imzml 0.0.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/data/Example_Continuous.ibd +0 -0
- data/data/Example_Continuous.imzML +373 -0
- data/data/Example_Processed.ibd +0 -0
- data/data/Example_Processed.imzML +373 -0
- data/data/imagingMS.obo +560 -0
- data/data/psi-ms.obo +14317 -0
- data/data/unit.obo +2585 -0
- data/lib/core_ext/string.rb +11 -0
- data/lib/imzml/metadata/data_processing.rb +24 -0
- data/lib/imzml/metadata/file_description/file_content.rb +42 -0
- data/lib/imzml/metadata/file_description.rb +10 -0
- data/lib/imzml/metadata/point.rb +7 -0
- data/lib/imzml/metadata/run/spectrum.rb +52 -0
- data/lib/imzml/metadata/scan_settings/image.rb +11 -0
- data/lib/imzml/metadata/scan_settings.rb +42 -0
- data/lib/imzml/metadata/spectrum.rb +79 -0
- data/lib/imzml/metadata.rb +36 -0
- data/lib/imzml/obo.rb +57 -0
- data/lib/imzml/parser.rb +332 -0
- data/lib/imzml/version.rb +5 -0
- data/lib/imzml.rb +23 -0
- data/lib/obo_ext/parser.rb +20 -0
- data/lib/obo_ext/stanza.rb +19 -0
- metadata +115 -0
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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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