ProMetheusDB: an in-depth analysis of the high-quality human methyl-proteome

Abstract

Protein Arginine (R) methylation is a post-translational modification involved in various biological processes, such as RNA splicing, DNA repair, immune response, signal transduction, and tumour development. Although several advancements were made in the study of this modification by mass spectrometry, researchers still face the problem of a high false discovery rate. We present a dataset of high-quality methylations obtained from several different heavy methyl SILAC (hmSILAC) experiments analysed with a machine learning-based tool doublets and show that this model allows for improved high-confidence identification of real methyl-peptides. Overall, our results are consistent with the notion that protein R methylation modulates protein:RNA interactions and suggest a role in rewiring protein:protein interactions, for which we provide experimental evidence for a representative case (i.e. NONO:PSPC1). Upon intersecting our R-methyl-sites dataset with a phosphosites dataset, we observed that R methylation correlates differently with S/T-Y phosphorylation in response to various stimuli. Finally, we explored the application of hmSILAC to identify unconventional methylated residues and successfully identified novel histone methylation marks on Serine 28 and Threonine 32 of H3.

Dynamicin vivomapping of the methylproteome using a chemoenzymatic approach

“…Our proteomics data also indicated enrichment of the SAM synthetase enzymes MAT2A/B, which are responsible for the coupling of ATP and L-Met to produce SAM 53 . While we cannot discount the possibility that these enzymes were identified because of ProSeAM present in their binding pockets, MAT2A is purportedly methylated on a critical Arg residue in the binding pocket (R264) and this methylation event may serve as a biological switch to control cellular SAM levels 54 . Similarly, our MS data indicates enrichment of several methyltransferases, including the Lys methyltransferases KMT2A/B, the Arg methyltransferases PRMT1, 3, 5 and CARM1, and the RNA methyltransferase NSUN2, all of which are known to be methylated 38 .…”

An Occupational Health Survey for Port Employees in Shenzhen and A Dataset Management System based on R

“…The OHSPEIMS provides a simple, fast, free solution for constructing a private, highly customized database management system. Shiny is often used to build interactive Web apps, and more and more apps are being published online to simplify some complex analysis processes and data visualization, such as genomic analysis 23 , proteomic analysis 24 , transcriptome analysis 25 , prediction model 26 , complex model 27 and visualization system for COVID-19 pandemic 27 . Hence, it is entirely possible to build a customized dataset management system using Shiny.…”