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ThermoRawFileParser produces files, which can not be processed with msconvert

See original GitHub issue

When converting raw file to mzML with ThermoRawFileParser: $ mono /opt/ThermoRawFileParser/ThermoRawFileParser.exe -f=2 -m=0 -i=170413_12mix_DIA_14.raw -b=170413_12mix_DIA_14.mzML -p

The mscovert can not process the converted file, but gives an error message about invalid cvParam $ msconvert 170413_12mix_DIA_14.mzML --32 --zlib --filter "peakPicking false 1-" --mzXML -o ./ Invalid cvParam accession "1003145 I am not sure if this is a problem is in use-case or in ThermoRawFileParser or in msconvert (ProteoWizard release: 3.0.18344)

The raw file can be found from https://www.ebi.ac.uk/pride/archive/projects/PXD008738

Issue Analytics

State:
Created 2 years ago
Reactions:1
Comments:13 (3 by maintainers)

Top GitHub Comments

3reactions

nielshulstaertcommented, Apr 20, 2021

Ok thanks for all the input, I’ll release a new version later today.

2reactions

caeteracommented, Apr 20, 2021

@nielshulstaert Yes, I think we have to release some sort of quick-fix for now. I was not expecting this small change will have such a huge effect. @martenson I agree that I should have been more aware of downstream tools when implementing the change. Sorry

It would be nice, however, to let the developers of the downstream tools aware that the change is to be implemented soon. Display some sort of warning, but I cannot come with a good idea how that is to be implemented

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