Benchmarking Cleavable Biotin Tags for Peptide-Centric Chemoproteomics

• DOI: 10.1021/acs.jproteome.2c00174
• Publication Date: 2022-04-25T12:49:16Z
• Authors: Zongmin Li; Keke Liu; Ping Xu; Jing Yang
• Keywords: Proteome

Click chemistry─specifically the copper-catalyzed azide-alkyne cycloaddition─has enabled development of a wide range chemical probes to analyze subsets functional proteome. The "clickable" proteome can be selectively enriched by using diverse cleavable biotin tags, but direct identification probe/tag-modified peptides (or peptide-centric analysis) remains challenging. Here, we evaluated performance five commercially available tags in three most common chemoproteomic workflows, resulting comparative analysis 15 methods. An acid-cleavable tag with dialkoxydiphenylsilane moiety, combination protein "click", peptide "capture" workflow, outperforms all other methods terms enrichment efficiency, yield, and reproducibility, although its may slightly compromised formation an unwanted formate product revealed blind search. Despite being inferior, photocleavable, reduction-cleavable, also find their applicable sceneries, especially when dealing acid-sensitive or probe-derived modifications. Furthermore, systematic comparison LC–MS/MS characteristics tag-modified provides valuable information for future reagents. Taken together, our data much-needed practical guidance researchers interested developing and/or applying ideal chemoproteomics.