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Main observation and conclusionrnBioorthogonal click chemistry has emerged as a powerful tool for the specific modification of proteins in complex mixtures.Metabolic labeling of proteins with azide followed by the copper-catalyzed azide-alkyne cycloaddition (CuAAC) with alkyne-based affinity probes/beads is widely applied to study protein turnover and post-translational modifications (PTMs).However,it has long been known that the alkyne-based enrichment of high concentration protein samples (e.g.,serum) is not sufficient to remove high abun-dant contaminating proteins.Herein,we demonstrate that the protein contamination is mainly caused by thiol-yne addition between terminal alkyne and cysteine residue.Furthermore,we report that azide-based enrichment combined with metabolic labeling with alkyne can significantly reduce contamination and improve the enrichment efficiency of secreted proteins in serum-containing condi-tioned medium.