msn-kit 0.2.5

Library and CLI for working with Mass Spec data.
Documentation 
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<?xml version="1.0" encoding="ISO-8859-1"?>
<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xs="http://www.w3.org/2001/XMLSchema-instance"
	xs:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd"
	accession="0815" id="handcraftedpda" version="20080325">
  <cvList count="2">
    <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.18.2" URI="http://psidev.info/ms/mzML/psi-ms.obo"/>
    <cv id="UO" fullName="Unit Ontology" version="1.20" URI="http://obo.cvs.sourceforge.net/viewvc/obo/obo/ontology/phenotype/unit.obo?revision=1.20"/>
  </cvList>
  <fileDescription>

    <fileContent>
      <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" value=""/>
      <cvParam cvRef="MS" accession="MS:1000806" name="absorption spectrum" value=""/>
    </fileContent>

    <sourceFileList count="1">
      <sourceFile id="sf1" name="MM48pos_20uM_1-A,8_01_9112.u2" location="file:///data/MM48pos_1uM_1-A,4_01_9122.d/">
        <cvParam cvRef="MS" accession="MS:1000816" name="Bruker U2 file" value=""/>
        <cvParam cvRef="MS" accession="MS:1000823" name="Bruker U2 nativeID format" value=""/>
        <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="71be39fb2700ab2f3c8b2234b91274968b6899b1"/>
      </sourceFile>
      <sourceFile id="sf2" name="analysis.baf" location="file:///data/MM48pos_1uM_1-A,4_01_9122.d/">
        <cvParam cvRef="MS" accession="MS:1000815" name="Bruker BAF file" value=""/>
	    <cvParam cvRef="MS" accession="MS:1000772" name="Bruker BAF nativeID format" value=""/>
        <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="71be39fb2700ab2f3c8b2234b91274968b6899b1"/>
      </sourceFile>


   </sourceFileList>

    <contact>
      <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="William Pennington"/>
      <cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="Higglesworth University, 12 Higglesworth Avenue, 12045, HI, USA"/>
      <cvParam cvRef="MS" accession="MS:1000588" name="contact URL" value="http://www.higglesworth.edu/"/>
      <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="wpennington@higglesworth.edu"/>
      <cvParam cvRef="MS" accession="MS:1000590" name="contact organization" value="dort"/>
    </contact>

    <contact>
      <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Drek'Thar"/>
			<cvParam cvRef="MS" accession="MS:1000590" name="contact organization" value="da"/>
 			<userParam name="name" value="contact2"/>
    </contact>

  </fileDescription>

  <referenceableParamGroupList count="2">
    <referenceableParamGroup id="CommonPDASpectrumParams">
      <cvParam cvRef="MS" accession="MS:1000619" name="lowest observed wavelength" value="200" unitAccession="UO:0000018" unitName="nanometer" unitCvRef="UO"/>
      <cvParam cvRef="MS" accession="MS:1000618" name="highest observed wavelength" value="600" unitAccession="UO:0000018" unitName="nanometer" unitCvRef="UO"/>
    </referenceableParamGroup>
  </referenceableParamGroupList>

  <sampleList count="1">
    <sample id="sample1" name="Sample1">
 			<cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="11.7" unitAccession="UO:0000021" unitName="gram" unitCvRef="UO"/>
 			<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="5"/>
 			<cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="3.1" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO"/>
 			<cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="5.5" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO"/>
 			<cvParam cvRef="MS" accession="MS:1000053" name="sample batch" value="4.4"/>
 			<cvParam cvRef="MS" accession="MS:1000052" name="suspension"/>
      <userParam name="name" value="sample"/>
    </sample>
    <sample id="sample2"/>
  </sampleList>

  <softwareList count="1">
    <software id="CompassXport" version="2.4.9">
      <cvParam cvRef="MS" accession="MS:1000717" name="CompassXport"/>
    </software>
  </softwareList>

  <scanSettingsList count="1">
    <scanSettings id="as1">
      <sourceFileRefList count="1">
        <sourceFileRef ref="sf1"/>
      </sourceFileRefList>
    </scanSettings>
  </scanSettingsList>

  <instrumentConfigurationList count="1">
    <instrumentConfiguration id="IPBmicrOTOFq">
      <cvParam cvRef="MS" accession="MS:1000703" name="micrOTOF-Q" value=""/>
      <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="23433"/>
      <cvParam cvRef="MS" accession="MS:1000275" name="collision quadrupole" value=""/>

      <componentList count="4">
        <source order="101">
		  <cvParam cvRef="MS" accession="MS:1000057" name="electrospray inlet" value=""/>
          <cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization" value=""/>
          <userParam name="name" value="source1"/>
        </source>
        <analyzer order="201">
          <cvParam cvRef="MS" accession="MS:1000081" name="quadrupole" value=""/>
          <userParam name="name" value="analyzer1"/>
        </analyzer>
        <analyzer order="202">
          <cvParam cvRef="MS" accession="MS:1000084" name="time-of-flight" value=""/>
          <userParam name="name" value="analyzer2"/>
        </analyzer>

        <detector order="1">
          	<cvParam cvRef="MS" accession="MS:1000621" name="photodiode array detector" value=""/>
          	<!-- cvParam cvRef="MS" accession="MS:9999999" name="Acquity UPLC PDA" name="" value=""/-->
	        <cvParam cvRef="MS" accession="MS:1000029" name="sampling frequency" value="1.1" unitAccession="UO:0000106" unitName="hertz" unitCvRef="UO"/>
            <userParam name="name" value="detector1"/>
        </detector>
        <detector order="301">
          <cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier" value=""/>
          <cvParam cvRef="MS" accession="MS:1000028" name="detector resolution" value="5.1"/>
          <cvParam cvRef="MS" accession="MS:1000029" name="sampling frequency" value="1.1" unitAccession="UO:0000106" unitName="hertz" unitCvRef="UO"/>
          <cvParam cvRef="MS" accession="MS:1000117" name="analog-digital converter" value=""/>
          <userParam name="name" value="detector1"/>
        </detector>
      </componentList>
    </instrumentConfiguration>
  </instrumentConfigurationList>

  <dataProcessingList count="1">
    <dataProcessing id="default_pda_dp">
      <processingMethod order="1" softwareRef="CompassXport">
        <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
        <cvParam cvRef="MS" accession="MS:1000747" name="completion time" value="2001-02-03+04:10"/>
        <userParam name="p2" value="value2"/>
      </processingMethod>
    </dataProcessing>
  </dataProcessingList>

  <run id="Exp01-PDA" defaultInstrumentConfigurationRef="IPBmicrOTOFq"
       sampleRef="sample1" defaultSourceFileRef="sf1"
  	   startTimeStamp="2007-06-27T15:23:45.00035">
    <spectrumList count="1" defaultDataProcessingRef="default_pda_dp">
      <spectrum index="0" sourceFileRef="sf2" id="declaration=0 collection=0 scan=0" defaultArrayLength="15">
        <referenceableParamGroupRef ref="CommonPDASpectrumParams"/>
        <cvParam cvRef="MS" accession="MS:1000806" name="absorption spectrum" value=""/>
       	<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value=""/>
       	<cvParam cvRef="MS" accession="MS:1000618" name="highest observed wavelength" value="200" unitAccession="UO:0000018" unitName="nanometer" unitCvRef="UO"/>
       	<cvParam cvRef="MS" accession="MS:1000619" name="lowest observed wavelength" value="600" unitAccession="UO:0000018" unitName="nanometer" unitCvRef="UO"/>
       <binaryDataArrayList count="2">
          <binaryDataArray encodedLength="160" >
            <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
            <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
            <cvParam cvRef="MS" accession="MS:1000617" name="wavelength array" unitAccession="UO:0000018" unitName="nanometer" unitCvRef="UO"/>
            <binary>AAAAAAAAAAAAAAAAAADwPwAAAAAAAABAAAAAAAAACEAAAAAAAAAQQAAAAAAAABRAAAAAAAAAGEAAAAAAAAAcQAAAAAAAACBAAAAAAAAAIkAAAAAAAAAkQAAAAAAAACZAAAAAAAAAKEAAAAAAAAAqQAAAAAAAACxA</binary>
          </binaryDataArray>
          <binaryDataArray encodedLength="160" >
            <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
            <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
            <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value=""
		     unitAccession="UO:0000269" unitName="absorbance unit" unitCvRef="UO"/>
        		<userParam name="itname" value="itarray1"/>
            <binary>AAAAAAAALkAAAAAAAAAsQAAAAAAAACpAAAAAAAAAKEAAAAAAAAAmQAAAAAAAACRAAAAAAAAAIkAAAAAAAAAgQAAAAAAAABxAAAAAAAAAGEAAAAAAAAAUQAAAAAAAABBAAAAAAAAACEAAAAAAAAAAQAAAAAAAAPA/</binary>
          </binaryDataArray>
        </binaryDataArrayList>
	  </spectrum>
    </spectrumList>

      <chromatogramList count="1" defaultDataProcessingRef="default_pda_dp">
      <chromatogram index="0" id="242nm" defaultArrayLength="15" >
        <cvParam cvRef="MS" accession="MS:1000812" name="absorption chromatogram" value=""/>
       	<cvParam cvRef="MS" accession="MS:1000618" name="highest observed wavelength" value="241" unitAccession="UO:0000018" unitName="nanometer" unitCvRef="UO"/>
       	<cvParam cvRef="MS" accession="MS:1000619" name="lowest observed wavelength" value="241" unitAccession="UO:0000018" unitName="nanometer" unitCvRef="UO"/>
        <binaryDataArrayList count="2">
          <binaryDataArray encodedLength="160" >
            <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
            <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
            <cvParam cvRef="MS" accession="MS:1000595" name="time array" unitAccession="UO:0000010" unitName="second" unitCvRef="UO"/>
            <binary>AAAAAAAAAAAAAAAAAADwPwAAAAAAAABAAAAAAAAACEAAAAAAAAAQQAAAAAAAABRAAAAAAAAAGEAAAAAAAAAcQAAAAAAAACBAAAAAAAAAIkAAAAAAAAAkQAAAAAAAACZAAAAAAAAAKEAAAAAAAAAqQAAAAAAAACxA</binary>
          </binaryDataArray>
          <binaryDataArray encodedLength="160" >
            <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
            <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
            <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value=""
		     unitAccession="UO:0000269" unitName="absorbance unit" unitCvRef="UO"/>
            <binary>AAAAAAAALkAAAAAAAAAsQAAAAAAAACpAAAAAAAAAKEAAAAAAAAAmQAAAAAAAACRAAAAAAAAAIkAAAAAAAAAgQAAAAAAAABxAAAAAAAAAGEAAAAAAAAAUQAAAAAAAABBAAAAAAAAACEAAAAAAAAAAQAAAAAAAAPA/</binary>
          </binaryDataArray>
        </binaryDataArrayList>
      </chromatogram>
    </chromatogramList>
  </run>
</mzML>

<!--  History:
      * 15.07.2008: Validates against final mzML-1.1
      * 25.03.2008: Validates against mzML-1.1rc5
      * 18.02.2008: Validates against mzML-1.1rc4
      * 09.02.2008: Working on Chromatogram
      * 06.02.2008: First PDA Spectra Mockup
      * 05.02.2008: Used MzMLFile_1.mzML from Marc Sturm as Template
 -->