Comments on a 'Proposal for a common nomenclature for sequence ions in mass spectra of peptides'

An expanded nomenclature scheme for labeling peptide fragmentations and its use with 'AMASS', a computer program for generating all possible fragment ion structures from known precursors

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.

Analysis of the amino acid sequence of peptides by mass spectrometry. An ion notation proposal

A new nomenclature is proposed that allows a precise and concise description of mass spectrometric fragments derived from peptides. The nomenclature differs from existing methods by specifically accommodating (1) extended or unusual amino acid residues, (2) cyclic- and cyclodepsipeptides, and (3) residues contained in branches of the main chain.

Contributions of mass spectrometry to peptide and protein structure

With the advent of recombinant deoxyribonucleic acid (DNA) technology which allows a wide range of manipulation of genes and their expression in cell lines other than the natural ones, many aspects of protein structure have become more important than ever. In addition to the determination of the amino acid sequence questions relating to homogeneity, the nature of post-translational modifications, the verification of the structure of a protein produced by a synthetically modified gene or the detection of a natural mutant are all questions that are more and more frequently asked and with the demand for more detail. Mass spectrometry has emerged as an important contributor to this field, particularly since the advent of fast atom bombardment (FAB) ionization, which makes it possible to ionize directly large polar molecules such as peptides and small proteins. As such, FAB mass spectrometry provides mainly molecular weight information which, in itself, often suffices to answer certain questions, particularly because the mass of many peptides can be determined directly from a single mass spectrum of a mixture. However, in order to obtain detailed structural information, such as the amino acid sequence, fragmentation has to be induced by collision processes and the product ions separated, preferably in the second mass spectrometer of a tandem system. This approach is particularly suited for the determination of the sequence of N-blocked peptides and the nature of the blocking group; the type and location of modified (i.e. phosphorylated, sulfated, glycosylated) amino acids; detection or verification of amino acid replacements; confirmation of the structure of synthetic peptides; and last but not least, the determination of the primary structure of proteins.

Fast atom bombardment mass spectrometry in the pharmaceutical analysis of drugs

The principles, techniques and value of fast atom bombardment mass spectrometry are summarized in this revïew. Applications of the method in such areas as molecular weight determination, standard and metabolic studies, and peptide sequencing, as well as direct quantitative analysis, are surveyed, with examples from several classes of compounds with pharmacological activity.