The development of the receptor concept by Langley, Ehrlich, Clark and others at the end of the nineteenth and the beginning of the twentieth century provided the basis for understanding pharmacological effects on a molecular basis [1, 2]. Today pharmacological receptors are understood to be signal transducing proteins that selectively and reversibly bind an endogenous signal molecule (or a synthetic analog), and then undergo a conformational change and mediate a cellular answer as a consequence. Among them are intracellular receptors of the nuclear receptor superfamily and membrane-bound receptors such as ion channel-coupled receptors, kinase-coupled receptors or G protein-coupled receptors [3].

For a long time no highly sensitive detection methods existed for the analysis of pharmacological effects, in the sense of receptor-ligand interactions, at a molecular level, even though receptors were already accepted as primary targets for biologically active compounds. Direct characterization of receptors, which are usually present in tissue preparations only in subnanomolar concentrations, was only possible after pure radioisotopes such as 3H or 1251 were available that allowed the production of radioligands [4]. The beginnings of radioligand binding assays are dated differently in the literature [1, 5-7]. They have definitely found widespread use since the mid 1970s [8]. Since the early 1990s radioligand binding assays have been increasingly automated, miniaturized and adapted to the requirements of high-throughput screening [9]. Recently, with the advent of modern fluorescence techniques, binding assays based on fluorophore-labeled ligands were established and gained importance for a variety of targets [10-15].

As binding assays provide a means to characterize the affinity of test compounds to defined targets, they play a very important, not to say an essential role in the drug discovery process. Next to the advantage of effective quantitation, the use of a marker, i.e. a labeled ligand - either with a radioisotope or a fluorophore - has, however, also serious immanent disadvantages. As the performance of mass spectrometry continues to improve, it appears therefore obvious to conduct binding assays in analogy to radioligand binding assays employing a native, i.e. unlabeled, ligand as a marker and to quantify this marker by mass spectrometry. In this chapter the feasibility of this approach, named MS binding assays in analogy to radioligand binding assays, will be outlined.

Since MS binding assays closely resemble conventional radioligand binding assays, the most important fundamentals and the relevance of radioligand binding assays but also their limitations are discussed first. Next, the basic considerations for the establishment of the MS binding assays are described and finally some applications addressing typical, pharmacologically relevant membrane-bound targets are presented.

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