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ThermoRawFileParser not recognizing some instruments?

See original GitHub issue

Hi, we have discovered that many of our ThermoRawFileParser converted files do not have the correct instrument model encoded in them. Example:

    <referenceableParamGroupList count="1">
      <referenceableParamGroup id="commonInstrumentParams">
        <cvParam cvRef="MS" accession="MS:1000483" value="" name="Thermo Fisher Scientific instrument model" />
        <cvParam cvRef="MS" accession="MS:1000529" value="SN03468B" name="instrument serial number" />
      </referenceableParamGroup>
    </referenceableParamGroupList>
    <softwareList count="1">
      <software id="ThermoRawFileParser" version="1.3.0-pre">
        <cvParam cvRef="MS" accession="MS:1000799" value="ThermoRawFileParser" name="custom unreleased software tool" />
      </software>
    </softwareList>

The instrument model is not provided, just the ambiguous parent term. For the same file, msconvert provides this:

    <referenceableParamGroupList count="1">
      <referenceableParamGroup id="CommonInstrumentParams">
        <cvParam cvRef="MS" accession="MS:1001742" name="LTQ Orbitrap Velos" value=""/>
        <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN03468B"/>
      </referenceableParamGroup>
    </referenceableParamGroupList>
    </sampleList>
    <softwareList count="2">
      <software id="Xcalibur" version="2.7.0">
        <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>
      </software>
      <software id="pwiz" version="3.0.20155">
        <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
      </software>
    </softwareList>

This seems to happen for both instruments: “name”: “LTQ Orbitrap Velos” “name”: “LTQ Orbitrap Elite”

Would you add those instruments to ThermoRawFileParsers list of recognized instruments? The above example comes from the raw files in: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/02/PXD000660

Issue Analytics

State:
Created 3 years ago
Comments:9

Top GitHub Comments

1reaction

caeteracommented, Jul 1, 2020

I have updated the mapping in ThermoRawParser with new terms. I will talk with @nielshulstaert to get the new release.

0reactions

caeteracommented, Aug 26, 2020

Release is published.

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