Labeling and Characterization of Phenol‐Containing Glycopeptides Using Chemoselective Probes with Isotope Tags

Abstract Secondary metabolites are structurally diverse natural products (NPs) and have been widely used for medical applications. Developing new tools to enrich NPs can be a promising solution to isolate novel NPs from the native and complex samples. Here, we developed native and deuterated chemoselective labeling probes to target phenol‐containing glycopeptides by the ene‐type labeling used in proteomic research. The clickable azido‐linker was included for further biotin functionalization to facilitate the enrichment of labeled substrates. Afterward, our chemoselective method, in conjunction with LC‐MS and MSn analysis, was demonstrated in bacterial cultures. A vancomycin‐related phenol‐containing glycopeptide was labeled and characterized by our labeling strategy, showing its potential in glycopeptide discovery in complex environments.