The IDFileConverter does not import the peptide-protein mappings correctly.
For example, in this pepXML [1] the peptide MGESDDSILR is correctly associated with a single protein, P63220. In the corres…
It has previously been demonstrated that trypsin has digestion problems if the AA in the vicinity of the K|R in the cleavage sites are
1) P; trypsin is incapable of cutting if P is in +1 position. Ar…