A strategy to assign a series of fragment ions: investigation of fragment ions involving peptide side chain and backbone cleavage

Abstract

We illustrate a strategy for identifying the possible structures which can be assigned to a series of fragment ions. The strategy uses the computer program amass to generate a list of all possible fragment structures for each ion and discards those structures that were not common within each list. We illustrate this strategy by comparing several “d” fragment ions present in the plasma desorption (PD) mass spectrum of peptide 1 (H-Arg-Arg-Arg-Glu-Glu-Glu-Thr-Glu-Glu-Ala-Ala-OH). From this comparison only three fragment structures were consistently observed; the “x/z” internal sequence fragment, the “z/a” internal sequence fragment and the “d” backbone, and sidechain fragment. On the basis of the measurement of an analog of peptide 1, both the “x/z” and “z/a” internal sequence fragment structures could be excluded. This strategy was used to help assign a series of unassigned fragment ions observed for peptide 1. The unassigned fragment ions were each observed about 14Da above the “d” series of fragment ions. Comparison of the possible fragment structures indicated that an internal sequence fragment could not explain the series of fragment ions. Only two fragment structures were consistently observed for all of the fragment ions. These fragment structures involve “a” type backbone cleavage with side chain cleavage between the γ—γ atoms or “b” type backbone cleavage with side chain cleavage between α—β atoms.