Peptides derived from enzymatic digestions (cathepsin D and trypsin) were characterized and amino acid sequences determined by using their LC/MS spectra. A Frit-FAB Interface that produces extensive peptide fragmentation and permits amino acid sequencing at the low picomole level Is described for a model antigen, Staphylococcus aureus nuclease (Nase), and an enzyme of unknown structure, yeast amlnopeptidase B. The amino acid sequences of peptides derived from digestion of Nase with cathepsln D (a relatively nonspecific endoprotease) were readily deduced and have provided Insights Into the nature of antigen processing. Frtt-FAB LC/MS spectra of the Nase peptides contained a sufficient number of fragment Ions to conclusively Identify peptides with a mass below 2000 Da. Capillary LC/MS provided a means for the separation and Identification of these enzymatically derived peptides In a fraction of the time that would have been required by gas-phase Edman sequence analysis. The optimized Frtt-FAB experiment was consequently evaluated for the partial characterization of amlnopeptldase B recently purified to homogeneity from Saccharomyces cerevislae. Sequence-specific Ions observed In the Frtt-FAB mass spectra of these tryptic peptides were Identical with those commonly observed In high-energy collision-induced dissociation (CID) spectra and included side-chain fragment ions that differentiated leucine from Isoleuclne. These fragment lons were used to deduce entire amino acid sequences for several of the tryptlc peptides. © 1991, American Chemical Society. All rights reserved.