Identifying nonspecific ligand binding in electrospray ionization mass spectrometry using the reporter molecule method

The application of the reporter molecule (M_rep) method for identifying nonspecific complexes in the ES-MS analysis of protein-ligand and DNA-ligand interactions in vitro is described. To test the reliability of the method, it was applied to the ES-MS analysis of protein-carbohydrate complexes originating from specific interactions in solution and from nonspecific interactions in the ES process. These control experiments confirm the basic assumptions underlying the M_rep method, namely that nonspecific ligand binding is a random process, and that the ES droplet histories for specific and nonspecific complexes are distinct. The application of the M_rep method to the ES-MS analysis of the sequential binding of the ethidium cation, a DNA intercalator, to single and double strand oligodeoxynucleotides is also described, and highlights the general utility of the method.