Helium droplets are large helium clusters that are capable of picking up individual atoms and molecules and show promise as nano-reactors for the synthesis of unique nanoparticles. In particular, the sequential addition of materials of different types offers opportunities for the fabrication of novel core-shell nanoparticles that cannot be synthesised by other methods. To exploit this potential, here we have carried out a mass spectrometry investigation on metal clusters in order to establish how to control the doping conditions for the fabrication of nanoparticles in superfluid helium droplets, and in particular to develop a recipe to control core and shell ratios in the case of core-shell nanoparticles. Several types of metal nanoparticles, including pure Ag, Au and Ni nanoparticles, and Ag/Au and Ni/Au core-shell systems, have been synthesised and then removed from the helium droplets by deposition on substrates for ex situ investigations using high-resolution transmission electron microscopy (TEM) and X-ray photoelectron spectroscopy (XPS). The TEM imaging has been used to estimate the sizes of nanoparticles, which show a bimodel distribution under the conditions employed. We also present the first evidence that crystalline metal nanoparticles are formed by self-assembly of metal atoms in helium droplets. The XPS investigation of Ni/Au core-shell nanoparticles shows an absence of any Au 4f core-level shift that would occur on alloying of Au and Ni, which provides the first direct evidence for the successful formation of core-shell nanoparticles using superfluid helium droplets.