Tandem mass tag-based thermal proteome profiling for the discovery of drug-protein interactions in cancer cells

Identification of effector targets is imperative to the characterization of the mechanisms of action of novel small molecules. Here, we describe steps to identify effector drug-protein interactions in lysates derived from cancer cell lines using a thermal proteome profiling (TPP) protocol. Building on existing TTP approaches, we detail the use of an in-solution trypsin digestion technique to streamline sample preparation, a nonparametric analysis to rank proteins for prioritization, and a follow-up strategy for identifying effector interactors. For complete details on the use and execution of this protocol, please refer to Johnson et al. (2022).1

Automated summary

In this study, the authors present a protocol using thermal proteome profiling (TPP) to identify effector drug-protein interactions in lysates from cancer cell lines. The protocol includes a streamlined sample preparation technique, nonparametric analysis for protein ranking, and a follow-up strategy for identifying effector interactors. Overall, this study is valuable for understanding the mechanisms of action of novel small molecules.