Electrospray ionization ion trap multiple-stage mass spectrometric fragmentation pathways of leucine and isoleucine: an ab initio computational study

We recently demonstrated the possibility to distinguish between leucine and isoleucine in several tryptic peptides by means of consecutive tandem mass steps (Armirotti et al. J. Am. Soc. Mass Spectrom. 2007; 18: 57), exploiting a gas-phase rearrangement of the immonium ion of Ile. In the present paper we explore the tandem mass spectrometric behaviour of the two amino acids. We propose a plausible structure for the diagnostic m/z 69 ion of Ile, that was reported for the first time in 1996 (Hulst and Kientz J. Mass. Spectrom. 1996; 31: 1188), and we explain why its formation is favoured with respect to Leu. Our conclusions are supported by ab initio quantum chemistry calcultations and isotope-labelled standards experiments.