The techniques of Microscale Thermophoresis (MST), and recently introduced Spectral Shift (SpS) have become valuable tools in target-based drug discovery owned to their ability of immobilization-free detection, low sample requirements, sensitivity, and scalability. These techniques allow fast detection and quantitative characterization of protein-ligand interactions and have found utility in library screening for hit compounds and characterization of interactions in the later stages of compound development. In this article, we highlight the advantages and limitations of MST and SpS in drug discovery and discuss how they can facilitate the characterization of new drug candidates. Our discussion is supported by case studies that demonstrate the successful application of the techniques in hit validation and optimization. In general, MST and SpS offer indispensable tools in drug discovery that support or even replace some of the earlier established approaches. •Utility of Microscale Thermophoresis (MST) and Spectral Shift (SpS) in drug discovery is discussed.•Advantages and disadvantages of both approaches are clearly presented.•The methods are benchmarked against other popular screening/ligand binding characterizing approaches.•Case studies are highlighted which demonstrate the utility of the methods at various stages of drug discovery.