Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis

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Cantin GT, Yi W, Lu B, Park SK, Xu T, Lee JD, Yates JR 3rd.
J Proteome Res. 2008 Mar;7(3):1346-51.
Immobilized metal affinity chromatography (IMAC) is a common strategy used for the enrichment of phosphopeptides from digested protein mixtures. However, this strategy by itself is inefficient when analyzing complex protein mixtures. Here, we assess the effectiveness of using protein-based IMAC as a pre-enrichment step prior to peptide-based IMAC. Ultimately, we couple the two IMAC-based enrichments and MudPIT in a quantitative phosphoproteomic analysis of the epidermal growth factor pathway in mammalian cells identifying 4470 unique phosphopeptides containing 4729 phosphorylation sites.

http://pubs.acs.org/doi/abs/10.1021/pr0705441
Departments of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.