Schiff base derivatives of peptide esters: Relative abundance of N-terminal,C-terminal and ‘internal’ fragments as a function of the blocking group

Electron-impact (EI) mass spectrometry of peptide derivatives is usually interpreted in terms of fragmentation where the charge resides on the N-terminal fragments and to a lesser degree on the less common, charged C-terminal fragments. Substituted and unsubstituted benzylidene, cinnamylidene, α- and β-naphthylidene derivatives of a reference tripeptide, valileala, gave both N- and C-terminal fragments as well as molecular ions. The order of increasing ion current (normalized) in C-terminal fragments was: acetylacetonyl, 4-dimethylaminonaphthylidene, p-dimethyl-aminobenzylidene, 3-pyridylmethylidene, p-diethylaminocinnamylidene, benzylidene, 2-hydroxy-naphthylidene, 4-pyridylmethylidene, p-nitrobenzylidene, p-methoxybenzylidene, p-cyanobenzylidene, cinnamylidene, p-dimethylaminocinnamylidene, β-indolylmethylidene, β-naphthylidene, 2-pyridylmethylidene and α-naphthylidene. The order for this value among the N-terminal fragments is significantly different, however (Day, Falter, Lehman and Hamilton, J. Org. Chem. in press). In addition to N- and C-terminal fragments, many spectra contain internal fragments, arising from loss of fragments from both ends, which provide sequence information. These fragments are found in the mass spectra of Schiff bases formed from various aromatic aldehydes with peptide esters. The interpretation of the latter pattern is facilitate in some cases by deuterium labeling at the α-carbon of the N-terminal amino acid residue of peptides. Such a pattern provides sequence information supplemental to that available involving N- and C-terminal fragmentations. In derivatives of hexaglycine, tetraphenylalanine and tryptophylmethionylaspartyl (β-OEt) phenylalanine amide, for example, substantial sequence information was contained in the internal fragments; in some cases the sequence could be deduced only if the internal fragments were utilized. The 4-dimethylamino-naphthylidene derivatives have proven to be the most useful to date in terms of volatility, tendency to maximize cleavage into N-terminal fragments, intensity of molecular ions and generation of useful mass spectra of certain peptide esters refractory to mass spectrometry in the form of any other derivative investigated.