Laboratory facilities house three Hewlett-Packard gas chromatography-mass spectrometry (GC–MS) systems (a 5972 and two 5973s). These instruments can operate in either the electron impact or chemical ionization mode. Additional interferences for techniques such as supercritical fluid chromatography (SFC)-MS are available in addition to the standard GC interface.

When GC is interfaced to a mass spectrometer, the identity of the eluting organic compounds can be positively determined. Electron impact ionization of organic molecules produces fragmentation patterns that can be used (within limitations) to identify individual compounds present in a GC peak. Many compounds do not produce a recognizable molecular ion under electron impact conditions. Reducing the amount of energy used in the ionization process (e.g., chemical ionization methods) generally produces a detectable pseudomolecular ion that can be used to confirm the molecular weight of the compound.