Abstract: The present invention relates to a method for the determination of the species profile of a protein-interacting compound, comprising the steps of a) providing a protein preparation derived from one species (species-1) containing a species-1-variant of said protein, b) providing a protein preparation derived from another species (species-2) containing a species-2-variant of said protein, c) mixing said preparations, d) contacting said mixed protein preparations with a ligand of said protein and with a given protein-interacting compound under conditions allowing the formation of a complex between said ligand and said protein, and e) detecting the complexes formed in step d) with the help of mass spectrometry.

Abstract: The present invention relates to methods for the identification and characterization (e.g. selectivity profiling) of HDAC interacting compounds using protein preparations derived from cells endogenously expressing HDACs or cell preparations containing said HDACs.

Abstract: The present invention relates to methods for the characterization of enzymes or of enzyme-compound complexes, wherein the enzyme is obtained from a protein preparation with the help of at least one broad spectrum ligand immobilized on a solid support and wherein the enzyme is characterized by mass spectrometry. These methods are useful for the screening of non-immobilized compound libraries, selectivity profiling of lead compounds and mechanism of action studies in living cells.