Phosphopantetheinyl transferase (PPTase) catalyzed protein modification has been demonstrated as an efficient method for site specific protein labeling with small molecules of diverse structures. Previously coenzyme A conjugated small molecule probes have been used as the substrates of PPTase for the covalent attachment of the probes to a specific Ser residue in the carrier proteins or short peptide tags through a phosphopantetheinyl linkage. Here we discovered that small molecules directly conjugated to the 5'-diphosphate moiety of ADP can serve as the substrates of a mutant Sfp PPTase, R4-4. Based on this, we used R4-4 to transfer small molecule labels to the carrier protein or peptide tags fused to the target protein through structurally simplified synthetic linkers. The synthesis of ADP conjugated small molecule probes can be easily accomplished by one-step coupling between phosphate derivatized probes and morpholidate-activated AMP. The use of ADP-small molecule conjugates for PPTase catalyzed protein labeling would further expand the structural and functional diversity of the chemical probes attached to the target protein to elucidate or engineer their biological activities.