Fragmentations of (M-H)- anions of underivatised peptides. Part 2: Characteristic cleavages of Ser and Cys and of disulfides and other post-translational modifications, together with some unusual internal processes

In a previous review (Bowie, Brinkworth, & Dua (2002); Mass Spectrom Rev 21:87-107) we described the characteristic backbone cleavages and side chain fragmentations which occur from (M-H)(-) parent anions of underivatized peptides. This work is briefly summarized in the present review. Cys was not described in the previous review: here we describe the Cys characteristic side chain loss of H(2)S, together with its gamma backbone cleavage. These processes are compared with those of the related Ser. All experimental observations are backed up with theoretical studies at the HF/6-31G(d)//AM1 level of theory, a level of theory which we have shown gives good geometries and acceptable relative energies. The negative ion cleavages of a number of post-translational modifications are described. Negative ion mass spectrometry is the method of choice for identification of disulfides in both peptides and proteins. Intramolecular disulfides are identified by the presence of the fragment anion [(M-H)(-)-H(2)S(2)], and CID MS2 of this fragment normally identifies the positions of the two Cys residues and often the full sequence of the peptide. An unsymmetrically substituted intermolecular disulfide can give up to eight characteristic fragment anions, and CID MS2 of some, or all of these often provides the full sequence of those peptides which form the initial intermolecular disulfide linkage. Negative ion cleavages of disulfides are the most energetically favored of all peptide negative cleavages studied to date. Negative ion mass spectrometry is also valuable for the identification of pyroglutamates, sulfates and phosphates. Finally, some unusual fragmentations are described which involve cyclization/elimination reactions which require the decomposing (M-H)(-) parent anions to adopt the same helical conformation that these peptides have in solution.