Do all b2 ions have oxazolone structures? Multistage mass spectrometry and ab initio studies on protonated N-acyl amino acid methyl ester model systems

Abstract

The tandem mass spectrometry fragmentation reactions of 21 protonated N-acyl amino acid methyl esters are examined as models for more complicated peptides. Four main types of reactions are observed: loss of CH2CO from the N-terminal acetyl group; loss of CH3OH from the C-terminal ester group to yield a model system for a b2 ion structure; loss of water from amino acids without an OH side chain group; fragmentation of the side chain by way of small molecule loss (e.g. H2O, NH3, and CH3SH). CH3OH loss is the only common reaction observed for all systems. The resultant [M+H-CH3OH]+ ions were examined in further detail by way of MS3 experiments because previous studies have shown that the oxozol..