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Proteobench / ProteoBench

ProteoBench is an open and collaborative platform for community-curated benchmarks for proteomics data analysis pipelines. Our goal is to allow a continuous, easy, and controlled comparison of proteomics data analysis workflows. https://proteobench.cubimed.rub.de/
https://proteobench.readthedocs.io
Apache License 2.0
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Peptidoform module #347

Open RobbinBouwmeester opened 2 months ago

RobbinBouwmeester commented 2 months ago

We need to figure out what is currently supported, what input files we need exactly, and what we can add.

mlocardpaulet commented 2 months ago

I think that in the peptidoform module we could add WOMBAT-P data. Maybe @veitveit could generate some for us? And maybe Proteome Discoverer has an output at peptidoform level that we could use.

RobbinBouwmeester commented 2 months ago

I am indeed currently testing the module with WOMBAT-P, that works.

mlocardpaulet commented 2 months ago

I think that we could also use some MQ outputs from the same searches as the ones done for the ion module. Not the evidence.txt but there is another text export with peptides (I think). Should I send you some?

mlocardpaulet commented 2 months ago

It will be super great to have the WOMBAT-P runs because they should already cover several pipelines ❤️