Technologies and challenges in large-scale phosphoproteomics

Authors

  • Kasper Engholm-Keller,

    1. Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
    2. Center for Clinical Proteomics, Odense University Hospital, Odense, Denmark
    3. Children's Medical Research Institute, Westmead, Sydney, Australia
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  • Martin R. Larsen

    Corresponding author
    1. Center for Clinical Proteomics, Odense University Hospital, Odense, Denmark
    • Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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  • Colour Online: See the article online to view Figs. 1, 2 and 4–6 in colour.

Correspondence: Dr. Martin R. Larsen, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark

E-mail: mrl@bmb.sdu.dk

Fax: +45 6593 2661

Abstract

Phosphorylation, the reversible addition of a phosphate group to amino acid side chains of proteins, is a fundamental regulator of protein activity, stability, and molecular interactions. Most cellular processes, such as inter- and intracellular signaling, protein synthesis, degradation, and apoptosis, rely on phosphorylation. This PTM is thus involved in many diseases, rendering localization and assessment of extent of phosphorylation of major scientific interest. MS-based phosphoproteomics, which aims at describing all phosphorylation sites in a specific type of cell, tissue, or organism, has become the main technique for discovery and characterization of phosphoproteins in a nonhypothesis driven fashion. In this review, we describe methods for state-of-the-art MS-based analysis of protein phosphorylation as well as the strategies employed in large-scale phosphoproteomic experiments with focus on the various challenges and limitations this field currently faces.

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