The development of systems for the analysis of membrane proteins is of fundamental importance for the identification of pharmaceutically active substances. A particular focus is on the pharmacological characterization, modification and functional investigation of cell-free membrane proteins. In particular ion channels, transport proteins and G protein-coupled receptors are in the focus of research. By introducing fluorescent groups at selected positions, multimeric membrane proteins can be introduced into the analysis. The incorporation of modified non-canonical amino acids during protein synthesis is carried out with the help of chemically or enzymatically preacylated tRNAs. Defined protein conjugates with biotinylated or fluorescence-labeled groups are prepared in pro- as well as in eukaryotic cell-free systems. The site-specific protein labeling serves as a gentle method for the functional analysis of the synthesized membrane proteins. Ligand-controlled and voltage-dependent ion channels are electrophysiologically characterized and analyzed with regard to the identification of new drugs.