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.