Effect of the sarcosine residue on sequence scrambling in peptide b5 ions

The effect of N‐methylation on sequence scrambling in the fragmentation of b₅ ions has been investigated by studying a variety of peptides containing sarcosine (N‐methylglycine). The product ion mass spectra for the b₅ 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 b₅ ions where the Sar residue is replaced by Ala and sequence scrambling occurs. The b₅ ion derived from Y‐Sar‐A‐A‐A‐A shows a product ion mass spectrum essentially identical to the spectrum of the b₅ 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 b₅ 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 b₅ ions and further fragmentation of these species. Copyright © 2014 John Wiley & Sons, Ltd.