Understanding protein interactions in the presence of biological metabolites is critical for unraveling biological processes and advancing therapeutic interventions. This study focuses on α,β-unsaturated carbonyls, particularly acrolein-derived protein modifications, unveiling a one-pot, four-step, selective chemistry that results in the formation of a heterocyclic α,β-unsaturated carbonyl, termed 3-formyl-3,4-dehydropiperidino (FDP), exclusively on lysine residues. Remarkably, this chemistry transforms lysine, a nucleophile, into an electrophilic warhead. We demonstrate its versatility in late-stage peptide diversification, precision protein engineering, and homogeneous protein labeling with diverse payloads. Additionally, FDP-lysine smoothly transforms into another heterocycle, 3-methylpyridinium (3-MP) lysine via deoxygenation and aromatization in reagentless conditions. This transformation facilitates late-stage peptide functionalization and homogeneous engineering of proteins, with MP-lysine acting as a mass booster. Leveraging this chemistry, we discovered hyperreactive sites responsible for acrolein-induced modification through chemoproteomic profiling of FDP- and MP-modified proteins. Our findings revealed changes in protein-protein interactions mediated by FDP-modified proteins and uncovered ∼1548 novel cross-linking partners of an FDP-modified protein.