The present invention relates to a method for determining the three dimensional structure of biomolecules, such as proteins, protein fragments, and peptides. The biomolecule is encapsulated in an amorphous silica matrix, from which a needle specimen is prepared. Atom probe tomography is then used to analyze the needle specimen and the data is used to reconstruct the three dimensional structure of the biomolecule. The present invention greatly facilitates determination of the three dimensional structure of biomolecules.