mzml 0.3.1 → 0.3.2
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.
- data/lib/mzml/spectrum.rb +3 -2
- data/lib/mzml/version.rb +1 -1
- data/test/test_mzml.rb +2 -0
- metadata +10 -24
- data/spec/mzml_spec.rb +0 -114
- data/spec/sample.compressed.mzML +0 -3108
- data/spec/sample.mgf +0 -10705
- data/spec/sample.mzML +0 -3108
- data/spec/sample.unindexed.mzML +0 -221
- data/spec/spec.opts +0 -1
- data/spec/spec_helper.rb +0 -29
data/spec/sample.unindexed.mzML
DELETED
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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.xsd" accession="" version="1.1.0">
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<cvList count="2">
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<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
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<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.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:1000294" name="mass spectrum" />
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</fileContent>
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<sourceFileList count="1">
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<sourceFile id="sf_ru_0" name="file://MSALLY2/S/RAW/HEK_cells/Hek_cells_100904050914.RAW" location="">
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<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2b6ebe1d5f900a445f82adb40b24cd77ed476ecb" />
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<cvParam cvRef="MS" accession="MS:1000564" name="PSI mzData file" />
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<cvParam cvRef="MS" accession="MS:1000777" name="spectrum identifier nativeID format" />
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</sourceFile>
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</sourceFileList>
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</fileDescription>
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<sampleList count="1">
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<sample id="sa_0" name="">
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<cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="0" unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />
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<cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="0" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />
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<cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="0" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />
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</sample>
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</sampleList>
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<softwareList count="4">
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<software id="so_in_0" version="2.5.5" >
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<cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" />
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</software>
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<software id="so_default" version="" >
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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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<software id="so_dp_sp_0_pm_0" version="4.3.1(build Sep 9 2009 12:30:29)" >
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<cvParam cvRef="MS" accession="MS:1000541" name="ReAdW" />
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</software>
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<software id="so_dp_sp_0_pm_1" version="1.7.0" >
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<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="SpectrumCanvas" />
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</software>
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</softwareList>
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<instrumentConfigurationList count="1">
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<instrumentConfiguration id="ic_0">
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<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />
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<componentList count="3">
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<source order="0">
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<cvParam cvRef="MS" accession="MS:1000008" name="ionization type" />
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</source>
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<analyzer order="0">
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<cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO" />
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<cvParam cvRef="MS" accession="MS:1000022" name="TOF Total Path Length" value="0" unitAccession="UO:0000008" unitName="meter" unitCvRef="UO" />
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<cvParam cvRef="MS" accession="MS:1000024" name="final MS exponent" value="0" />
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<cvParam cvRef="MS" accession="MS:1000025" name="magnetic field strength" value="0" unitAccession="UO:0000228" unitName="tesla" unitCvRef="UO" />
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<cvParam cvRef="MS" accession="MS:1000443" name="mass analyzer type" />
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</analyzer>
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<detector order="0">
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<cvParam cvRef="MS" accession="MS:1000028" name="detector resolution" value="0" />
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<cvParam cvRef="MS" accession="MS:1000029" name="sampling frequency" value="0" unitAccession="UO:0000106" unitName="hertz" unitCvRef="UO" />
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<cvParam cvRef="MS" accession="MS:1000026" name="detector type" />
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</detector>
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</componentList>
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<softwareRef ref="so_in_0" />
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</instrumentConfiguration>
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</instrumentConfigurationList>
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<dataProcessingList count="1">
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<dataProcessing id="dp_sp_0">
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<processingMethod order="0" softwareRef="so_dp_sp_0_pm_0">
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<cvParam cvRef="MS" accession="MS:1000035" name="peak picking" />
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<userParam name="#type" type="xsd:string" value="conversion"/>
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</processingMethod>
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<processingMethod order="0" softwareRef="so_dp_sp_0_pm_1">
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<cvParam cvRef="MS" accession="MS:1001486" name="data filtering" />
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<cvParam cvRef="MS" accession="MS:1000747" name="completion time" value="2011-02-07+21:50" />
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</processingMethod>
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</dataProcessing>
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</dataProcessingList>
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<run id="ru_0" defaultInstrumentConfigurationRef="ic_0" sampleRef="sa_0" defaultSourceFileRef="sf_ru_0">
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<spectrumList count="5" defaultDataProcessingRef="dp_sp_0">
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<spectrum id="scan=9033" index="562" defaultArrayLength="75">
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<cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
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<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
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<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
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<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
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<scanList count="1">
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<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
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<scan>
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<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="5207.31" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
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</scan>
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</scanList>
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<binaryDataArrayList count="2">
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<binaryDataArray encodedLength="800">
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<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
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<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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<binary>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</binary>
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</binaryDataArray>
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<binaryDataArray encodedLength="400">
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<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of counts" unitCvRef="MS"/>
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<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />
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<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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<binary>CZMLRfdvCEWM1ydFdZ/pRDWvDUapXF5FlQ4eRRgd20W1P3BFe9EqRecTCEWk6gdF1TyQRf3eDEblhfxEGkkWRua92UXCoaVFknjfRD2F80RS3hxFwbDrRHJiRkUUbSBFv2McRTEaQ0VvUwlFi68fRUv5hkVEwIZFBrRRRdTF6UVEzxJF+UYTRd/nH0Ui83tFox8MRUrwG0X3gWpFmtUURQjH20UWMTRFwc8pRTNRCEWsaQlFcrUXRSkJwUWZkBxGrgIxRuMio0WU/etEmWwtReGvbEUa4JZFyoffRPtHlEUI/lBFsW2ARV4xUEWtvS5FBi06RdwJEkWojBJGPIxHRvKcE0UAqGNGzdmkRQ+aFkXsqlpFvtcwRRLkYUV/WFRFSJQLRQy4BkV29CNF</binary>
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</binaryDataArray>
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</binaryDataArrayList>
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</spectrum>
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<spectrum id="scan=9034" index="563" defaultArrayLength="79">
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<cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
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<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
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<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
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<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
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<scanList count="1">
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<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
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<scan>
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<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="5208.68" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
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</scan>
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</scanList>
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<binaryDataArrayList count="2">
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<binaryDataArray encodedLength="844">
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<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
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<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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<binary>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</binary>
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</binaryDataArray>
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<binaryDataArray encodedLength="424">
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<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of counts" unitCvRef="MS"/>
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<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />
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<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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<binary>pb8PRZMGWEVVn1lFubaqRfkR9kQDlm9FT/ACRWNkKEWd/O9Ep2c3RawNg0XKUEtFGxvcRdjRFUZWyWdFw0hhRVb/BkUlNVtFoqkRRZLe+USzSApFXQv6RLsYMkWBsjFFk6OBRXLSNUVydedEVt7jRE/ECkUVMA5FHQ4YRbGREUWA9fZE+j5lRY5hx0UBRAxFY6cBRc2+OkU4JBBFsFsiRcmD+0Q9B4dF327GRZ1oDkVZ1w5FF5sLRfppFEW51lJFmBM4RXZCpEUdjvREDS6TRftxVUY/pL1FGRb1RCPjUEU0HGVFckCBRfDWH0V+wx9FkXcrRlr3bEVTNjdFvosIRVkXc0U5klxGCiYnRt0xHEa/RsVF1IQNRUNWNEXMaftEvNkPRRWB+ETuG19FMOLURL+sQUUdew5FuDkARQ==</binary>
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</binaryDataArray>
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</binaryDataArrayList>
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</spectrum>
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<spectrum id="scan=9035" index="564" defaultArrayLength="0">
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<cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
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<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2" />
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<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
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<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
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<scanList count="1">
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<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
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<scan>
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<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="5209.18" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
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</scan>
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</scanList>
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<precursorList count="1">
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<precursor>
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<isolationWindow>
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<cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="868.46765137" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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<cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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<cvParam cvRef="MS" accession="MS:1000829" name="isolation window upper offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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</isolationWindow>
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<selectedIonList count="1">
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<selectedIon>
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<cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="868.46765137" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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<cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="3" />
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<cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="12840.7001953125" unitAccession="MS:1000132" unitName="percent of base peak" unitCvRef="MS" />
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</selectedIon>
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</selectedIonList>
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<activation>
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<cvParam cvRef="MS" accession="MS:1000509" name="activation energy" value="0" unitAccession="UO:0000266" unitName="electronvolt" unitCvRef="UO" />
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<cvParam cvRef="MS" accession="MS:1000044" name="dissociation method" />
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</activation>
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</precursor>
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</precursorList>
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</spectrum>
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<spectrum id="scan=9036" index="565" defaultArrayLength="83">
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<cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
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<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
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<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
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<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
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<scanList count="1">
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<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
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<scan>
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<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="5209.63" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
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</scan>
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</scanList>
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<binaryDataArrayList count="2">
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<binaryDataArray encodedLength="888">
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<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
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<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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<binary>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</binary>
|
|
178
|
-
</binaryDataArray>
|
|
179
|
-
<binaryDataArray encodedLength="444">
|
|
180
|
-
<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of counts" unitCvRef="MS"/>
|
|
181
|
-
<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />
|
|
182
|
-
<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
|
|
183
|
-
<binary>Q4ImReexMkXWN0VF1fbbRA9nB0Xe/Q1Fa/urRX8rTEWmbiRFiZoORfixFUUuPEZFPmYCRftqzURuxC9FfZg1RbgrYEYmLB5FsK+FRoIRlEUDV4NF+TAaRecZNUW5phhFoIsjRa5JBUU+ezVFC3PqRNAl80TsNepE+vMgRfW5hEVv6VxFHYMFRV2NEUXvJCpFvHYNRQXMUUVMBFBFvGrvRLUEBEXs2OpEd8n6RBYJJkWzmyhFEaklRXVEp0UrKVtGKosjRUYeJEUJ8FVGN5knRjHQ7kX6AUNFxeEpRdmiD0V8QjpFpaUaRSSwn0UBmPZFtF8TRYJfB0VugzZF+AwJRf/G8EWjC4hGhv0sRYyvq0XuxoxFuKYdRaJqBEWvwCFFaZYgRdncL0W/dR1FrHL4REkECkUJ8lJFRDYXRatv+0Tha01Fr8E2RWCNDkU=</binary>
|
|
184
|
-
</binaryDataArray>
|
|
185
|
-
</binaryDataArrayList>
|
|
186
|
-
</spectrum>
|
|
187
|
-
<spectrum id="scan=9037" index="566" defaultArrayLength="0">
|
|
188
|
-
<cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
|
|
189
|
-
<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2" />
|
|
190
|
-
<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
|
|
191
|
-
<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
|
|
192
|
-
<scanList count="1">
|
|
193
|
-
<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
|
|
194
|
-
<scan>
|
|
195
|
-
<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="5210.17" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
|
|
196
|
-
</scan>
|
|
197
|
-
</scanList>
|
|
198
|
-
<precursorList count="1">
|
|
199
|
-
<precursor>
|
|
200
|
-
<isolationWindow>
|
|
201
|
-
<cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="1045.84021" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
|
|
202
|
-
<cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
|
|
203
|
-
<cvParam cvRef="MS" accession="MS:1000829" name="isolation window upper offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
|
|
204
|
-
</isolationWindow>
|
|
205
|
-
<selectedIonList count="1">
|
|
206
|
-
<selectedIon>
|
|
207
|
-
<cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="1045.84021" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
|
|
208
|
-
<cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="3" />
|
|
209
|
-
<cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="17405.5" unitAccession="MS:1000132" unitName="percent of base peak" unitCvRef="MS" />
|
|
210
|
-
</selectedIon>
|
|
211
|
-
</selectedIonList>
|
|
212
|
-
<activation>
|
|
213
|
-
<cvParam cvRef="MS" accession="MS:1000509" name="activation energy" value="0" unitAccession="UO:0000266" unitName="electronvolt" unitCvRef="UO" />
|
|
214
|
-
<cvParam cvRef="MS" accession="MS:1000044" name="dissociation method" />
|
|
215
|
-
</activation>
|
|
216
|
-
</precursor>
|
|
217
|
-
</precursorList>
|
|
218
|
-
</spectrum>
|
|
219
|
-
</spectrumList>
|
|
220
|
-
</run>
|
|
221
|
-
</mzML>
|
data/spec/spec.opts
DELETED
|
@@ -1 +0,0 @@
|
|
|
1
|
-
--color
|
data/spec/spec_helper.rb
DELETED
|
@@ -1,29 +0,0 @@
|
|
|
1
|
-
$LOAD_PATH.unshift(File.dirname(__FILE__))
|
|
2
|
-
$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
|
|
3
|
-
require 'rubygems'
|
|
4
|
-
require 'mzml'
|
|
5
|
-
require 'spec'
|
|
6
|
-
require 'spec/autorun'
|
|
7
|
-
|
|
8
|
-
class Mgf < Struct.new(:title, :mz, :intensity); end
|
|
9
|
-
|
|
10
|
-
def parse_mgf(fname)
|
|
11
|
-
mgf = Mgf.new(nil,[],[])
|
|
12
|
-
File.open(fname).each do |l|
|
|
13
|
-
l.chomp!
|
|
14
|
-
case l
|
|
15
|
-
when /^TITLE=(.+)/
|
|
16
|
-
mgf.title = $1
|
|
17
|
-
when /^\d/
|
|
18
|
-
m,i = l.split(' ').map{|e| (e.to_f * 1000).to_i() / 1000.0 }
|
|
19
|
-
mgf.mz << m
|
|
20
|
-
mgf.intensity << i
|
|
21
|
-
when /^END IONS/
|
|
22
|
-
break
|
|
23
|
-
end
|
|
24
|
-
end
|
|
25
|
-
return mgf
|
|
26
|
-
end
|
|
27
|
-
|
|
28
|
-
Spec::Runner.configure do |config|
|
|
29
|
-
end
|