This platform generates compound libraries in situ, allowing proteins to template the formation of optimal ligands, while ABPP provides a high-throughput, mass spectrometry-based readout for ligand screening. We applied this platform to discover covalent inhibitors for serine hydrolases, including PPME1, ABHD11, and PNPLA6, achieving nanomolar potency. Using the PNPLA6 inhibitor as a tool compound, lipidomics studies revealed its role in lipid metabolism and cancer cell proliferation, providing new insights into the enzyme's biological function. We also extended this approach to cysteine-targeting covalent ligand discovery by introducing novel scaffolds—chloroacetohydrazone and acrylohydrazone—that are compatible with DCL and selectively label cysteine residues. By integrating a TMT-based workflow, we identified over 2,600 ligandable cysteine sites across the proteome, with EC50 values determined for each site. This method enabled the discovery of first reported inhibitors for enzymes such as NIT2, PRDX5, and TXNDC17. Additionally, we used a cytotoxic ligand identified through cell viability assays as a tool compound to study the regulatory proteins re-translated following VCP inhibition, which induces paraptosis by causing the accumulation of degraded proteins.