Does anyone knows of a way to easily convert between the mass-spec database search result formats (specifically, converting from pep.XML to id.csv), preferably within the R environment? We have a series of pep.XML files which we would like to import into the Bioconductor package "isobar". However, the readIBSpectra() function included in this package only seems to recognize id.csv or mzIdentML file formats. (PS: I am new to working with mass-spec data, so please pardon any naivete intrinsic to this question!)
I don't know too much about R but Python's XML parser does an excellent job in doing what you want. Once you know the fields within this id.csv file that ISOBAR accepts, extract the information with the parser, store them as lists and push them to a writing file,
Please ignore this post if Python is not the way you want to go.