Covalent chemistry represents an attractive strategy for expanding the ligandability of the proteome, and chemical proteomics has revealed numerous electrophile-reactive cysteines residing at cryptic, non-orthosteric pockets on diverse human proteins. Determining which of these covalent binding events impact protein function, however, remains challenging. In this seminar, I will first describe a base-editing strategy to infer the functionality of cysteines by quantifying the impact of their missense mutation on cancer cell proliferation. Building on this strategy and chemical proteomics, I will then highlight our discovery of a potent and selective covalent probe HL-1B that targets an allosteric cysteine in the RNA exonuclease TOE1. I will show that this compound functions as a “molecular clamp” to stabilize TOE1 interactions with the spliceosome, trigger over-trimming of snRNAs, rewire splicing and synthetic-lethal vulnerabilities in cancer cells. Together, these studies establish a framework for developing covalent probes against cancer dependencies and for modulating protein–RNA interactions in cells, enabling precise chemical perturbation of fundamental biological processes and the development of next-generation of therapeutics.