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compomics / psm_utils

Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python
https://psm-utils.readthedocs.io
Apache License 2.0
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Getting Name Error with MSGFplus mzid file #72

Closed thulasis closed 1 month ago

thulasis commented 9 months ago

Hi there,

I am using ms2resocre on my msgfplus resulted PSM files. I am using the following command to execute the ms2resocre ms2rescore -p Desktop/Demo_data/data/20072102.mzid -s Desktop/Demo_data/data/20072102.mzML -c Desktop/Demo_data/config_file.json I am running the version 3.0.0 OS: Linux

I am getting the KeyError Name Error. Herewith I attached the error log ms2rescore.log.

Please help me with this.

I request you provide a good user manual or documentation for using ms2resocre program. ms2rescore.readthedocs.io isn't so helpful for executing the ms2rescore.

Thank you, Tulasi

RalfG commented 5 months ago

Hi @thulasis,

Thanks for using MS²Rescore! It seems that there is an issue while parsing one of the amino acid modifications from the mzIdentML file from MS-GF+. Could you share the mzIdentML file that generated the issue? That would help us tremendously to fix the issue.

Thanks, Ralf

RalfG commented 5 months ago

Regarding the documentation, do let us know which parts of using MS²Rescore or from the documentation were unclear to you. We are always looking to improve user experiences.