Methods and systems for detecting, comparing, or evaluating proteins in an folded conformation, a particular bound state, or an aggregate state, and methods and systems for comparing amounts of labeling of a protein in a natural or control conformation and a denatured conformation. The methods of the present invention may be used for a variety of applications including but not limited to evaluation of protein aggregates levels related to a particular disease (e.g., aggregate-associated disease, etc.), possibly for diagnostic purposes.