Expanding the Chemoproteomic Toolkit to Asparagine and Glutamine.

Chemoproteomic strategies have revolutionized proteome annotation by targeting nucleophilic and redox-active side chains. However, the primary amides of asparagine (Asn) and glutamine (Gln) have long lacked robust chemical tools for proteome-wide interrogation. We report a chemoselective palladium-mediated dehydration that converts Asn/Gln amides to nitriles under mild aqueous conditions. This transformation enables the first proteome-wide mapping of chemically addressable Asn/Gln sites in lysates and living cells. Leveraging this reactivity, we establish an inverse chemoproteomic framework in which reduced nitrile formation reports PTM-mediated protection of Asn/Gln sites, including those impacted by deamidation and N-glycosylation. This approach reveals sites masked by post-translational modifications (PTMs), specifically those associated with deamidation and N-glycosylation. In yeast, this framework expanded the known N-glycoproteome, identifying numerous candidates missed by traditional glycopeptide enrichment due to low abundance or noncanonical motifs. Furthermore, comparative profiling in Candida albicans captured the dynamic remodeling of glycosylation patterns during morphogenesis. This dehydration-to-nitrile platform establishes a scalable handle on the amide proteome to map residue accessibility and PTM-linked site dynamics across biological states.