Identification, Quantification, and Site Localization of Protein Posttranslational Modifications via Mass Spectrometry-Based Proteomics

Abstract

Posttranslational modifications (PTMs) are important biochemical processes for regulating various signaling pathways and determining specific cell fate. Mass spectrometry (MS)-based proteomics has been developed extensively in the past decade and is becoming the standard approach for systematic characterization of different PTMs on a global scale. In this chapter, we will explain the biological importance of various PTMs, summarize key innovations in PTMs enrichment strategies, high-performance liquid chromatography (HPLC)-based fractionation approaches, mass spectrometry detection methods, and lastly bioinformatic tools for PTMs related data analysis. With great effort in recent years by the proteomics community, highly efficient enriching methods and comprehensive resources have been developed. This chapter will specifically focus on five major types of PTMs; phosphorylation, glycosylation, ubiquitination/sumosylation, acetylation, and methylation.

Understanding Camellia sinensis using Omics Technologies along with Endophytic Bacteria and Environmental Roles on Metabolism: A Review

“…MS-based proteomics is becoming the standard approach for systematic characterization of post-translational modifications, e.g., phosphorylation, glycosylation, ubiquitination or sumosylation, acetylation, and methylation [22]. Post-translational modifications are important biochemical processes for regulating various signaling pathways and determining specific cell fate.…”

Orchestrating the proteome with post-translational modifications

“…Increasingly, PTMs are recognized as critical directors of proteome function and as major determinants of plant phenotypes. The arrival of advanced PTM-enrichment techniques, such as tandem metal oxide affinity chromatography for phosphoproteins and linkage-specific ubiquitin sensors, to name but a few (Ikeda et al , 2010; Hoehenwarter et al , 2013), as well as advances in quantitative proteomics and bioinformatics of PTMs, is heralding a golden age of PTM research (Ke et al , 2016). While several major PTMs already enjoy widespread recognition, lesser-known modifications are now slowly gaining equally important reputations.…”

The Effects of Storage on Platelet Proteome Assessed by Protein Expression Changes and Lysine Modification Changes Using Tmt Isobaric Labeling

“…Tandem mass tag (TMT) [7,8],composed of a mass reporter, a mass normalizer, and a reactive moiety, has beencommercially employedfor simultaneously labeling and analyzing6, 10 or 11 samples ata time.The quantitative methods are based on amino-group labelling with isobaric TMT [9].It has been used to quantify the relative peptide intensities of the rst dimensional MS, while the second dimensional MS is to sequence peptide fragment ions for protein identi cation. In addition, certain enrichment and puri cation method, including but not limited to phosphorylation, acetylation,succinylation, and ubiquitination can be applied to modi ed peptides in order to achieve post-translational modi cation (PTM) proteome pro ling [10,11].With various types of PTMs diversifying proteomes speci cally, PTMshave been demonstrated to play important roles in regulating protein functions [12]. More widespread applications of modi ed "omics" have contributed to our knowledge of the complexity of biological processes mediated by PTMs [13,14], which iscritical in understanding protein dynamics and mechanisms of biological functions at the molecular level [15].…”