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Genome Technology s Peer Review: A Weekly Forum of Recently Published Journal Articles: Feb 22, 2005

Following is a description of a recently published research paper recommended by a scientist involved in integrated biology. The recommender, John Yates, is a professor in the department of cell biology at the Scripps Research Institute.


For a complete list of recommended papers, read Genome Technology, a GenomeWeb News sister publication.

Large-scale characterization of HeLa cell nuclear phosphoproteins

Beausoleil S, Jedrychowski M, Schwartz D, Elias J, Villén J, Li J, Cohn M, Cantley, L, Gygi S. PNAS. 2004; 101: 12130-12135.


Steven Gygi and his colleagues at HarvardMedicalSchooldescribe in this paper in PNAS how they applied strong cation exchange chromatography and tandem mass spectrometry to isolate and identify phosphorylation sites. Determining the site of a regulatory phosphorylation event, the authors write, is often essential for elucidating specific kinase-substrate relationships, providing a handle for understanding essential signaling pathways and ultimately allowing insights into numerous disease pathologies. Their experimental strategy enriched phosphopeptides from the nuclear fraction of HeLa cell lysate, and then used tandem MS to identify 2,002 phosphorylation sites from 967 proteins. This unprecedented large collection of sites permitted a detailed accounting of known and unknown kinase motifs and substrates, the authors conclude. Yates says the paper is significant because it demonstrates how MS3 can be used to create a more complex ion fragmentation pattern as a means of identifying a large number of phosphorylation sites.


John Yates

Professor, Department of Cell Biology

Scripps Research Institute


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