search

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

Proteome Discoverer node / PSM file support #73

Closed rolivella closed 8 months ago

rolivella commented 1 year ago

Hello! I would like to ask if you are planning to make a Proteome Discoverer node for you tool. It would be very usefull for our facility and I think that for the entire community. Thanks!

RalfG commented 1 year ago

Hi @rolivella,

Unfortunately, implementing (non-C#) software in PD is not that straightforward. So, it is currently not on our priority list. We are, however, implementing support for PD result files as input to our proteomics ML tools (MS²PIP, DeepLC, and MS²Rescore) with our in-development package psm_utils.

What is the exact use case for MS²PIP you would have in mind as PD node? Simple validation of PSMs, or full rescoring (with MS²Rescore)?

Best, Ralf

rolivella commented 1 year ago

Hi @RalfG ,

Yes, we're using PD with Mascot and we would like to do a full rescoring. In any case, at the moment we can wait for the psm_utils implementation and test it.

Thank you,

Roger

RalfG commented 8 months ago

Hi, @rolivella,

Happy to announce that ProteomeDiscoverer MSF files are now supported in MS²Rescore 3.0. Exported mzIdentML files should also work.

Let us know how it works out for you!

Ralf

rolivella commented 8 months ago

@RalfG thanks! I'll try it and let youb know!