229 integration of i2masschroq results in dda quantification ion level module

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.readthedocs.io

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229 integration of i2masschroq results in dda quantification ion level module #247

Closed mlocardpaulet closed 4 months ago

mlocardpaulet commented 4 months ago

I have made the toml, and added "i2MassChroQ" where needed (included to set up the colors of the dots, maybe we want to make this bit automatic). I have not work at all on tests. I am happy to do so but may need pointers, never did testing before. There is an error, and I think that it is connected to proforma parsing. The error message is triggered from get_proforma_bracketed (from what I understood):

mlocardpaulet commented 4 months ago

here is an example of a modified sequence in the input table: "AALQEELQLC[MOD:00397]K"

mlocardpaulet commented 4 months ago

looks good. @wolski , we turned off some features of the plots that you added because it was becoming too slow. We can discuss this.