single python script to convert .idXML files to PMSs format, which is generated by proteome discoverer.
This particular pipeline was used to generate PSMs outputs for Calisp-2 without needing to use proteome discoverer.
Script was designed to be run in Spyder 5.15
The variable 'files' should be edited to contain the full filepaths of the files that need to be processed.
outputs are written to the directory of the input files.
There are two script versions, one for inputs where modifications are listed in the idXML file with a delimiter '_modifications', and one where modifications of unknown masses are matched to unimod.
The unimod version is also avaiable to convert pepXML to PSMs format for Calis-p