Enhancing Cysteine Chemoproteomic Coverage through Systematic Assessment of Click Chemistry Product Fragmentation
| Autor: | Tianyang Yan, Andrew B. Palmer, Daniel J. Geiszler, Daniel A. Polasky, Lisa M. Boatner, Nikolas R. Burton, Ernest Armenta, Alexey I. Nesvizhskii, Keriann M. Backus |
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| Rok vydání: | 2022 |
| Předmět: | |
| Zdroj: | Analytical Chemistry. 94:3800-3810 |
| ISSN: | 1520-6882 0003-2700 |
| DOI: | 10.1021/acs.analchem.1c04402 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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