Here we set out to identify protein targets of Lipoic acid and Lipoamide by chemical proteomics approaches. We generated Lipoamide-based affinity matrices to pulldown target proteins and quantify them via bottom-up proteomics. Use of the same affinity matrix in dose dependent compeition assays allowed us to identify HDACs as potently bound by Lipoic acid and Lipoamide and to derive the affinty of drug target interactions. These findings were confirmed by further competiiton assays with already established HDAC inhibitor based affinity matrices.