title: Quantitative dynamics of phosphoproteome: the devil is in the details.
abstract: Recent advances in peptide-based (bottom-up) quantitative proteomics and bioinformatics have opened unprecedented opportunities for extensive investigation of cellular proteomes and their dynamics. Here we discuss two approaches currently used to investigate the global dynamics of phosphorylation based on the isolation of phosphorylated proteins or peptides. We evaluate the accuracy of these methodologies to grasp the global dynamics of phosphorylation, and we raise awareness on ambiguities inherent to these analyses. We conclude that further development of targeted approaches should prevent inaccurate conclusions about the nature of biological regulations and in particular kinase-substrate networks.
authors.affiliation: T cell Signaling Laboratory, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, United Kingdom. mogjibs@gmail.com
authors.forename: Mogjiborahman
authors.initials: M
authors.lastname: Salek
authors.forename: Oreste
authors.initials: O
authors.lastname: Acuto
mesh_terms: D000818:Animals; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D010748:Phosphopeptides / Q000737:chemistry* / Q000302:isolation & purification; D010750:Phosphoproteins / Q000737:chemistry* / Q000302:isolation & purification; D010766:Phosphorylation; D020543:Proteome / Q000737:chemistry* / Q000302:isolation & purification; D040901:Proteomics / Q000379:methods*
chemical_list: D010748:Phosphopeptides; D010750:Phosphoproteins; D020543:Proteome