <userParam name="MALDIquant object(s) exported to mzML" value=""/>
   </processingMethod>
  </dataProcessing>
 </dataProcessingList>
 <run id="run0" defaultInstrumentConfigurationRef="IC0">
  <spectrumList count="9" defaultDataProcessingRef="export">
   <spectrum index="0" id="scan=0" defaultArrayLength="3">
    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
    <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="329.152786254883" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="367.645835876465" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
    <scanList count="1">
     <scan>
      <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
      <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
     </scan>
    </scanList>
    <binaryDataArrayList count="2">
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="mzArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="3"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="24"/>
      <binary/>
     </binaryDataArray>
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="intensityArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="40"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="3"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="24"/>
      <binary/>
     </binaryDataArray>
    </binaryDataArrayList>
   </spectrum>
   <spectrum index="1" id="scan=1" defaultArrayLength="3">
    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
    <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="329.152786254883" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="366.562515258789" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
    <scanList count="1">
     <scan>
      <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>
      <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
     </scan>
    </scanList>
    <binaryDataArrayList count="2">
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="mzArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="64"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="3"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="24"/>
      <binary/>
     </binaryDataArray>
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="intensityArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="88"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="3"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="24"/>
      <binary/>
     </binaryDataArray>
    </binaryDataArrayList>
   </spectrum>
   <spectrum index="2" id="scan=2" defaultArrayLength="2">
    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
    <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="329.152786254883" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="366.562515258789" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
    <scanList count="1">
     <scan>
      <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
      <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
     </scan>
    </scanList>
    <binaryDataArrayList count="2">
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="mzArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="112"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="16"/>
      <binary/>
     </binaryDataArray>
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="intensityArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="128"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="16"/>
      <binary/>
     </binaryDataArray>
    </binaryDataArrayList>
   </spectrum>
   <spectrum index="3" id="scan=3" defaultArrayLength="1">
    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
    <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="308.266668701172" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="308.266668701172" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
    <scanList count="1">
     <scan>
      <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
      <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
     </scan>
    </scanList>
    <binaryDataArrayList count="2">
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="mzArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="144"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8"/>
      <binary/>
     </binaryDataArray>
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="intensityArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="152"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8"/>
      <binary/>
     </binaryDataArray>
    </binaryDataArrayList>
   </spectrum>
   <spectrum index="4" id="scan=4" defaultArrayLength="2">
    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
    <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="308.266668701172" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="329.697925567627" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
    <scanList count="1">
     <scan>
      <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>
      <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
     </scan>
    </scanList>
    <binaryDataArrayList count="2">
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="mzArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="160"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="16"/>
      <binary/>
     </binaryDataArray>
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="intensityArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="176"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="16"/>
      <binary/>
     </binaryDataArray>
    </binaryDataArrayList>
   </spectrum>
   <spectrum index="5" id="scan=5" defaultArrayLength="1">
    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
    <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="308.266668701172" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="308.266668701172" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
    <scanList count="1">
     <scan>
      <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
      <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
     </scan>
    </scanList>
    <binaryDataArrayList count="2">
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="mzArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="192"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8"/>
      <binary/>
     </binaryDataArray>
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="intensityArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="200"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8"/>
      <binary/>
     </binaryDataArray>
    </binaryDataArrayList>
   </spectrum>
   <spectrum index="6" id="scan=6" defaultArrayLength="2">
    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
    <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="329.697925567627" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="387.850006103516" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
    <scanList count="1">
     <scan>
      <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
      <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
     </scan>
    </scanList>
    <binaryDataArrayList count="2">
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="mzArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="208"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="16"/>
      <binary/>
     </binaryDataArray>
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="intensityArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="224"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="16"/>
      <binary/>
     </binaryDataArray>
    </binaryDataArrayList>
   </spectrum>
   <spectrum index="7" id="scan=7" defaultArrayLength="2">
    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
    <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="387.850006103516" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="394.791679382324" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
    <scanList count="1">
     <scan>
      <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>
      <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
     </scan>
    </scanList>
    <binaryDataArrayList count="2">
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="mzArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="240"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="16"/>
      <binary/>
     </binaryDataArray>
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="intensityArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="256"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="16"/>
      <binary/>
     </binaryDataArray>
    </binaryDataArrayList>
   </spectrum>
   <spectrum index="8" id="scan=8" defaultArrayLength="3">
    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
    <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="329.697925567627" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="394.791679382324" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
    <scanList count="1">
     <scan>
      <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
      <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
     </scan>
    </scanList>
    <binaryDataArrayList count="2">
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="mzArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="272"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="3"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="24"/>
      <binary/>
     </binaryDataArray>
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="intensityArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="296"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="3"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="24"/>
      <binary/>
     </binaryDataArray>
    </binaryDataArrayList>
   </spectrum>
  </spectrumList>
 </run>
</mzML>