Impacts of high kinetic energy massive gold clusters (~ 500 keV Au400+4) exhibit significantly enhanced secondary ion yields relative to traditional atomic or polyatomic primary ions (e.g. Au3 and C60). The one-of-a-kind instrument used to generate these hypervelocity nanoparticles (~2 nm diameter, ~30 km/s) and monitor emissions from their impacts (SIMS) is described in detail for the first time. The projectile range of 520 keV Au400+4 is measured to be ~20 nm in amorphous carbon and projectile disintegration is observed at the exit of carbon foils as thin as 5 nm. These experiments were performed by monitoring carbon cluster ions emitted from both sides of a foil impacted by the projectile. Surprisingly, clusters emitted in the forward direction are larger than those emitted backward. The composition of the mass spectra is shown to depend on both the thickness of the foil and the size of the projectile. Secondary ion yields for a variety of materials including peptides, lipids, drugs, polymers, inorganic salts, and various small molecules have been measured and molecular ion yields for many of these species exceed unity. Multiplicity measurements show that up to seven molecular ions of leucine-enkephalin (YGGFL) can be detected from the impact of a single projectile. SI yields measured with ~500 keV Au400+4 are generally one to two orders of magnitude greater than those obtained with 130 keV Au3+ and 50 keV C60+ projectiles. The high molecular ion yields observed suggest the internal energies of ions emitted from massive cluster impacts are relatively low. In order to address this hypothesis, a novel method for measuring secondary ion internal energies was developed using a series of benzylpyridinium salts. Using this method, the internal energies were measured to be ~0.19 eV/atom, which is a factor of five less than that seen in atomic-SIMS. Sample metallization is shown to be ineffective for further increasing secondary ion yields with Au400, despite observations from previous molecular dynamic simulations. Coincidence mass spectrometry is applied to nanometric chemical segregations found on samples coated with thin layers of gold and silver. It is possible to measure the surface coverages of the metallic and underlying organic layers using mass spectrometry in a non-imaging mode.