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 b(2) 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 oxozolone structures liberate CO. Only lysine and arginine do not fragment by way of CO, which is suggestive of alternative cyclic structures involving the side chain. Ab initio calculations (at the MP2/6-31G*//HF/6-31G*) were carried out on isomeric b(2) ions of both types (oxazolone and that involving side-chain interaction) derived from arginine, histidine, lysine, methionine, asparagine, glutamine, and serine. For arginine, histidine, and lysine the cyclic structures involving the side chain are more stable than the oxozolone structures. Finally, solution phase data relevant to the gas phase processes are highlighted. (C) 2001 Elsevier Science B.V.
