The identification of compounds with a desired biological activity is a key step in the drug discovery process. There is a growing need for efficient methods, capable of reliably identifying compounds in a relatively short time span with desired binding affinity.Several NMR-based screening methods have been developed using chemical shift perturbation, 1-3 transferred NOE 4,5 and diffusion and relaxation editing methods. [6][7][8] In the development of NMR techniques for measuring binding affinity, one of the main aims is the reduction of experiment time and of sample usage without isotope enrichment. Although a high resolution structure of protein-ligand complex is preferable in rational drug design, the mapping of specific interaction sites obtained by NMR techniques often provides valuable insights for identifying lead compounds or analyzing their mode of binding.In designing NMR-based screening methods, it is critical to develop the technique capable of screening a large pool of new drug candidates and capable of identifying lead compounds with high affinity towards the target proteins. The most straightforward way to achieve this is by detecting only ligand signals while suppressing signals from target proteins. Recently, it has been shown that diffusion-based NOE-pumping experiment 9-11 can effectively be used to directly detect ligands that bind to the macromolecules. One of the disadvantages in this method is the technical difficulty to quickly optimize a diffusion filter for suppressing the ligand signals at a short NOE mixing time in preparation of the acquisition. For aim of developing an efficient and practical screening method to identify a lead compound with high affinity towards the protein receptor, a simple approach using the difference NOE-pumping experiment is implemented in this study.Besides NMR spectroscopy, mass spectrometry has played an important role in library screening for determining the bound molecule either by MALDI-TOF 12 or ESI-MS. 13 Recently CSI-MS, a variant of ESI-MS operating at low temperature, was developed.14,15 It facilitates observation of weaker associations among proteins, since the temperature at the spray interface is much lower. Although ESI-MS has been used for the detection of non-covalent macromolecular associations, [16][17][18][19] it is shown that CSI-MS is more sensitive in observations of macromolecular interaction. CSI-MS was successfully used to observe hyper-stranded DNA molecules that were unable to be detected by the ESI method 20 indicating the significant advance Pharmacy and Life Science, Hachioji, Japan *5 NM Application & Research Group, Application & Research Center, Analytical Instruments Division, JEOL Ltd., Musashino, Akishima, Japan *6 Department of Chemistry, Faculty of Science, Tokyo Metropolitan University, Hachioji, Japan A difference diffusion-based NMR technique and cold-spray ionization mass spectrometry were employed as a solutionbased approach for identifying a ligand binding with a protein receptor. The difference diffusion-b...