Protonated dipeptide losses from b(5) and b(4) ions of side chain hydroxyl group containing pentapeptides

In this study, C-terminal protonated dipeptide eliminations were reported for both b5 and b4 ions of side chain hydroxyl group (-OH) containing pentapeptides. The study utilized the model C-terminal amidated pentapeptides having sequences of XGGFL and AXVYI, where X represents serine (S), threonine (T), glutamic acid (E), aspartic acid (D), or tyrosine (Y) residue. Upon low-energy collision-induced dissociation (CID) of XGGFL (where X = S, T, E, D, and Y) model peptide series, the ions at m/z 279 and 223 were observed as common fragments in all b5 and b4 ion (except b4 ion of YGGFL) mass spectra, respectively. By contrast, peptides, namely SMeGGFL-NH2 and EOMeGGFL-NH2, did not show either the ion at m/z 279 or the ion at m/z 223. It is shown that the side chain hydroxyl group is required for the possible mechanism to take place that furnishes the protonated dipeptide loss from b5 and b4 ions. In addition, the ions at m/z 295 and 281 were detected as common fragments in all b5 and b4 ion (except b4 ion of AYVYI) mass spectra, respectively, for AXVYI model peptide series. The MS(4) experiments exhibited that the fragment ions at m/z 279, 223, 295, and 281 entirely reflect the same fragmentation behavior of [M + H](+) ion generated from commercial dipeptides FL-OH, GF-OH, YI-OH, and VY-OH. These novel eliminations reported here for b5 and b4 ions can be useful in assigning the correct and reliable peptide sequences for high-throughput proteomic studies.