Functional Proteomic Analysis to Characterize Signaling Crosstalk

Methods Mol Biol. 2019;1871:197-224. doi: 10.1007/978-1-4939-8814-3_14.

Abstract

The biological activities of a cell are determined by its response to external stimuli. The signals are transduced from either intracellular or extracellular milieu through networks of multi-protein complexes and post-translational modifications of proteins (PTMs). Most PTMs including phosphorylation, acetylation, ubiquitination, and SUMOylation, among others, modulate activities of proteins and regulate biological processes such as proliferation, differentiation, as well as host pathogen interaction. Conventionally, reverse genetics analysis and single molecule-based studies were employed to identify and characterize the function of PTMs and enzyme-substrate networks regulated by them. With the advent of high-throughput technologies, it is now possible to identify and quantify thousands of PTM sites in a single experiment. Here, we discuss recent advances in enrichment strategies of various PTMs. We also describe a method for the identification and relative quantitation of proteins using a tandem mass tag labeling approach combined with serial enrichment of phosphorylation, acetylation and succinylation using antibody enrichment strategy.

Keywords: Crosstalk; Mass spectrometry; Phosphorylation; Quantitation; Signaling pathways.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatography, Liquid
  • Computational Biology / methods
  • Data Analysis
  • Data Mining
  • Mass Spectrometry / methods
  • Protein Binding
  • Protein Interaction Mapping / methods*
  • Protein Processing, Post-Translational
  • Proteomics* / methods
  • Signal Transduction*
  • Workflow