compomics / ThermoRawFileParser

Thermo RAW file parser that runs on Linux/Mac and all other platforms that support Mono
Apache License 2.0
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ThermoRawFileParser not recognizing some instruments? #80

Closed edeutsch closed 4 years ago

edeutsch commented 4 years ago

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

caetera commented 4 years ago

Hi Eric,

thank you for reporting the problem. The instrument in the files you refrence is provided as "Orbitrap Velos Pro", that does not have a specific CV term, the closest one is "LTQ Orbitrap Velos". As a fix I added "Orbitrap Velos Pro" resolving to "LTQ Orbitrap Velos", but none of the the referenced files was from Orbitrap Elite, thus I will need an example to add Oribtrap Elite in the same way.

edeutsch commented 4 years ago

Thanks for this. I have requested a new term for LTQ Orbitrap Velos Pro: https://github.com/HUPO-PSI/psi-ms-CV/pull/31/files Please review that PR.

As for the Orbitrap Elite, please see the first few files here: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/08/PXD013646 Apparently the "LTQ Orbitrap Elite" and the "Orbitrap Elite" are the same instrument, just different names.

caetera commented 4 years ago

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

edeutsch commented 4 years ago

Any news on a new release?

chambm commented 4 years ago

I've added these in msconvert as well (actually the PR is building so it's not quite ready) . The Exploris 120 and 240 and the Orbitrap ID-X too. (NB for @caetera: that is the instrument model string to check for)

edeutsch commented 4 years ago

Thanks, @chambm !

@caetera , new term is here: https://github.com/HUPO-PSI/psi-ms-CV/pull/37/files

caetera commented 4 years ago

Added Orbitrap ID-X in ded9953

Sorry, no updates on the new release. I talked with @nielshulstaert to review my changes (two pair of eyes are better, than one) and do a release some time ago, but I haven't heard from him since then.

edeutsch commented 4 years ago

okay, thank you! We're still using 1.3.0-pre (or some version of that if there's more than one) but it would be super nice to have an official 1.3.0 or whatever version with these changes in there and whatever else has happened. Thanks!

caetera commented 4 years ago

Release is published.