PTM Repositories and Data Mining Tools

There are a number of online PTM repositories including PhosphoSitePlus [120], SysPTM 2.0 [121], PTMCode [122], and ProteomeScout [123]. PTMCode indicates functional links between individual and multiple PTMs including acetylation and methylation [122]. Another software, ProteomeScout, provides a compendium of public PTM data, including quantitative proteomics and details on functional annotation [123]. These repositories aid design of follow-on experimental work and provide data for the development of in silico prediction tools.

Computational Prediction Tools for Acetylation and Methylation Sites

There has been a focus on the development and application of tools to predict acetylation and methylation sites to complement and extend analysis performed in vitro in a cost-effective manner. The challenges around site prediction have been outlined by review and evaluation of PMeS, PLMLA, MeMo, MASA, BPB-PPMS, MethK, and iMethyl-PseAAC using a common dataset of methylation sites [124]. It was concluded that performance needs to be optimized and that it would be of benefit to adopt different feature information for methyl-arginine and methyl-lysine predictors [124]. The PLMLA tool also predicts acetylation sites and has been compared with the LAceP, EnsemblePail, PHOSIDA, and PSKAcePred acetylation site prediction software [125]. The comparison utilized information on 13,810 acetylation sites from 6388 proteins, which was obtained from SysPTM 2.0 and PhosphoSitePlus databases. LAceP performed best, employing a logistic regression method to integrate information on amino acid sequence adjacent to acetylated sites, physicochemical properties, and the transition probability of adjacent amino acids [125].

A comprehensive and comparative analysis of acetylation, methylation, ubiq- uitinylation, and SUMOylation has identified conserved amino acid sequence association with secondary structure [126]. Information, combined with site specificity data for enzymes mediating addition and removal of acetyl and methyl groups, can benefit site prediction as has been demonstrated for lysine acetyltransferases [127]. Chemoselective reactions provide an MS method for the experimental determination of acetyl and methyl transferase activities. Examples include alkynyl-acetyl-CoA and SAM analogs for bioorthogonal click chemistry analysis of proteins that are substrates for acetylation and methylation, respectively [128-130]. These complement other MS-based analyses (Table 4.2).

Table 4.2 Biochemical methods coupled to MS for analysis of protein acetylation and methylation.

Notes: Lysine acylations other than acetylation can be analyzed [129].