How to convert msgf+ output to peprec?

compomics / ms2pip

MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.

https://ms2pip.readthedocs.io

Apache License 2.0

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How to convert msgf+ output to peprec? #208

Closed JannikSchneider12 closed 3 months ago

JannikSchneider12 commented 7 months ago

Hey everyone,

I have used msgf+ and now have either an mzid and/or a tsv results file. Now I wanted to convert this to a valid peprec file for ms2pip. I tried the conversion scripts but it seems like non of them is specified for this kind of files?

Thanks for your time and help

RalfG commented 7 months ago

Hi Jannik,

Depending on your use case, it might be better to try out v4.0 of MS²PIP, which is currently in 'dev' releases. This version uses compomics/psm_utils to read the peptide information, and .mzid is one of the natively supported file formats. The only drawback currently is that not all spectral library formats have been implemented yet.

MS²PIP 4.0 can be installed with:

pip install ms2pip --pre

Let us know if this solves your issue.

Best, Ralf