A nomenclature system for labeling cyclic peptide fragments
- Cite this article as:
- Ngoka, L.C.M. & Gross, M.L. J Am Soc Mass Spectrom (1999) 10: 360. doi:10.1016/S1044-0305(99)00006-9
A nomenclature system for labeling fragment ions of cyclic peptides is proposed. A fragment ion is labeled with a four-part descriptor of the general formula xnJZ, where x is the designation for the ion (e. g., lower case a or b, as are used for peptide fragments) and n is the number of amino acid residues in the ion. A b ion is the usual acylium ion or isomeric equivalent consisting of n amino-acid residues, and this ion may lose carbon monoxide to form an a ion. The subscripts J and Z are the one-letter (upper-case) codes for the two amino-acid residues connecting the backbone amide or ester bond, J-Z, that can be viewed as broken to form the decomposing linear ion. The symbol J is for the N-terminal amino-acid residue, and Z is that for the C-terminal amino-acid residue that result from the bond cleavage. The nomenclature system is applicable to a wide range of cyclic peptides, including depsipeptides, cyclic peptides containing modified or unusual amino acids, cyclic peptides bearing a linear peptide moiety, and cyclic peptides that are introduced into the gas phase as metal-ion cationized species.