Collision-induced dissociation of singly charged peptide ions in a matrix-assisted laser desorption ionization ion trap mass spectrometer

We document the systematics of collision-induced dissociation of singly cha rged peptide ions in a matrix-assisted laser desorption/ionization (MALDI) ion trap mass spectrometer. We show that singly charged peptide ions with m /z ratios extending to 3500 can be effectively fragmented using a newly dev ised excitation scheme, termed red shifted off-resonance large amplitude ex citation (RSORLAE), and classify the dominant features of the resulting col lision-induced dissociation spectra as follows. (1) Peptides ions with a m/ z value of <1500 can be effectively fragmented independent of their amino a cid composition. (2) Peptides ions with m/z <3000 that contain lysine but n ot arginine can be extensively fragmented. (3) Arginine-containing peptide ions undergo highly preferential fragmentation at the C-termini of aspartic /glutamic acid residues. (4) Peptide ions containing a C-terminal lysine re sidue as well as one or more arginine residues readily rearrange to lose th e terminal lysine. (5) Proline-containing peptide ions fragment preferentia lly at the N-termini of the proline residues. These systematics are helpful for the verification of peptide primary structures and for formulating eff icient strategies for protein identification using tandem MALDI ion trap ma ss spectrometric data. (Int J Mass Spectrom 190/191 (1999) 313-320) (C) 199 9 Elsevier Science B.V.