Bioorthogonal chemistry is a mainstay of
chemoproteomic sample preparation workflows. While numerous transformations are
now available, chemoproteomic studies still rely overwhelmingly on
copper-catalyzed azide –alkyne cycloaddition (CuAAC) or 'click' chemistry. Here
we demonstrate that gel-based activity-based protein profiling (ABPP) and
mass-spectrometry-based chemoproteomic profiling can be conducted using Suzuki–Miyaura
cross-coupling. We identify reaction conditions that proceed in complex cell
lysates and find that Suzuki –Miyaura cross-coupling and CuAAC yield comparable
chemoproteomic coverage. Importantly, Suzuki–Miyaura is also compatible with
chemoproteomic target deconvolution, as demonstrated using structurally matched
probes tailored to react with the cysteine protease caspase-8. Uniquely enabled
by the observed orthogonality of palladium-catalyzed cross-coupling and CuAAC,
we combine both reactions to achieve dual protein labeling.
Assessment of MS/MS Search Algorithms with Parent-Protein Profiling
