Could not find matching spectra

[JesusCastano01]

Hi, I've been trying to run MS2Rescore from the Command Line, and I ran into an issue. I'm using MaxQuant search results, and it looks like I have to specify something for the parameters below, which are currently set at "null."

"psm_id_pattern": null, "spectrum_id_pattern": null,

I've checked the documentation, but I haven't been able to find a solution to this. There's an example for MGF, but not for MaxQuant. Do you have any ideas about how to solve this problem?

I'd appreciate any advice.

This is what my config.json file looks like, just in case it's useful.

[RalfG]

Hi @JesusCastano01,

You will indeed have to set one (or both) of those settings. Could you share the top of the MaxQuant msms.txt file and a section of an mzML file that contains a spectrum header? Depending on what the spectra are named in both files, we need to set regular expression patterns to match the two to each other.

Best, Ralf

[RalfG]

Relevant documentation: https://ms2rescore.readthedocs.io/en/stable/userguide/configuration/#mapping-psms-to-spectra