Chemoproteomics has enabled the rapid and proteome-wide discovery of functional, redox-sensitive, and ligandable cysteine residues. Despite widespread adoption and considerable advances in both sample-preparation workflows and MS instrumentation, chemoproteomics experiments still typically only identify a small fraction of all cysteines encoded by the human genome. Here, we develop an optimized sample-preparation workflow that combines enhanced peptide labeling with singlepot, solid-phase-enhanced sample-preparation (SP3) to improve the recovery of biotinylated peptides, even from small sample sizes. By combining this improved workflow with on-line highfield asymmetric waveform ion mobility spectrometry (FAIMS) separation of labeled peptides, we achieve unprecedented coverage of > 14000 unique cysteines in a single-shot 70 min experiment. Showcasing the wide utility of the SP3-FAIMS chemoproteomic method, we find that it is also compatible with competitive small-molecule screening by isotopic tandem orthogonal proteolysis-activity-based protein profiling (isoTOP-ABPP). In aggregate, our analysis of 18 samples from seven cell lines identified 34225 unique cysteines using only~28 h of instrument time. The comprehensive spectral library and improved coverage provided by the SP3-FAIMS chemoproteomics method will provide the technical foundation for future studies aimed at deciphering the functions and druggability of the human cysteineome.
Mass-spectrometry-based
chemoproteomics has enabled the rapid and
proteome-wide discovery of functional and potentially ’druggable’
hotspots in proteins. While numerous transformations are now available,
chemoproteomic studies still rely overwhelmingly on copper(I)-catalyzed
azide–alkyne cycloaddition (CuAAC) or ’click’
chemistry. The absence of bio-orthogonal chemistries that are functionally
equivalent and complementary to CuAAC for chemoproteomic applications
has hindered the development of multiplexed chemoproteomic platforms
capable of assaying multiple amino acid side chains in parallel. Here,
we identify and optimize Suzuki–Miyaura cross-coupling conditions
for activity-based protein profiling and mass-spectrometry-based chemoproteomics,
including for target deconvolution and labeling site identification.
Uniquely enabled by the observed orthogonality of palladium-catalyzed
cross-coupling and CuAAC, we combine both reactions to achieve dual
labeling. Multiplexed targeted deconvolution identified the protein
targets of bifunctional cysteine- and lysine-reactive probes.
Mass spectrometry-based chemoproteomics
has enabled functional
analysis and small molecule screening at thousands of cysteine residues
in parallel. Widely adopted chemoproteomic sample preparation workflows
rely on the use of pan cysteine-reactive probes such as iodoacetamide
alkyne combined with biotinylation via copper-catalyzed azide–alkyne
cycloaddition (CuAAC) or “click chemistry” for cysteine
capture. Despite considerable advances in both sample preparation
and analytical platforms, current techniques only sample a small fraction
of all cysteines encoded in the human proteome. Extending the recently
introduced labile mode of the MSFragger search engine, here we report
an in-depth analysis of cysteine biotinylation via click chemistry
(CBCC) reagent gas-phase fragmentation during MS/MS analysis. We find
that CBCC conjugates produce both known and novel diagnostic fragments
and peptide remainder ions. Among these species, we identified a candidate
signature ion for CBCC peptides, the cyclic oxonium-biotin fragment
ion that is generated upon fragmentation of the N(triazole)–C(alkyl)
bond. Guided by our empirical comparison of fragmentation patterns
of six CBCC reagent combinations, we achieved enhanced coverage of
cysteine-labeled peptides. Implementation of labile searches afforded
unique PSMs and provides a roadmap for the utility of such searches
in enhancing chemoproteomic peptide coverage.
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