Statistical analysis of mass spectral data obtained from singly protonated peptides under high-energy collision-induced dissociation conditions.

A statistical study of the fragmentation behaviour of 138 model peptides, containing 3-9 amino acid residues (n = 3-9) under high-energy collision conditions is presented. The aim was to identify characteristic patterns of ions in the spectra of peptides which can be translated into general rules to be used in the spectral interpretation and provide a better insight into their fragmentation behaviour. It was found that both number and nature of the amino acids are important factors directing the fragmentation behaviour. The spectra of tri- and tetrapeptides exhibit a comparable probability for the formation of B2- and Y"n-2 ions, whereas larger peptides show a preference for the formation of Bn-1 ions. This generally observed fragmentation pattern of peptides is changed significantly when basic amino acid residues (Arg, Lys and His) and/or Pro are present Arginine appears to have the most pronounced influence on the fragmentation behaviour and overrules that of the other amino acid residues.