, Volume 19, Issue 12, pp 1776-1780

Peptide sequence scrambling through cyclization of b5 ions


The CID mass spectra of the MH+ ions and the b5 ions derived therefrom have been determined for the hexapeptides YAAAAA, AYAAAA, AAYAAA, AAAYAA, and AAAAYA. The CID mass spectra for the b5 ions derived from the five isomers are essentially identical and show abundant ion signals for nonsequence b ions. This result is consistent with cyclization of the b5 ions to a cyclic pentapeptide before fragmentation; this cyclic peptide can open at various positions, leading to losses of amino acid residues that are not characteristic of the original amino acid sequence. These nonsequence b ions are also observed in the fragmentation of the MH+ ions and increase substantially in importance with increasing collision energy. A comparison of the fragmentation of AAAYAA and Ac-AAAYAA indicates that N-acetylation eliminates the cyclization of b5 ions and, thus, eliminates the nonsequence ions in the CID mass spectra of both b5 and MH+ ions.

Published online July 3, 2008