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Understanding protein–ligand interactions in a cellular context is an important goal in molecular biology and biochemistry, and particularly for drug development. Investigators must demonstrate that drugs penetrate cells and specifically bind their targets. Towards that end, we present a native mass spectrometry (MS)‐based method for analyzing drug uptake and target engagement in eukaryotic cells. This method is based on our previously introduced direct‐MS method for rapid analysis of proteins directly from crude samples. Here, direct‐MS enables label‐free studies of protein–drug binding in human cells and is used to determine binding affinities of lead compounds in crude samples. We anticipate that this method will enable the application of native MS to a range of problems where cellular context is important, including protein–protein interactions, drug uptake and binding, and characterization of therapeutic proteins.

Intracellular Protein–Drug Interactions Probed by Direct Mass Spectrometry of Cell Lysates