search

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
Apache License 2.0
27 stars 7 forks source link

Peptidoform and peptide modules #258

Open RobbinBouwmeester opened 4 months ago

wolski commented 4 months ago

The files in io_parse_settings in dda_quant_base and dda_quant_ion are identical. They can be removed from "dda_quant_base".

Regarding the test/data folder, should we have subfolders for each module, e.g. test/data/DDA_ion etc?

Do we have peptidoform files in test/data for the peptideform module? Maxquant reports peptide level quantification in the peptide.txt file. But this is the peptide (stripped sequence) level. Do we benchmark software not reporting quantification on the peptidoform level with this module, e.g., by rolling up (aggregating) precursor or PSM intensities to the peptidoform level, or do we exclude those tools?

wolski commented 4 months ago

When running the "Parse bench" in the Qunat Peptidoform Level - BETA -

image

Tested on 70fa3a7 and later commits

wolski commented 4 months ago

Also, there are now three parse.py files in dda_quant_base in dda_quant_ion and dda_quant_peptidoform There is some code duplication among those files, e.g. convert_to_standard_format is present in base and peptidoform, aggregate_modification_column in base and peptidoform, etc.