A general method for the specific and covalent labeling of fusion proteins in vivo is described. The approach is based on the unusual mechanism of the human DNA repair protein O6-alkylguanine-DNA alkyl-transferase, which irreversibly transfers an alkyl group from O6-alkylguanine-DNA to one of its cysteine residues. Labeling is possible in bacterial as well as eukaryotic cells and is independent of the nature of the label, thereby opening up new ways to study proteins in vivo. [on SciFinder (R)]