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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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MSFragger-DIA output parsing #396

Closed rodvrees closed 2 months ago

rodvrees commented 2 months ago

By default, quantification output from MSFraggerDIA is a DIA-NN report.tsv file. I'm assuming the user should still specify MSFragger-DIA and not DIA-NN in the web interface. However, it is possible to do quantification with Ionquant as well, which will result in an MSFragger output file. What should we do about this? Have multiple parsing options for MSFragger-DIA, stick to the default workflow, ...?

Originally posted by @rodvrees in https://github.com/Proteobench/ProteoBench/issues/395#issuecomment-2333458456_

rodvrees commented 2 months ago

Another (bigger) problem: DIA-NN quant output from MSFraggerDIA also loses species (gene names) information, just like spectronaut. @brvpuyve

rodvrees commented 2 months ago

As discussed during the hackathon, there should be two options: MSFraggerDIA + DIA-NN and MSFraggerDIA + Ionquant