Mercurial > repos > galaxyp > cardinal_spectra_plots

view test-data/Example_Processed.imzML @ 0:de334e98f1c1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
author galaxyp
date Mon, 01 Oct 2018 01:01:41 -0400
parents
children 889c9e3a2526
line wrap: on
line source

<?xml version="1.0" encoding="ISO-8859-1"?>
<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_idx.xsd" version="1.1">
  <cvList count="3">
    <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo"/>
    <cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/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" value=""/>
      <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value=""/>
      <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{9D501BDC-5344-4916-B7E9-7E795B02C856}"/>
      <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7E8FDB93053915D3EDB51B70AA0619AC209964DF"/>
      <cvParam cvRef="IMS" accession="IMS:1000031" name="processed" value=""/>
    </fileContent>
    <sourceFileList count="1">
      <sourceFile id="sf1" name="Example.raw" location="C:\Users\Thorsten Schramm\Documents\Promotion\imzML\Website\files\Beispiel-Dateien\Example images\">
        <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW file" value=""/>
        <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>
        <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7623BE263B25FF99FDF017154B86FAB742D4BB0B"/>
      </sourceFile>
    </sourceFileList>
    <contact>
      <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Thorsten Schramm"/>
      <cvParam cvRef="MS" accession="MS:1000590" name="contact organization" value="Institut für Anorganische und Analytische Chemie"/>
      <cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="Schubertstraße 60, Haus 16, Gießen, Germany"/>
      <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="thorsten.schramm@anorg.chemie.uni-.giessen.de"/>
    </contact>
  </fileDescription>
  <referenceableParamGroupList count="4">
    <referenceableParamGroup id="mzArray">
      <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
      <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
      <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
      <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>
    </referenceableParamGroup>
    <referenceableParamGroup id="intensityArray">
      <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
      <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>
      <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
      <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>
    </referenceableParamGroup>
    <referenceableParamGroup id="scan1">
      <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value=""/>
      <cvParam cvRef="MS" accession="MS:1000095" name="linear" value=""/>
      <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="ITMS - p NSI Full ms [100,00-800,00]"/>
    </referenceableParamGroup>
    <referenceableParamGroup id="spectrum1">
      <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
      <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
      <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value=""/>
      <cvParam cvRef="MS" accession="MS:1000129" name="negative scan" value=""/>
    </referenceableParamGroup>
  </referenceableParamGroupList>
  <sampleList count="1">
    <sample id="sample1" name="Sample1">
      <cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1"/>
    </sample>
  </sampleList>
  <softwareList count="2">
    <software id="Xcalibur" version="2.2">
      <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>
    </software>
    <software id="TMC" version="1.1 beta">
      <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value=""/>
    </software>
  </softwareList>
  <scanSettingsList count="1">
    <scanSettings id="scansettings1">
      <cvParam cvRef="IMS" accession="IMS:1000401" name="top down" value=""/>
      <cvParam cvRef="IMS" accession="IMS:1000413" name="flyback" value=""/>
      <cvParam cvRef="IMS" accession="IMS:1000480" name="horizontal line scan" value=""/>
      <cvParam cvRef="IMS" accession="IMS:1000491" name="linescan left right" value=""/>
      <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"/>
      <cvParam cvRef="MS" accession="MS:1000836" name="dried dropplet" value=""/>
      <cvParam cvRef="MS" accession="MS:1000835" name="matrix solution concentration" value="10"/>
      <cvParam cvRef="MS" accession="MS:1000834" name="matrix solution" value="DHB"/>
    </scanSettings>
  </scanSettingsList>
  <instrumentConfigurationList count="1">
    <instrumentConfiguration id="LTQFTUltra0">
      <cvParam cvRef="MS" accession="MS:1000557" name="LTQ FT Ultra" value=""/>
      <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="none"/>
      <componentList count="3">
        <source order="1">
          <cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization" value=""/>
          <cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet" value=""/>
          <cvParam cvRef="MS" accession="MS:1000843" name="wavelength" value="337"/>
          <cvParam cvRef="MS" accession="MS:1000844" name="focus diameter x" value="10"/>
          <cvParam cvRef="MS" accession="MS:1000845" name="focus diameter y" value="10"/>
          <cvParam cvRef="MS" accession="MS:1000846" name="pulse energy" value="10"/>
          <cvParam cvRef="MS" accession="MS:1000847" name="pulse duration" value="10"/>
          <cvParam cvRef="MS" accession="MS:1000848" name="attenuation" value="50"/>
          <cvParam cvRef="MS" accession="MS:1000850" name="gas laser" value=""/>
          <cvParam cvRef="IMS" accession="IMS:1000202" name="target material" value="Conductive Glas"/>
        </source>
        <analyzer order="2">
          <cvParam cvRef="MS" accession="MS:1000264" name="ion trap" value=""/>
          <cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
        </analyzer>
        <detector order="3">
          <cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier" value=""/>
          <cvParam cvRef="MS" accession="MS:1000120" name="transient recorder" value=""/>
        </detector>
      </componentList>
      <softwareRef ref="Xcalibur"/>
    </instrumentConfiguration>
  </instrumentConfigurationList>
  <dataProcessingList count="2">
    <dataProcessing id="XcaliburProcessing">
      <processingMethod order="1" softwareRef="Xcalibur">
        <cvParam cvRef="MS" accession="MS:1000594" name="low intensity data point removal" value=""/>
      </processingMethod>
    </dataProcessing>
    <dataProcessing id="TMCConversion">
      <processingMethod order="2" softwareRef="TMC">
        <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
      </processingMethod>
    </dataProcessing>
  </dataProcessingList>
  <run defaultInstrumentConfigurationRef="LTQFTUltra0" defaultSourceFileRef="sf1" id="Experiment01" sampleRef="sample1" startTimeStamp="2009-08-11T15:59:44">
    <spectrumList count="9" defaultDataProcessingRef="XcaliburProcessing">
      <spectrum id="Scan=1" defaultArrayLength="0" index="0">
        <referenceableParamGroupRef ref="spectrum1"/>
        <scanList count="1">
          <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
          <scan instrumentConfigurationRef="LTQFTUltra0">
            <referenceableParamGroupRef ref="scan1"/>
            <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:1000103" name="external array length" value="8399"/>
            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/>
            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
            <binary/>
          </binaryDataArray>
          <binaryDataArray encodedLength="0">
            <referenceableParamGroupRef ref="intensityArray"/>
            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="33612"/>
            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
            <binary/>
          </binaryDataArray>
        </binaryDataArrayList>
      </spectrum>
      <spectrum id="Scan=2" defaultArrayLength="0" index="1">
        <referenceableParamGroupRef ref="spectrum1"/>
        <scanList count="1">
          <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
          <scan instrumentConfigurationRef="LTQFTUltra0">
            <referenceableParamGroupRef ref="scan1"/>
            <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:1000103" name="external array length" value="8399"/>
            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="67208"/>
            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
            <binary/>
          </binaryDataArray>
          <binaryDataArray encodedLength="0">
            <referenceableParamGroupRef ref="intensityArray"/>
            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="100804"/>
            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
            <binary/>
          </binaryDataArray>
        </binaryDataArrayList>
      </spectrum>
      <spectrum id="Scan=3" defaultArrayLength="0" index="2">
        <referenceableParamGroupRef ref="spectrum1"/>
        <scanList count="1">
          <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
          <scan instrumentConfigurationRef="LTQFTUltra0">
            <referenceableParamGroupRef ref="scan1"/>
            <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:1000103" name="external array length" value="8399"/>
            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="134400"/>
            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
            <binary/>
          </binaryDataArray>
          <binaryDataArray encodedLength="0">
            <referenceableParamGroupRef ref="intensityArray"/>
            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="167996"/>
            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
            <binary/>
          </binaryDataArray>
        </binaryDataArrayList>
      </spectrum>
      <spectrum id="Scan=4" defaultArrayLength="0" index="3">
        <referenceableParamGroupRef ref="spectrum1"/>
        <scanList count="1">
          <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
          <scan instrumentConfigurationRef="LTQFTUltra0">
            <referenceableParamGroupRef ref="scan1"/>
            <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:1000103" name="external array length" value="8399"/>
            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="201592"/>
            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
            <binary/>
          </binaryDataArray>
          <binaryDataArray encodedLength="0">
            <referenceableParamGroupRef ref="intensityArray"/>
            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="235188"/>
            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
            <binary/>
          </binaryDataArray>
        </binaryDataArrayList>
      </spectrum>
      <spectrum id="Scan=5" defaultArrayLength="0" index="4">
        <referenceableParamGroupRef ref="spectrum1"/>
        <scanList count="1">
          <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
          <scan instrumentConfigurationRef="LTQFTUltra0">
            <referenceableParamGroupRef ref="scan1"/>
            <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:1000103" name="external array length" value="8399"/>
            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="268784"/>
            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
            <binary/>
          </binaryDataArray>
          <binaryDataArray encodedLength="0">
            <referenceableParamGroupRef ref="intensityArray"/>
            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="302380"/>
            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
            <binary/>
          </binaryDataArray>
        </binaryDataArrayList>
      </spectrum>
      <spectrum id="Scan=6" defaultArrayLength="0" index="5">
        <referenceableParamGroupRef ref="spectrum1"/>
        <scanList count="1">
          <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
          <scan instrumentConfigurationRef="LTQFTUltra0">
            <referenceableParamGroupRef ref="scan1"/>
            <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:1000103" name="external array length" value="8399"/>
            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="335976"/>
            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
            <binary/>
          </binaryDataArray>
          <binaryDataArray encodedLength="0">
            <referenceableParamGroupRef ref="intensityArray"/>
            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="369572"/>
            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
            <binary/>
          </binaryDataArray>
        </binaryDataArrayList>
      </spectrum>
      <spectrum id="Scan=7" defaultArrayLength="0" index="6">
        <referenceableParamGroupRef ref="spectrum1"/>
        <scanList count="1">
          <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
          <scan instrumentConfigurationRef="LTQFTUltra0">
            <referenceableParamGroupRef ref="scan1"/>
            <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:1000103" name="external array length" value="8399"/>
            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="403168"/>
            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
            <binary/>
          </binaryDataArray>
          <binaryDataArray encodedLength="0">
            <referenceableParamGroupRef ref="intensityArray"/>
            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="436764"/>
            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
            <binary/>
          </binaryDataArray>
        </binaryDataArrayList>
      </spectrum>
      <spectrum id="Scan=8" defaultArrayLength="0" index="7">
        <referenceableParamGroupRef ref="spectrum1"/>
        <scanList count="1">
          <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
          <scan instrumentConfigurationRef="LTQFTUltra0">
            <referenceableParamGroupRef ref="scan1"/>
            <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:1000103" name="external array length" value="8399"/>
            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="470360"/>
            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
            <binary/>
          </binaryDataArray>
          <binaryDataArray encodedLength="0">
            <referenceableParamGroupRef ref="intensityArray"/>
            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="503956"/>
            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
            <binary/>
          </binaryDataArray>
        </binaryDataArrayList>
      </spectrum>
      <spectrum id="Scan=9" defaultArrayLength="0" index="8">
        <referenceableParamGroupRef ref="spectrum1"/>
        <scanList count="1">
          <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
          <scan instrumentConfigurationRef="LTQFTUltra0">
            <referenceableParamGroupRef ref="scan1"/>
            <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:1000103" name="external array length" value="8399"/>
            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="537552"/>
            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
            <binary/>
          </binaryDataArray>
          <binaryDataArray encodedLength="0">
            <referenceableParamGroupRef ref="intensityArray"/>
            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="571148"/>
            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
            <binary/>
          </binaryDataArray>
        </binaryDataArrayList>
      </spectrum>
    </spectrumList>
  </run>
</mzML>