Identification of the targets of biologically active small molecules using quantitative proteomics

Currently, cell-based screenings yield a multitude of small molecule modulators of diverse biological processes. The most demanding step in the course of elucidation of the mode of action of biologically active compounds is the identification of the target proteins. Although there is no generic approach available, affinity-based chemical proteomics is the most widely applied methodology. Particularly, quantitative chemical proteomics has proven very powerful in the identification of the putative targets of small molecules. Here we describe the procedure for identification of target proteins for small molecules employing affinity chromatography and the stable isotope labeling in cell culture (SILAC) for quantitative proteomics.