Drug Affinity Responsive Target Stability is a general methodology for identifying and studying protein-ligand interactions. The technique is based on the principle that when a small molecule compound binds to a protein, the interaction stabilizes the target protein's structure such that it becomes protease resistant. DARTS is particularly useful for the initial identification of the protein targets of small molecules, but can also be used to validate potential protein-ligand interactions predicted or identified by other means and to estimate the affinity of interactions. The approach is simple and advantageous because it can be performed using crude cell lysates and other complex protein mixtures (without requiring purified proteins), and uses native, unmodified small molecules. The protocols provided in this article describe the general approach for performing DARTS experiments, which can be easily modified and scaled to fit the criteria and purpose of any individual project.