We report the results of experiments, simulations, and DFT calculations that focus on describing the reaction dynamics observed within the collision-induced dissociation of l-lysine-H and its side-chain methylated analogues, -methyl-l-lysine-H (Me-lysine-H), ,-dimethyl-l-lysine-H (Me-lysine-H), and ,,-trimethyl-l-lysine-H (Me-lysine-H). The major pathways observed in the experimental measurements were / 130 and 84, with the former dominant at low collision energies and the latter at intermediate to high collision energies. The / 130 peak corresponds to loss of N(CH)H, while / 84 has the additional loss of HCO likely in the form of HO + CO. Within the time frame of the direct dynamics simulations, / 130 and 101 were the most populous peaks, with the latter identified as an intermediate to / 84. The simulations allowed for the determination of several reaction pathways that result in these products. A graph theory analysis enabled the elucidation of the significant structures that compose each peak. Methylation results in the preferential loss of the side-chain amide group and a reduction of cyclic structures within the / 84 peak population in simulations.
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