I have MS/MS data that I searched with MS-GF+. Unfortunately, MS-GF+ doesn't do protein inference, so I have a list of peptides in .mzid format. Our workflow is in R.
Putting all that together - does there exist an R package which will perform protein inference (i.e. give protein IDs) and accepts .mzid files?
I know there are R packages that do protein inference, and I know there are protein inference tools that accept .mzid, but I don't know of any tools that are both an R package and accept .mzid. Any help?