Structural and Mechanistic Information on c1 Ion Formation in Collision-Induced Fragmentation of Peptides

The formation of c1 ions during collision-induced fragmentation of peptides with asparagine, ornithine, or glutamine at the N-terminal position 2 has been studied. For this purpose, the corresponding fragment ion spectra of a large set of synthetic peptides were investigated. It is demonstrated that the c1 ion intensity depends on the nature of the second residue in the N-terminal dipeptide motif as well as on the peptide length. It is shown that the formation of c1 ions proceeds by two competing mechanisms. One mechanism is the secondary fragmentation of the b2 ion, the efficiency of which shows only a minor dependency on the complete peptide sequence. The other mechanism is the direct formation from the molecular ion, which is identified to be connected with sequence-specific c1 ion intensities. A model for this latter mechanism is proposed based on the analysis of the formation and secondary fragmentation of the zmax-1 ion, which is the complementary ion to the c1 ion. Additional evidence is obtained by investigation of peptides with ornithine in N-terminal position 2, which in general exhibit c1 ion intensities intermediate between the asparagine- and glutamine-containing species. The data presented support the reliable assignment of N-terminal dipeptide motifs using collision-induced dissociation.

Graphical AbstractIdentification of a new mechanism for the formation of c1 ions from peptides containing glutamine or asparagine in N-terminal position 2.Figure optionsDownload high-quality image (33 K)Download as PowerPoint slide