Fragmentations of Protonated Arginine, Lysine and Their Methylated Derivatives:  Concomitant Losses of Carbon Monoxide or Carbon Dioxide and an Amine

Abstract

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.

Arginine methylation in yeast proteins during stationary-phase growth and heat shock

“…The structures in Fig. 2c, and d are supported by our current and previous work (Lakowski and Frankel 2009;Lakowski et al 2010a;Lakowski et al 2013;Thomas et al 2014) and by other studies (Shek et al 2006). The structures of dimethylated primary product ions derived from aDMA and sDMA and having 158.1 m/z are proposed based on primary product ion spectra of arginine that showed a 130.0 m/z product ion with a similar structure but no methyl groups (Shek et al 2006).…”

A Pseudo MS3Approach for Identification of Disulfide-Bonded Proteins: Uncommon Product Ions and Database Search

“…The neutral loss of HN=C(NH 2 ) 2 is proposed to involve the nucleophilic attack of C δ atom by the negatively charged oxygen of the C-terminal carboxyl group. The neutral loss of HN=C(NH 2 ) 2 has also been reported in MS/MS analysis of Arg derivatives [59], and MS/MS analysis of peptides Arg-Gly and Gly-Arg [25]. The HN=C(NH 2 ) 2 loss did not show up for y 10 cluster ions, which could be due to higher energy required for the formation of a nine-membered ring transition state compared with a six-membered ring.…”

Fragmentation of protonated dipeptides containing arginine. Effect of activation method

“…One notes, for example, the elimination of HNCO to form m/z 172; this fragmentation route implies a cyclization on loss of NH 3 involving a carbonyl oxygen. (We assume that NH 3 loss occurs from the guanidino group, as observed for protonated arginine [27,28]. The m/z 172 ion is a major product in the fragmentation of the [MH Ϫ NH 3 ] ϩ ions in the quadrupole ion trap ( Figure 5), although we cannot confirm that this also represents loss of HNCO.…”

“…This appears to be the case for b 1 ions derived from lysine [36], histidine [37], methionine [38], and arginine. For the latter case, the MH ϩ of arginine shows [26,28] (Tables 1 and 2) are distinctly different, indicating that we are dealing with different ion structures under the observation times and excitation energies pertaining to the QqTOF experiments.…”