Figure 1. Major chemical proteomic methodologies utilized to study CSCs. Chemical proteomics strategies could employ different experimental procedures, including global proteome comparison between drug treated and control cells (A-D) and affinity-based target protein profiling using modified (E) or unmodified (F) compound of interest. Main chemical proteomic techniques include gel-based and gel-free methods. Gel-based methods employ 1- or 2-D gel electrophoresis followed by MS (A). Quantitative proteomic analyses eliminate the need to visualize target proteins by gel electrophoresis. For quantitative comparison of a number of samples in parallel, several popular peptide labeling methods can be utilized. These methods employ isotopic labeling of proteins followed by identification by LC-MS/MS (B, C).