Effect of the sarcosine residue on sequence scrambling in peptide b(5) ions.

The effect of N-methylation on sequence scrambling in the fragmentation of b(5) ions has been investigated by studying a variety of peptides containing sarcosine (N-methylglycine). The product ion mass spectra for the b(5) ions derived from Sar-A-A-A-Y-A and Sar-A-A-Y-A-A show only minor signals for non-direct sequence ions the major fragmentation reactions occurring from the unrearranged structures. This is in contrast to the b(5) ions where the Sar residue is replaced by Ala and sequence scrambling occurs. The b(5) ion derived from Y-Sar-A-A-A-A shows a product ion mass spectrum essentially identical to the spectrum of the b(5) ion derived from Sar-A-A-A-Y-A, indicating that in the former case macrocyclization has occurred but the macrocyclic form shows a strong preference to reopen to put the Sar residue in the N-terminal position. Similar results were obtained in the comparison of b(5) ions derived from A-Sar-A-A-Y-A and Sar-A-A-Y-A-A. The product ion mass spectra of the MH+ ions of Y-Sar-A-A-A-A and A-Sar-A-A-Y-A show substantial signals for non-direct sequence ions indicating that fragmentation of the MH+ ions channels extensively through the respective b(5) ions and further fragmentation of these species. Copyright (c) 2014 John Wiley & Sons, Ltd.