Isomer differentiation via collision-induced dissociation: the case of protonated alpha-, beta2- and beta3-phenylalanines and their derivatives.

A combination of electrospray ionisation (ESI), multistage and high-resolution mass spectrometry experiments is used to examine the gas-phase fragmentation reactions of the three isomeric phenylalanine derivatives, alpha-phenylalanine, beta(2)-phenylalanine and beta(3)-phenylalanine. Under collision-induced dissociation (CID) conditions, each of the protonated phenylalanine isomers fragmented differently, allowing for differentiation. For example, protonated beta(3)-phenylalanine fragments almost exclusively via the loss of NH(3), only beta(2)-phenylalanine via the loss of H(2)O, while alpha- and beta(2)-phenylalanine fragment mainly via the combined losses of H(2)O + CO. Density functional theory (DFT) calculations were performed to examine the competition between NH(3) loss and the combined losses of H(2)O and CO for each of the protonated phenylalanine isomers. Three potential NH(3) loss pathways were studied: (i) an aryl-assisted neighbouring group; (ii) 1,2 hydride migration; and (iii) neighbouring group participation by the carboxyl group. Finally, we have shown that isomer differentiation is also possible when CID is performed on the protonated methyl ester and methyl amide derivatives of alpha-, beta(2)- and beta(3)-phenylalanines.