[Version: Any] Proteome Discoverer doesn't parse MGF scan numbers correctly

[michabirklbauer]

Proteome Discoverer doesn't read scan numbers from MGF files correctly and just numbers spectra from 0 to n. This messes up down-stream analysis as CSMs can't be properly mapped back to the spectra they originate from. This can't be fixed in MS Annika as MS Annika doesn't read the MGF file, Proteome Discoverer does - however it is possible to remap output files with the this tool we implemented: https://github.com/hgb-bin-proteomics/Proteome_Discoverer_MGF_Scan_Number_Repair_Tool