A nomenclature system for labeling cyclic peptide fragments

L. C.M. Ngoka, M. L. Gross

Research output: Contribution to journalArticlepeer-review

58 Scopus citations


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.

Original languageEnglish
Pages (from-to)360-363
Number of pages4
JournalJournal of the American Society for Mass Spectrometry
Issue number4
StatePublished - 1999


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