Identifying Nonspecific Ligand Binding in Electrospray Ionization Mass Spectrometry Using the Reporter Molecule Method

The application of the reporter molecule (Mrep) 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 Mrep 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 Mrep 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