In this study, C-terminal protonated dipeptide eliminations were reported for both b (5) and b (4) 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 b (5) and b (4) ion (except b (4) ion of YGGFL) mass spectra, respectively. By contrast, peptides, namely S(Me)GGFL-NH2 and E(OMe)GGFL-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 b (5) and b (4) ions. In addition, the ions at m/z 295 and 281 were detected as common fragments in all b (5) and b (4) ion (except b (4) ion of AYVYI) mass spectra, respectively, for AXVYI model peptide series. The MS4 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 b (5) and b (4) ions can be useful in assigning the correct and reliable peptide sequences for high-throughput proteomic studies.