I have analysed a label-free phosphoproteomics dataset with Progenesis QI. I am now trying to filter out my phosphopeptides with the PhosphoRS algorithm to only keep the phosphopeptides with high confidence for the phosphosite localisation (>75%) for further analysis. I have an .mgf file and .mzIdentML file from the Progenesis analysis. I am trying to find a script to run the PhosphoRS algorithm on R. The isobar package has that function but I'm unsure if it works for label-free phosphoproteomics as well. Moreover, I can't find the full script to merge my .mgf and .mzIdentML files in order to create the PhosphoRS input file. Any advice on how to run this analysis would be great. I am a beginner on R. Thanks!

Isaline Mees PhD student, Florey Institute of Neurosciences Melbourne, Australia