Unusual behavior of gem-diamino peptides in fast atom bombardment and electrospray ionization mass spectrometry

Backbone modified peptides are commonly investigated in the frame of therapeutic chemistry because of their increased stability towards enzymatic degradation. For these pseudopeptides, the standard analytical procedures using amino acid analysis and Edman degradation, which require proteinogenic residues, fail to provide structural identification. In contrast, mass spectrometry is particularly well suited for their characterization since informative spectra have been recorded for a vast variety of biomolecules using Gem-diamino peptides were studied by fast atom bombardment (FAB) and electrospray ionization (ESI) mass spectrometry to evidence specific fragmentations involving the labile modified bonds. Base peaks recorded in the positive mode were attributed to fragment ions even with soft atmospheric pressure ionization. The criterion that one ion corresponds to one molecule in ESI mass spectra commonly encountered in high throughput analysis of combinatorial libraries must be considered with caution when fragile structures are analyzed.