quantms.io protein groups representation. #559
Description
Description of feature
We have the protein groups in quantms.io representation here the section https://io.quantms.org/#protein. For all our datasets, Im producing quantms.io using the library. We can now produce for the DIA workflow the following:
- feature.parquet
- psm.parquet
- pg.parquet
However, for the TMT and LFQ workflow, we don't have support; this is mainly because we rely on MSStats. I want to gradually produce these files and convert from the mzTab protein tables to quantms.io. Here are two of the mzTab I recently produced for a TMT and an LFQ experiment:
- TMT: https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/absolute-expression-2025/tissues/PXD016999-second-instrument/quant_tables/ (A quick note here, apart of the mzTab we do have here other files like protein and peptide tables from proteinquantifier)
- LFQ: https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/absolute-expression-2025/tissues/PXD020192/quant_tables/
Can you @timosachsenberg @jpfeuffer help me to understand this information from the proteins to make sure that we are exporting the right information to quantms.io.
Please, if you need smaller files, let me know I can try to produce the mzTab examples. These ones are also updated: