imzml 0.0.2

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Files changed (25) hide show
  1. checksums.yaml +7 -0
  2. data/data/Example_Continuous.ibd +0 -0
  3. data/data/Example_Continuous.imzML +373 -0
  4. data/data/Example_Processed.ibd +0 -0
  5. data/data/Example_Processed.imzML +373 -0
  6. data/data/imagingMS.obo +560 -0
  7. data/data/psi-ms.obo +14317 -0
  8. data/data/unit.obo +2585 -0
  9. data/lib/core_ext/string.rb +11 -0
  10. data/lib/imzml/metadata/data_processing.rb +24 -0
  11. data/lib/imzml/metadata/file_description/file_content.rb +42 -0
  12. data/lib/imzml/metadata/file_description.rb +10 -0
  13. data/lib/imzml/metadata/point.rb +7 -0
  14. data/lib/imzml/metadata/run/spectrum.rb +52 -0
  15. data/lib/imzml/metadata/scan_settings/image.rb +11 -0
  16. data/lib/imzml/metadata/scan_settings.rb +42 -0
  17. data/lib/imzml/metadata/spectrum.rb +79 -0
  18. data/lib/imzml/metadata.rb +36 -0
  19. data/lib/imzml/obo.rb +57 -0
  20. data/lib/imzml/parser.rb +332 -0
  21. data/lib/imzml/version.rb +5 -0
  22. data/lib/imzml.rb +23 -0
  23. data/lib/obo_ext/parser.rb +20 -0
  24. data/lib/obo_ext/stanza.rb +19 -0
  25. metadata +115 -0
data/data/Example_Processed.imzML ADDED
@@ -0,0 +1,373 @@
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+ <?xml version="1.0" encoding="ISO-8859-1"?>
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+ <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">
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+ <cvList count="3">
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+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo"/>
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+ <cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>
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+ <cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo"/>
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+ </cvList>
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+ <fileDescription>
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+ <fileContent>
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+ <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
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+ <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value=""/>
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+ <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{9D501BDC-5344-4916-B7E9-7E795B02C856}"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7E8FDB93053915D3EDB51B70AA0619AC209964DF"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000031" name="processed" value=""/>
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+ </fileContent>
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+ <sourceFileList count="1">
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+ <sourceFile id="sf1" name="Example.raw" location="C:\Users\Thorsten Schramm\Documents\Promotion\imzML\Website\files\Beispiel-Dateien\Example images\">
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+ <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW file" value=""/>
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+ <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>
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+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7623BE263B25FF99FDF017154B86FAB742D4BB0B"/>
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+ </sourceFile>
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+ </sourceFileList>
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+ <contact>
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+ <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Thorsten Schramm"/>
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+ <cvParam cvRef="MS" accession="MS:1000590" name="contact organization" value="Institut f�r Anorganische und Analytische Chemie"/>
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+ <cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="Schubertstra�e 60, Haus 16, Gie�en, Germany"/>
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+ <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="thorsten.schramm@anorg.chemie.uni-.giessen.de"/>
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+ </contact>
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+ </fileDescription>
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+ <referenceableParamGroupList count="4">
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+ <referenceableParamGroup id="mzArray">
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+ <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
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+ <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
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+ <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>
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+ </referenceableParamGroup>
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+ <referenceableParamGroup id="intensityArray">
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+ <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
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+ <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
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+ <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>
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+ </referenceableParamGroup>
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+ <referenceableParamGroup id="scan1">
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+ <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value=""/>
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+ <cvParam cvRef="MS" accession="MS:1000095" name="linear" value=""/>
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+ <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="ITMS - p NSI Full ms [100,00-800,00]"/>
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+ </referenceableParamGroup>
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+ <referenceableParamGroup id="spectrum1">
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+ <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
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+ <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
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+ <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value=""/>
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+ <cvParam cvRef="MS" accession="MS:1000129" name="negative scan" value=""/>
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+ </referenceableParamGroup>
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+ </referenceableParamGroupList>
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+ <sampleList count="1">
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+ <sample id="sample1" name="Sample1">
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+ <cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1"/>
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+ </sample>
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+ </sampleList>
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+ <softwareList count="2">
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+ <software id="Xcalibur" version="2.2">
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+ <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>
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+ </software>
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+ <software id="TMC" version="1.1 beta">
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+ <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value=""/>
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+ </software>
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+ </softwareList>
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+ <scanSettingsList count="1">
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+ <scanSettings id="scansettings1">
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+ <cvParam cvRef="IMS" accession="IMS:1000401" name="top down" value=""/>
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+ <cvParam cvRef="IMS" accession="IMS:1000413" name="flyback" value=""/>
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+ <cvParam cvRef="IMS" accession="IMS:1000480" name="horizontal line scan" value=""/>
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+ <cvParam cvRef="IMS" accession="IMS:1000491" name="linescan left right" value=""/>
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+ <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="100" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="100" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
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+ <cvParam cvRef="MS" accession="MS:1000836" name="dried dropplet" value=""/>
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+ <cvParam cvRef="MS" accession="MS:1000835" name="matrix solution concentration" value="10"/>
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+ <cvParam cvRef="MS" accession="MS:1000834" name="matrix solution" value="DHB"/>
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+ </scanSettings>
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+ </scanSettingsList>
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+ <instrumentConfigurationList count="1">
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+ <instrumentConfiguration id="LTQFTUltra0">
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+ <cvParam cvRef="MS" accession="MS:1000557" name="LTQ FT Ultra" value=""/>
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+ <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="none"/>
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+ <componentList count="3">
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+ <source order="1">
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+ <cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization" value=""/>
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+ <cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet" value=""/>
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+ <cvParam cvRef="MS" accession="MS:1000843" name="wavelength" value="337"/>
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+ <cvParam cvRef="MS" accession="MS:1000844" name="focus diameter x" value="10"/>
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+ <cvParam cvRef="MS" accession="MS:1000845" name="focus diameter y" value="10"/>
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+ <cvParam cvRef="MS" accession="MS:1000846" name="pulse energy" value="10"/>
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+ <cvParam cvRef="MS" accession="MS:1000847" name="pulse duration" value="10"/>
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+ <cvParam cvRef="MS" accession="MS:1000848" name="attenuation" value="50"/>
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+ <cvParam cvRef="MS" accession="MS:1000850" name="gas laser" value=""/>
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+ <cvParam cvRef="IMS" accession="IMS:1000202" name="target material" value="Conductive Glas"/>
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+ </source>
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+ <analyzer order="2">
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+ <cvParam cvRef="MS" accession="MS:1000264" name="ion trap" value=""/>
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+ <cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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+ </analyzer>
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+ <detector order="3">
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+ <cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier" value=""/>
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+ <cvParam cvRef="MS" accession="MS:1000120" name="transient recorder" value=""/>
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+ </detector>
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+ </componentList>
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+ <softwareRef ref="Xcalibur"/>
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+ </instrumentConfiguration>
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+ </instrumentConfigurationList>
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+ <dataProcessingList count="2">
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+ <dataProcessing id="XcaliburProcessing">
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+ <processingMethod order="1" softwareRef="Xcalibur">
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+ <cvParam cvRef="MS" accession="MS:1000594" name="low intensity data point removal" value=""/>
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+ </processingMethod>
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+ </dataProcessing>
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+ <dataProcessing id="TMCConversion">
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+ <processingMethod order="2" softwareRef="TMC">
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+ <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
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+ </processingMethod>
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+ </dataProcessing>
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+ </dataProcessingList>
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+ <run defaultInstrumentConfigurationRef="LTQFTUltra0" defaultSourceFileRef="sf1" id="Experiment01" sampleRef="sample1" startTimeStamp="2009-08-11T15:59:44">
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+ <spectrumList count="9" defaultDataProcessingRef="XcaliburProcessing">
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+ <spectrum id="Scan=1" defaultArrayLength="0" index="0">
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+ <referenceableParamGroupRef ref="spectrum1"/>
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+ <scanList count="1">
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+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
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+ <scan instrumentConfigurationRef="LTQFTUltra0">
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+ <referenceableParamGroupRef ref="scan1"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
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+ </scan>
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+ </scanList>
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+ <binaryDataArrayList count="2">
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+ <binaryDataArray encodedLength="0">
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+ <referenceableParamGroupRef ref="mzArray"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
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+ <binary/>
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+ </binaryDataArray>
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+ <binaryDataArray encodedLength="0">
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+ <referenceableParamGroupRef ref="intensityArray"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="33612"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
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+ <binary/>
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+ </binaryDataArray>
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+ </binaryDataArrayList>
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+ </spectrum>
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+ <spectrum id="Scan=2" defaultArrayLength="0" index="1">
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+ <referenceableParamGroupRef ref="spectrum1"/>
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+ <scanList count="1">
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+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
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+ <scan instrumentConfigurationRef="LTQFTUltra0">
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+ <referenceableParamGroupRef ref="scan1"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
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+ </scan>
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+ </scanList>
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+ <binaryDataArrayList count="2">
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+ <binaryDataArray encodedLength="0">
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+ <referenceableParamGroupRef ref="mzArray"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="67208"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
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+ <binary/>
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+ </binaryDataArray>
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+ <binaryDataArray encodedLength="0">
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+ <referenceableParamGroupRef ref="intensityArray"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="100804"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
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+ <binary/>
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+ </binaryDataArray>
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+ </binaryDataArrayList>
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+ </spectrum>
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+ <spectrum id="Scan=3" defaultArrayLength="0" index="2">
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+ <referenceableParamGroupRef ref="spectrum1"/>
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+ <scanList count="1">
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+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
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+ <scan instrumentConfigurationRef="LTQFTUltra0">
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+ <referenceableParamGroupRef ref="scan1"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
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+ </scan>
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+ </scanList>
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+ <binaryDataArrayList count="2">
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+ <binaryDataArray encodedLength="0">
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+ <referenceableParamGroupRef ref="mzArray"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="134400"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
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+ <binary/>
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+ </binaryDataArray>
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+ <binaryDataArray encodedLength="0">
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+ <referenceableParamGroupRef ref="intensityArray"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="167996"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
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+ <binary/>
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+ </binaryDataArray>
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+ </binaryDataArrayList>
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+ </spectrum>
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+ <spectrum id="Scan=4" defaultArrayLength="0" index="3">
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+ <referenceableParamGroupRef ref="spectrum1"/>
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+ <scanList count="1">
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+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
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+ <scan instrumentConfigurationRef="LTQFTUltra0">
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+ <referenceableParamGroupRef ref="scan1"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
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+ </scan>
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+ </scanList>
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+ <binaryDataArrayList count="2">
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+ <binaryDataArray encodedLength="0">
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+ <referenceableParamGroupRef ref="mzArray"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="201592"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
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+ <binary/>
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+ </binaryDataArray>
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+ <binaryDataArray encodedLength="0">
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+ <referenceableParamGroupRef ref="intensityArray"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="235188"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
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+ <binary/>
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+ </binaryDataArray>
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+ </binaryDataArrayList>
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+ </spectrum>
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+ <spectrum id="Scan=5" defaultArrayLength="0" index="4">
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+ <referenceableParamGroupRef ref="spectrum1"/>
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+ <scanList count="1">
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+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
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+ <scan instrumentConfigurationRef="LTQFTUltra0">
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+ <referenceableParamGroupRef ref="scan1"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
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+ </scan>
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+ </scanList>
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+ <binaryDataArrayList count="2">
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+ <binaryDataArray encodedLength="0">
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+ <referenceableParamGroupRef ref="mzArray"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="268784"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
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+ <binary/>
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+ </binaryDataArray>
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+ <binaryDataArray encodedLength="0">
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+ <referenceableParamGroupRef ref="intensityArray"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="302380"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
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+ <binary/>
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+ </binaryDataArray>
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+ </binaryDataArrayList>
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+ </spectrum>
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+ <spectrum id="Scan=6" defaultArrayLength="0" index="5">
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+ <referenceableParamGroupRef ref="spectrum1"/>
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+ <scanList count="1">
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+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
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+ <scan instrumentConfigurationRef="LTQFTUltra0">
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+ <referenceableParamGroupRef ref="scan1"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
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+ </scan>
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+ </scanList>
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+ <binaryDataArrayList count="2">
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+ <binaryDataArray encodedLength="0">
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+ <referenceableParamGroupRef ref="mzArray"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="335976"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
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+ <binary/>
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+ </binaryDataArray>
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+ <binaryDataArray encodedLength="0">
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+ <referenceableParamGroupRef ref="intensityArray"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="369572"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
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+ <binary/>
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+ </binaryDataArray>
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+ </binaryDataArrayList>
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+ </spectrum>
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+ <spectrum id="Scan=7" defaultArrayLength="0" index="6">
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+ <referenceableParamGroupRef ref="spectrum1"/>
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+ <scanList count="1">
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+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
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+ <scan instrumentConfigurationRef="LTQFTUltra0">
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+ <referenceableParamGroupRef ref="scan1"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
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+ </scan>
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+ </scanList>
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+ <binaryDataArrayList count="2">
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+ <binaryDataArray encodedLength="0">
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+ <referenceableParamGroupRef ref="mzArray"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="403168"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
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+ <binary/>
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+ </binaryDataArray>
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+ <binaryDataArray encodedLength="0">
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+ <referenceableParamGroupRef ref="intensityArray"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="436764"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
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+ <binary/>
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+ </binaryDataArray>
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+ </binaryDataArrayList>
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+ </spectrum>
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+ <spectrum id="Scan=8" defaultArrayLength="0" index="7">
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+ <referenceableParamGroupRef ref="spectrum1"/>
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+ <scanList count="1">
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+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
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+ <scan instrumentConfigurationRef="LTQFTUltra0">
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+ <referenceableParamGroupRef ref="scan1"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
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+ </scan>
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+ </scanList>
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+ <binaryDataArrayList count="2">
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+ <binaryDataArray encodedLength="0">
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+ <referenceableParamGroupRef ref="mzArray"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="470360"/>
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+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
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+ <binary/>
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+ </binaryDataArray>
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