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Alzheimer's disease (AD) is a neurodegenerative disease that involves the misfolding of a normal protein, called amyloid beta, which has recently been associated with the binding of metal ions, such as iron, copper, and zinc. It is thought that metal imbalance is involved in protein misfolding and leads to oxidative damage and neuron degeneration. Yet, the functions of these metal ions and the misfolded proteins in the disease process are not well understood. In this pilot study, we used synchrotron Fourier transform infrared microscopy (FTIRM) to image the in situ secondary structure of amyloid plaques in brain tissue from a mouse model of AD. We also examined metal ion content within these plaques using X-ray fluorescence microprobe (XRFM). We found that all plaques examined contained zinc, with higher concentrations in the center of the plaque. The iron distribution was more dispersed and the copper concentration was below the detection limit. In addition, we found increasing misfolded protein, indicated by elevated beta-sheet content, from the outer rim to the core of the plaque. This suggests that zinc concentration correlates with the amount of protein misfolding. However, its exact role, as well as the role of iron and copper, remains unclear.