Proteomics to pathway data analysis R and Python packages

Question

[sbt_gvs]

Hello all.

Need some recommendations, have an excel file of proteomics data, below image is the example table. The database set Name is the mjdb_mouse-20150516

I tried using the DEP package in R, but since quantification is already normalized and not raw counts I get an error in building the SE object. Is there any other package in R or python that I can use to perform differential analysis and pathway analysis? Also, does this format of the table below work with IPA software, or do I need to add any metadata or transform it, if so how?

Any publication reference or example code is helpful.