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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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Add Spectronaut support #372

Closed brvpuyve closed 2 weeks ago

brvpuyve commented 3 months ago

=> Input files: https://cloud.cmb.ugent.be/index.php/s/zdGB3zZ7Fwed9gq?path=%2FModule_4_DIA_Quantification%2FSpectronaut

In the parameter file no clear definition of MS1 and MS2 tolerance: │ ├─ MS1 Mass Tolerance Strategy: System Default │ └─ MS2 Mass Tolerance Strategy: System Default

brvpuyve commented 2 months ago

Can someone also help out with the documentation on Spectronaut? @wolski @AnStaes

rodvrees commented 2 months ago

@brvpuyve, none of the input files have species information. E.g. there's no columns with _HUMAN or _YEAST output, which is necessary.

brvpuyve commented 2 months ago

@rodvrees Witold reran the analysis with some changed parameter settings which should have resolved the loss of species information. The files have been uploaded to the Cloud server.

rodvrees commented 2 months ago

Spectronaut output parsing is now ready (#399). Instead of the user having to fiddle with settings to assure the species information is present, we've implemented a mapping step so that gene names get mapped to the correct protein descriptor.

e.g. Q8WWZ7 (in spectronaut output) will be mapped to sp|Q8WWZ7|ABCA5_HUMAN.

This will also apply for FraggerDIA output, which has the same issue

brvpuyve commented 2 months ago

Great, thanks Robbe!

wolski commented 2 weeks ago

Spectronaut support completed with PR #437