We present a comprehensive structural investigation of the Ge wetting layer (WL) and island growth on Si(001) substrates by a combination of AFM, high resolution transmission electron microscopy and the energy-differential coherent Bragg rod analysis (COBRA) x-ray method. By considering the influence of the initial Si surface morphology on the deposited Ge, these techniques provide quantitative information on the Ge content and its distribution, in particular within the WL which plays a crucial role in the formation of epitaxial nanostructures. In the WL, the Ge content was found to be above 80% for our growth conditions. Furthermore, from the digital analysis of high-resolution transmission electron microscope images, quantitative information on the strain relaxation is obtained, which complements the COBRA analysis of the Ge distribution and content in these nanostructures.