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compomics / ms2rescore

Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
https://ms2rescore.readthedocs.io
Apache License 2.0
39 stars 14 forks source link

MSMS Parsing with MaxQuant #136

Open JesusCastano01 opened 3 months ago

JesusCastano01 commented 3 months ago

Hi,

I have been trying to do rescoring using the MS2rescore user interface on some MaxQuant results, but I keep getting this error message:

"File "psm_utils\io\maxquant.py", line 98, in _evaluate_columns raise MSMSParsingError( psm_utils.io.maxquant.MSMSParsingError: Missing columns: ['Raw file']"

I'm not sure how to fix this.

Any help would be greatly appreciated. Thanks, Jesus

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RalfG commented 3 months ago

Hi Jesus,

Most likely it is a file encoding issue. Could you open the MaxQuant file in an editor such as notepad, notepad++, or vscode and save it with utf-8 as encoding?

For instance, on Windows:

image

Let us know if that fixes the issue.

Best, Ralf

Potentially related to compomics/psm_utils#68.

JesusCastano01 commented 3 months ago

Hi, Thank you. This resolved the issue, and I could start the run. However, it seems that the software now gets stuck in one of the steps, as shown in the figure below. The error where it gets stuck says "Can't pickle local object 'create_engine..connect'" For what's worth, disabling MS2PIP allows you to finish the run successfully, but of course, disabling this is giving up one of the main reasons to use MS2Score in the first place. Therefore, I think there's a problem specifically with MS2PIP, but I'm unsure how to solve it.

Do you have any idea about what could fix this issue?

image

RalfG commented 2 months ago

Hi @JesusCastano01,

The pickling issue should be fixed in the Windows desktop installer for v3.0.3.

Best, Ralf