Quantitative analysis of phosphorylation-based protein signaling networks in the immune system by mass spectrometry

Program in Systems Immunology and Infectious Disease Modeling, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Wiley Interdisciplinary Reviews Systems Biology and Medicine (Impact Factor: 3.21). 05/2011; 3(3):368-76. DOI: 10.1002/wsbm.123
Source: PubMed

ABSTRACT Dynamic modification of cell proteins with phosphate is one of the key regulators of the cellular response to external stimuli. Phosphorylation-based signaling networks mediate cell proliferation, differentiation, and migration, and their dysregulation is the basis of multiple diseases. However, the transient nature of the regulatory protein phosphorylation and low site occupancy mean that only a fraction of the protein is phosphorylated at a given time, and it is a challenge to measure the degree and dynamics of phosphorylation using traditional biochemical means. Technological advances in the field of mass spectrometry (MS) made it possible to generate large sets of phosphoproteomics data, probing the phosphoproteome with great depth, sensitivity, and accuracy. Therefore, quantitative phosphoproteomics emerged as one of the essential components of the systems biology approach for profiling of complex biological networks. Nowadays, the challenge lies in validation of the information and in its integration into the comprehensive models of cell decision processes. This article reviews the role of phosphoproteomics in systems biology, the MS-based approach, and technical details of the methods. Recent examples of quantitative measurements and methodologies as well as applications to the studies of the immune system and infectious diseases are presented and discussed. WIREs Syst Biol Med 2011 3 368–376 DOI: 10.1002/wsbm.123
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    • "[3] In this context, phosphoproteomics is defined as the study of a proteome that undergoes phosphorylation, the stoichiometry of the protein phosphorylation status at individual residues, and the changes in phosphorylation in response to perturbations. [4] [5] Therefore, highly sensitive methods for isolation, detection and quantification of low abundance phosphorylation sites are needed. The strong need for quantitative information in phosphoproteomics requires the development of mass spectrometry (MS)-based analytical methods that are able to determine protein abundances. "
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