Amytracker fluorescence is one order of magnitude brighter than Congo Red. The affinity of Amytracker is in the nM range and thus, Amytracker is typically used at several fold lower concentrations. In a comparative study using human amyloidosis tissue, Amytracker detected amyloid deposits in 15 % of Congo Red negative samples. While the pathological relevance of Congo Red negative deposits is currently unclear, Amytracker staining might give an indication of earlier states of disease. Unlike Congo Red, Amytracker does not bind to collagen or other cytoskeletal proteins.
In the APP/PS1 and APP23 mouse models of Alzheimer's disease, Amytracker stains early fibrils already after 6 months, while Congo Red stains mainly mature fibrils showing up after 12 months in the APP/PS1 mouse model.