The in vivo and in vitro labeling of fusion proteins with synthetic mols. capable of probing and controlling protein function has the potential to become an important method in functional genomics and proteomics. We have recently introduced an approach for the specific labeling of fusion proteins, which is based on the generation of fusion proteins with the human DNA repair protein O6-alkylguanine-DNA alkyltransferase (hAGT) and the irreversible reaction of hAGT with O6-benzylguanine derivs. Here, we report optimized protocols for the synthesis of O6-benzylguanine derivs. and the use of such derivs. for the labeling of different hAGT fusion proteins in vivo and in vitro. [on SciFinder (R)]