Electron capture dissociation Fourier transform ion cyclotron resonance mass spectrometry of cyclodepsipeptides, branched peptides, and ε-peptides

Although electron capture dissociation (ECD) offers many advantages for structural elucidation, a fundamental understanding of all possible processes following electron capture is necessary if ECD is to succeed in the characterization of unknowns. Many biologically active compounds have non-standard structures, e.g, N-alkylation, branching, cyclization, and ester linkages. Here we report ECD of cyclodepsipeptides (valinomycin and beauvericin), including N-methylated structures (beauvericin), branched peptides (AcA3K(G3)A3–NH2 and A3K(G3)A3–NH2), and oligomers of ε-amino acids (ε-peptides) (Ac(Ahx)6K and (Ahx)6K) to establish the behavior of such non-standard structures. ECD of cyclodepsipeptides yielded numerous backbone fragments but no charge-reduced species, consistent with a radical cascade mechanism. ECD of ε-peptides resulted in a• and y fragments only, suggesting that the N–C c/z• fragmentation channel is impeded in those structures. ECD of branched peptides resulted in complex fragmentation patterns, characterized by the presence of the immonium related m ion from the modified residue. © 2004 Elsevier B.V. All rights reserved.