Cu-Catalyzed Azide-Alkyne-Thiol Reaction Forms Ubiquitous Background in Chemical Proteomics Studies

We report here a Cu-catalyzed azide-alkyne-thiol reaction forming thiotriazoles as the major by-product under widely used bioorthogonal protein labelling “click” conditions. The development of Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) had tremendous impact on many biological discoveries. However, the considered chemoselectivity of CuAAC is hampered by high reactivity of cysteine free thiols yielding thiotriazole protein conjugates. The reaction by-products generate false positive protein hits in “functional” proteomic studies. The reported detail investigation of conjugates between chemical probes containing terminal alkynes, azide-tags and cell lysates reveals formation of thiotriazoles, which can be readily detected by in-gel fluorescence scanning or after peptide and protein enrichment by MS-based proteomics. The produced fluorescent bands or enriched proteins may not result from the important enzymatically driven reaction and can be falsely assigned as hits. This study provides a complete list of the most common background proteins. The knowledge of this previously overlooked reactivity now leads to improved experimental design. Here, we present modified CuAAC conditions, which avoids the undesired product formation and diminishes the background.