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In the present chapter we propose to detail how mass spectrometry (MS) can be used to characterize protein/ligand systems. This original application of mass spectrometry, called native MS, appeared in the early 90s and has evolved continuously until now. Currently, native MS is fully integrated in structural biology programs and in drug discovery platforms.

This chapter will provide the reader with a description of the general approach allowing protein/ligand systems to be characterized by native MS. We then focus on the type of information native MS provides for protein/ligand systems, with emphasis on the determination of the binding stoichiometries, site-specificities and relative affinities. How native MS supports structure- and fragment- based drug research will be commented with examples from the literature.

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