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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.

Original publication

DOI

10.1021/ac301833k

Type

Journal article

Journal

Anal Chem

Publication Date

16/10/2012

Volume

84

Pages

8431 - 8436

Keywords

Animals, Humans, Mass Spectrometry, Phosphopeptides, Phosphoproteins, Phosphorylation, Proteome, Proteomics