We investigate the potential of elastic scattering of energetic ions for compositional analysis of magnetic colloidal nanocrystals. Thin layers of nanocrystals deposited by spin coating on Si-wafers are investigated by two different set-ups for Rutherford Backscattering Spectrometry (RBS), employing different projectile ions (4He, 12C) and primary energies (600 keV - 8 MeV). The advantages and disadvantages of the different approaches are discussed in terms of obtainable mass resolution, necessary primary particle fluence and deposited energy. It is shown that different isotopes of transition metals can be resolved by employing 8 MeV 12C3+ primary ions.