Related Experiment Video
Updated: Jun 30, 2026

Synthesis and Mass Spectrometry Analysis of Oligo-peptoids
Published on: February 21, 2018
An expanded nomenclature scheme for labeling peptide fragmentations and its use with 'AMASS', a computer program for
A G Craig1, S C Koerber, J Porter
1Clayton Foundation Laboratories for Peptide Biology, Salk Institute, San Diego, California 92138-9216.
Abstract:
A nomenclature scheme for exhaustively labeling peptide fragment ions is proposed. The scheme is based on IUPAC nomenclature and the previously proposed Roepstorff nomenclature scheme used to label fragment ions in linear peptides. The descriptor used is specifically defined in order to increase the number of peptide and side chain linkages to which the nomenclature scheme can be applied compared with the Roepstorff scheme. The proposed descriptor can be used unambiguously to assign all possible fragments from linear, cyclized, branched, extended (i.e. beta-amino acids) and retro inverso peptides. A significant advantage of the proposed scheme is its simple interface with the currently accepted Roepstorff scheme. This nomenclature scheme is able to label all theoretical fragments generated by the computer program 'AMASS'. AMASS is proposed as a means of systematically calculating the mass of all possible fragment ions from known precursor structures. The program can help determine whether a peptide fragment was derived from an internal sequence fragment or a combination of side chain and backbone cleavages. The program AMASS and the proposed nomenclature scheme are used to illustrate a procedure for identifying fragment ions in the metastable product ion spectrum of somatostatin-14. We envisage that this procedure will be useful for identifying fragment ions which are characteristic of particular structural arrangements in dicyclic and polycyclic peptides.
More Related Videos
Related Concept Videos
Mass Spectrometry: Molecular Fragmentation Overview
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can occur at...
Mass Spectrometry of Amines
Mass Spectrometry: Amine Fragmentation
In amines, the number of nitrogen atoms affects the mass of the molecular ion, which is described by the nitrogen rule of mass spectrometry. This rule states that a compound containing a single or...
Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation
For example, the fragmentation of...
Peptide Identification Using Tandem Mass Spectrometry
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
Mass Spectrum: Interpretation

