Drug target factor complex identification is necessary for evidence based drug discovery. Previous study showed that using small chemical immobilized magnetic nanobeads the chemical target factors were effectively purified and identified. Here we succeeded to purify the chemical target factor complex, so called cofactor(s). Arginine exhibits a variety of biological activities through a complex and highly regulated set of pathways that remain incompletely understood at both the whole-body and the cellular levels. The aim of this study is to develop and validate effective purification system for arginine target complex. New arginine target protein (arginine interacting factor 4, AIF4) was purified and identified. Using recombinant AIF4 protein and arginine-immobilized magnetic nanobeads, AIF4 cofactor, AIF4-BP1, were purified. Interaction of AIF4 and AIF4-BP1 was detected in arginine-dependent manner, suggesting arginine receptor complex formation. This nanobeads technology is more than 30-fold efficient purification efficient than general purification technology.