A comparative study of the collision induced dissociation and the electron capture dissociation of model peptides using ESI-FTMS.

Tandem mass spectra of several model peptides, including KG3WG3K, NG3WG3N, RG7R, RG3WG3R, RG3DG3R, RG3EG3R, RG3FG3R and RG5WG5R were studied using both SORI-CID and ECD methods. By cross comparing the fragmentation pattern of these peptides using the same dissociation method and the same peptide using different dissociation methods, interesting spectral features that are related to the mechanisms of dissociation under SORI-CID and ECD conditions were extracted. Both dissociation methods were believed to be charge-directed. Due presumably to the stepwise ion activation, peptide ion dissociation under SORI-CID conditions was influenced mainly by "localized" hydrogen bonds. Consistent with previous literature findings, mobility proton model could be used to account for the spectral features observed. Substantial changes in the fragmentation patterns of these peptides were observed by using ECD methods. By postulating that the initial tertiary structures of the peptide ions were retained prior to electron capture process, the changes in fragmentation pattern could be attributed to the directing effect of the "global" hydrogen-bonding network. From the present results, no special preference was observed for cleavage at the backbone linkages adjacent to tryptophan residue over other inter-residual linkages. The previous reported nine-times cleavage preference at the C-terminal side of the tryptophan residue should therefore be attributed to some sequence specific phenomena.