Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

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" />
    <softwareList count="1">
      <software id="ThermoRawFileParser" version="1.3.0-pre">
        <cvParam cvRef="MS" accession="MS:1000799" value="ThermoRawFileParser" name="custom unreleased software tool" />

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"/>
    <softwareList count="2">
      <software id="Xcalibur" version="2.7.0">
        <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>
      <software id="pwiz" version="3.0.20155">
        <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>

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:

Issue Analytics

  • State:closed
  • Created 3 years ago
  • Comments:9

github_iconTop GitHub Comments

caeteracommented, Jul 1, 2020

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

caeteracommented, Aug 26, 2020

Release is published.

Read more comments on GitHub >

github_iconTop Results From Across the Web

ThermoRawFileParser produces files, which can not be ...
I created an issue on pwiz and once this is handled, I can contribute to integrating it in mzR. Can't make any guarantees...
Read more >
Thermo RAW file parser that runs on Linux/Mac and all other platforms that support Mono ... The tool can output some RAW file...
Read more >
ThermoRawFileParser: modular, scalable and cross- ...
Unfortunately, the vast majority of cross-platform proteomics tools are not able to operate directly on the proprietary formats generated by ...
Read more >
OpenMS: FileConverter
Thermo raw files can be converted to mzML using the ThermoRawFileParser ... Enables compatibility with some tools that do not support compressed input...
Read more >
kduffy/thermorawfileparser - Docker Image
The tool can output some RAW file metadata -m=0|1 (0 for JSON, 1 for TXT) and the spectra file -f=0|1|2|3 (0 for MGF,...
Read more >

github_iconTop Related Medium Post

No results found

github_iconTop Related StackOverflow Question

No results found

github_iconTroubleshoot Live Code

Lightrun enables developers to add logs, metrics and snapshots to live code - no restarts or redeploys required.
Start Free

github_iconTop Related Reddit Thread

No results found

github_iconTop Related Hackernoon Post

No results found

github_iconTop Related Tweet

No results found

github_iconTop Related Post

No results found

github_iconTop Related Hashnode Post

No results found