Further studies on the fragmentation of protonated ions of peptides containing aspartic acid, glutamic acid, cysteine sulfinic acid, and cysteine sulfonic acid

Here we examined the fragmentation, on a quadrupole ion‐trap mass spectrometer, of the protonated ions of a group of peptides containing one arginine and two different acidic amino acids, one being aspartic acid (Asp) or glutamic acid (Glu) and the other being cysteine sulfinic acid [C(SO 2 H)] or cysteine sulfonic acid [C(SO 3 H)]. Our results showed that, upon collisional activation, the cleavage of the peptide bond C‐terminal to C(SO 2 H) is much more facile than that of the peptide bond C‐terminal to Asp, Glu, or C(SO 3 H). There is no significant difference, however, in susceptibility to cleavage of peptide bonds that are C‐terminal to Asp, Glu, and C(SO 3 H). To understand these experimental observations, we carried out B3LYP/6‐31G* density functional theory calculations for a model cleavage reaction of GXG → b 2  + Gly, in which X is Asp, Glu, C(SO 2 H), or C(SO 3 H). Our calculation results showed that the cleavage reaction is thermodynamically more favorable when X = C(SO 2 H) than when X = Asp or C(SO 3 H). We attributed the less facile cleavage of the amide bond after Glu to that the formation of a six‐membered ring b ion for Glu‐bearing peptides is kinetically not as favorable as the formation of a five‐membered ring b ion for peptides containing the other three acidic amino acids. The results from this study may provide useful tools for peptide sequencing. Copyright © 2004 John Wiley & Sons, Ltd.