J Proteome Res. 2006 Jan;5(1):127-34.

Quantitative phosphoproteomic analysis of the tumor necrosis factor pathway.

Cantin GT, Venable JD, Cociorva D, Yates JR 3rd.

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Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd. SR11, La Jolla, California 92037, USA.

Abstract

Protein phosphorylation has become a focus of many proteomic studies due to the central role that it plays in biology. We combine peptide-based gel-free isoelectric focusing and immobilized metal affinity chromatography to enhance the detection of phosphorylation events within complex protein samples using LC-MS. This method is then used to carry out a quantitative phosphoproteomic analysis of the tumor necrosis factor (TNF) pathway using HeLa cells metabolically labeled with 15N-containing amino acids, where 145 phosphorylation sites were found to be up-regulated upon the activation of the TNF pathway.

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