Electron capture dissociation (ECD) studies of two modified Amyloid βpeptides (20–29 and 25–35) were performed to investigate the role of H• radicals in the ECD of peptide ions and the free radical cascade (FRC) mechanism. 2,4,6-trimethylpyridinium (TMP) was used as the fixed charge tag, which is postulated to both trap the originally formed radical upon electron capture and inhibit the H• generation. It was found that both the number and locations of the fixed charge groups influenced the backbone and side-chain cleavages of these peptides in ECD. In general, the frequency and extent of backbone cleavages decreased and those of side-chain cleavages increased with the addition of fixed charge tags. A singly labeled peptide with the tag group farther away from the protonated site experienced a smaller decrease in backbone cleavage fragments than the one with the tag group closer to the protonated site. Despite the non-protonated nature of all charge carriers in doubly labeled peptide ions, several c and z• ions were still observed in their ECD spectra. Thus, while H• transfer may be important for the N-Cα bond cleavage, there also exist other pathways, which would require a radical migration via H• abstraction through space, or via an amide superbase mechanism. Finally, internal fragment ions were observed in the ECD of these linear peptides, indicating that the important role of the FRC in backbone cleavages is not limited to the ECD of cyclic peptides.
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