I am trying to work with MSF files (and RAW files) downloaded from a manuscript via PRIDE/ProteomeXchange. I am just trying to access the complete proteome (not just peptide sequence) with confident/coverage from the file.
Unfortunately, the Thermo Proteome Discoverer Software used to generated the MSF files was version 220.127.116.11, so the version of Proteome Discoverer (18.104.22.1685) I am working with needs MSF files in at least version 22.214.171.124 format. I do not have a great deal of expertise in PD so I do not know if there is a way to convert these files.
I have tried to converting the MSF files with M2Lite, ProCon, and Thermo MSF Parser with no luck.
Does anyone have advice? I greatly appreciate any and all help!