Investigation of peptide size, residue position, neighbor amino acid and side chain effect on macrocyclization of b(n) (n=5-7) ions

A systematic study was carried out to examine the effects of the side chain, peptide size, residue position, and neighboring amino acid on the macrocyclization of b ions. The work utilized isomeric model peptides YAGFLV-NH2, AGFLVY-NH2, GFLVYA-NH2, FLVYAG-NH2, LVYAGF-NH2, VYAGFL-NH2, which all have the same amino acid sequence in cyclic form. The b(6) ions derived from all these isomeric peptides form the same macrocyclic structure due to the generation of the same amino acid sequence order upon cyclization. Hence, the MS/MS spectra and breakdown graphs of b(6) ions derived from these peptides are similar to each other. However, the relative intensities of the non-direct sequence ions in both the MS/MS spectra and breakdown graphs of the b(6) ions derived from FAYVGL-NH2, GVYALF-NH2 and VFYLAG-NH2 show a different distribution from each other and the first series, even though they are all isomeric peptides. This could be due to the different amino acid sequence order in the cyclic forms of these peptides. It is clearly shown that the neighboring amino acid influences the selective opening of the macrocyclic form.