The influence of the ionisation energy on the quality of spectral fingerprints recorded by static head space-mass spectrometry (SHS-MS) was studied on cheese, wine and flavoured soda. The parameters used to assess signal quality were noise level of spectra, total signal abundance, range of mass fragments above noise, signal-to-noise ratio of each mass fragment, and discriminating power of the spectral fingerprints. These parameters were measured at eight levels of ionisation energy ranging from 35 to 95 eV. Overall, up to 70–80 eV the quality of the mass spectra increased. Fine analysis of the mass spectra shows that the levels of ionisation energy that yielded the best signal-to-noise ratios were specific to the material being studied. This work also shows that a thorough study of the spectral noise helps optimise the spectral acquisition parameters and their exploitation in predictive models.