Amyloid-beta (Ab) proteins play an important role in a number of neurodegenerative diseases. Ab is found in senile plaques in brains of Alzeimer's disease patients. The 42 residues of the monomer form dimers which stack to fibrils gaining several micrometers in length. Using Ab fibrils with 13C and 15N marker substitution, we developed an innovative approach to obtain insights to structural and chemical information of the protein. We deposited the modified protein fibrils to pre-sharped aluminium needles with >100-nm apex diameters and, using the position-sensitive mass-to-charge spectrometry technique of atom probe tomography, we acquired the chemically-resolved three dimensional information for every detected ion evaporated in small fragments from the protein. We also discuss the influence of experimental parameters such as pulse energy and pulse frequency of the used Laser beam which lead to differences in the size of the gained fragments, developing the capability of localising metal atom within Ab plaques.