Observation of the side chain O -methylation of glutamic acid or aspartic acid containing model peptides by electrospray ionization-mass spectrometry

Abstract

O-methylation of the side chains of glutamic acid (E) and aspartic acid (D) residues is generally observed modification when an acidified methanol/water (MeOH/dHO) mixture is used as a solvent system during sample preparation for proteomic research. This chemical modification may result misidentification with endogenous protein methylation; therefore, a special care should be taken during sample handling prior to mass spectrometric analysis. In the current study, we systematically examined the extent of E/D methylation and C-terminus carboxyl group of synthetic model peptides in terms of different incubation temperatures, storage times, and added acid types as well as its percentages. To monitor these effects, C-terminus amidated and free acid forms of synthetic model peptides comprised of E or D residue(s) have been analyzed by electrospray ionization-mass spectrometry (ESI-MS). Additionally, LC-MS/MS experiments were performed to confirm the formation of methylated peptide product. The results showed that the rate of methylation was increased as the temperature increases along with prolong incubation times. Moreover, the extent of methylation was remarkably high when formic acid (FA) used as a protonation agent instead of acetic acid (AA). In addition, it was found that the degree of methylation was significantly decreased by lowering acid percentages in ESI solution. More than one acidic residue containing model peptides have been also used to explore the extent of multiple methylation reaction. Lastly, the ethanol (EtOH) and isopropanol (iPrOH) have been substituted separately with MeOH in sample preparation step to investigate the extent of esterification reaction under the same experimental conditions. However, in the positive perspective of view, this method can be used as a simple, rapid and cheap method for methylation of acidic residues under normal laboratory conditions.

Characterization of Diagenetiforms in an Expanded Proteome of the Extinct Moa (Dinornithidae): Identifying Biological, Diagenetic, Experimental Artifact, and Mislabeled Modifications in Degraded Tissues

“…Methylation[+14]/Ethylation[+28]: The detection of methylation on aspartic acid and glutamic acid may result from the usage of methanol during the stage-tipping procedure [2]. Methanol has been shown to cause methylation at these sites in samples where a mixture of methanol and water has been used in sample preparation [56]. Additionally, previously reported methylation of serine in histones using tandem MS has been shown to in fact be a peculiar artifact of fragmentation when interrogated using MS/MS/MS, wherein the methylation was actually on the neighboring lysine [57].…”

Protein posttranslational modifications in health and diseases: Functions, regulatory mechanisms, and therapeutic implications

“…Protein methylation, formed by transferring a methyl group from S‐adenosylmethionine (SAM) to a specific methyl acceptor, usually occurs at the side chains of lysine, arginine, histidine, asparagine, and glutamine, among which the methylation of lysine and arginine is the most common. 709 , 710 …”

“…Protein methylation, formed by transferring a methyl group from S-adenosylmethionine (SAM) to a specific methyl acceptor, usually occurs at the side chains of lysine, arginine, histidine, asparagine, and glutamine, among which the methylation of lysine and arginine is the most common. 709,710 Lysine methylation, mediated by protein lysine methyltransferases (PKMTs), has three different methylation forms, including monomethylation (Kme1), dimethylation (Kme2), and trimethylation (Kme3) (Figure 12A), linked to heterochromatin formation, X chromosome inactivation, and transcriptional silencing or activation. 711,712 PKMTs can be divided into two broad categories.…”