Methods, systems, and compositions for detecting molecule aggregation, folding, or interactions featuring comparing the amount of labeling of a molecule of interest, such as a protein, in a test sample with an amount of labeling in a control, e.g., a sample wherein the molecule of interest is denatured. If less labeling is present in the test sample as compared to the control sample, the test sample may comprise the molecule of interest in aggregate form, folded form, or interactive form, e.g., interacting with another molecule such as a protein molecule, DNA molecule or RNA molecule. The present invention may be used for detecting or monitoring a disease or condition such as a protein misfolding disease (proteopathy), e.g., amyotrophic lateral sclerosis (ALS), etc.