Abstract: The invention is directed to methods to distinguish among different protein conformers of the same protein such as proteins which form amyloid deposits. Using the methods of the invention, one or more protein conformers in a sample can be detected, differentiated, and quantitated. An example of a protein which is known to exist in at least two conformations is the normal prion protein (PrPC) and its infectious isoform (PrPSc). The invention provides means to distinguish PrPC from PrPSc and allows quantitation of each individually, even when the conformers are present together in a mixture. Thus, the methods of the invention can provide important tools for human and animal health.