Proteome-Wide Quantitation by SILAC
Ongoing improvements in instrumentation, fractionation techniques, and enrichment procedures have dramatically increased the coverage of the proteome achievable via LC-MS/MS-based methodologies, opening the call for approaches to quantitatively assess differences at a proteome-wide scale. Stable isotope labeling by amino acids in cell culture (SILAC) has emerged as a powerful and versatile approach for proteome-wide quantitation by mass spectrometry. SILAC utilizes the cells’ own metabolism to incorporate isotopically labeled amino acids into its proteome which can be mixed with the proteome of unlabeled cells and differences in protein expression can easily be read out by comparing the abundance of the labeled versus unlabeled proteins. SILAC has been applied to numerous different cell lines and the technique has been adapted for a wide range of experimental procedures. In this chapter we provide detailed procedure for performing SILAC-based experiment for proteome-wide quantitation, including a protocol for optimizing SILAC labeling. We also provide an update on the most recent developments of this technique.
Key wordsSILAC quantitative proteomics mass spectrometry LC-MS/MS labeling isotope
We would like to thank all members of the Center for Experimental BioInformatics (CEBI) for useful discussions, especially Dr. Irina Kratchmarova for the critical reading of the chapter. The research leading to these results has received funding from the European Commission’s 7th Framework Programme (grant agreement HEALTH-F4-2008-201648/PROSPECTS), the Danish Natural Science Research Council and the Lundbeck Foundation.
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