Protein footprinting mass spectrometry (MS), an emerging approach to elucidate higher-order structure (HOS) and binding, benefits from the iterative development of reaction strategies to expand the covalent labeling toolbox. Herein, we introduce a footprinting reagent for nucleophiles and demonstrate its efficacy for differential covalent labeling MS analysis. Benzoyl fluoride (BF), although reactive with water, is more practical for modifying nucleophilic functional groups than other acid halides and serves as an acyl-transfer reagent for proteins. BF is 10 times more reactive with phenolic Tyr than the current generation nucleophile footprinter. BF modifies, in addition to Tyr, Lys, His, and the N-terminus, weak nucleophiles Ser and Thr, for which few footprinters exist, imparting broad applicability with a range of nucleophiles. We applied benzoylation to a model Ser- and Thr-rich protein-ligand binding system without perturbing the protein HOS. This efficacious footprinting method expands the toolbox of reagents and provides promise for future reaction strategies including possibly membrane proteins.