Phosphoproteomics: Methods and Challenges

Protein phosphorylation is a widespread post-translational modification that regulates many biological processes. This covalent modification alters the biochemical properties of proteins and can act as an activity switch or as a docking site for protein-protein interactions. Due to the increasing interest for studying cell signaling in various biological settings at a larger scale, phosphoproteomics, the quantitative study of protein phosphorylation using advanced tandem mass spectrometry, has gained significant interest during the last decade. Today phosphoproteomics is performed in many proteomics laboratories thanks to a significant focus on developing efficient phosphopeptide enrichment methods performed in several research groups. This article describes the current state-of-the-art within phosphoproteomics together with technical and theoretical perspectives and, discusses future challenges for researchers working in this area.