Exploring the Effects of Methylation on the CID of Protonated Lysine: A Combined Experimental and Computational Approach

Abstract

We report the results of experiments, simulations, and DFT calculations that focus on describing the reaction dynamics observed within the collision-induced dissociation of Llysine-H + and its side-chain methylated analogues, N ε -methyl-Llysine-H + (Me 1 -lysine-H + ), N ε ,N ε -dimethyl-L-lysine-H + (Me 2 -lysine-H + ), and N ε ,N ε ,N ε -trimethyl-L-lysine-H + (Me 3 -lysine-H + ). The major pathways observed in the experimental measurements were m/z 130 and 84, with the former dominant at low collision energies and the latter at intermediate to high collision energies. The m/z 130 peak corresponds to loss of N(CH 3 ) n H 3−n , while m/z 84 has the additional loss of H 2 CO 2 likely in the form of H 2 O + CO. Within the time frame of the direct dynamics simulations, m/z 130 and 101 were the most populous peaks, with the latter identified as an intermediate to m/z 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 m/z 84 peak population in simulations.

A Computational and Experimental Examination of the CID of Phosphorylated Serine

“…The initial structure of p-Ser was determined using Avogadro [25] with the phosphorylation occurring on the side-chain oxygen and the excess proton placed on the N-terminus. Direct dynamics simulations involving protonated peptides are commonly performed with PM6 [17,26] and the RM1 [16,21,22,[26][27][28][29] semi-empirical methods. In our study of s-Ser, we found that PM6 outperformed RM1 [17], and expect similar results to be seen here.…”

“…Proton motion can be correlated to fragmentation times, allowing for an analysis of the influence of these migrations on dissociation events [35]. It was recently illustrated that this type of information could be combined with a graph theory analysis [16,36,37] to define a modified ad-jacency matrix weighted by the atomic number whose lowest eigenvalue is used to identify unique structures. Graph theory and direct dynamics provide powerful tools for analyzing reaction mechanisms.…”

“…With the important structures identified using these tools, the energetics are obtained at the ωB97X-D/aug-cc-pVTZ level of theory as implemented in the Gaussian16 software package [38]. We note that many of the mechanisms described here are similar to those seen in s-Ser and were characterized at the same level in our previous work [16].…”

“…Direct dynamics simulations [15][16][17][18][19][20][21] and ab initio calculations have a history of providing significant and impactful insight into the dynamics taking place in tandem mass spectrometry. However, only a few systems that contain PTMs have been studied using these techniques.…”

A Computational and Experimental Examination of the CID of Phosphorylated Serine

“…Direct dynamics simulations [15][16][17][18][19][20][21] and ab initio calculations have a history of providing significant and impactful insight into the dynamics taking place in tandem mass spectrometry. However, only a few systems that contain PTMs have been studied using these techniques.…”