The fragmentation pathways of protonated arginine, protonated N R ,N R -dimethylarginine, the N R ,N R ,N Rtrimethylarginine ion, three protonated N ,N -dimethyllysines, and three permanent lysine ions in which the charge is fixed by trimethylation are reported. Ion assignment was facilitated by 15 N-labeling and deuterium substitution. The chemistries are dominated by charge-induced elimination of the amino groups as neutrals, including dimethylamine, trimethylamine and guanidine. Competitive losses of the R-amino and side-chain amino groups were observed; these losses led to intermediates that had different structures and different subsequent dissociation reactions. Concomitant losses of CO or CO 2 with these amines were also commonly observed. However, the ionic products of amine losses did not subsequently lose CO or CO 2 , suggesting strongly that in these concomitant eliminations, it is the CO or CO 2 that was first eliminated, followed immediately by the loss of the amine. Results of density functional theory calculations on protonated arginine and protonated N R ,N R -dimethylarginine reveal that, in such concomitant eliminations, the dissociating complex is vibrationally hot and the intermediate ion formed by losing CO or CO 2 can immediately dissociate to eliminate the amine.

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Stable radical cations of dimeric amino acid derivatives of tryptophan and tyrosine were generated by collision-induced dissociation of [Cu(II)(diethylenetriamine)(amino acid derivative)2]*2+. The yields of the dimer radical cations were dependent on both the auxiliary ligand and the tryptophan or tyrosine derivatives used. Amino acid derivatives with an unmodified carboxylic acid group did not generate dimer radical cations. For the amino acid derivatives Ac-Trp-OMe and Ac-Trp-NH2 (Ac is N-acetyl; OMe and NH2 are the methyl ester and amide modifications of the C-terminal carboxylic group), no auxiliary ligand was required for generating the dimer radical cations. Collision-induced dissociation of the [Cu(II)(amino acid derivative)4]*2+ precursor generated the dimer radical cation [(amino acid derivative)2]*+. Stabilizing interactions, most likely involving hydrogen bonding, between the two amino acid derivatives are proposed to account for observation of the dimer radical cations. Dissociation of these ions yields protonated or radical cationic amino acid derivatives; these observations are consistent with the expectation of proton competition between monomeric units, whose proton affinities were calculated using density functional theory.