Quantum theory states that orbiting electrons of an atom must occupy discrete energy levels in order to be stable. Bombardment with ions of sufficient energy (usually MeV protons) produced by an ion accelerator, will cause inner shell ionization of atoms in a specimen. Outer shell electrons drop down to replace inner shell vacancies, however only certain transitions are allowed. X-rays of a characteristic energy of the element are emitted. An energy dispersive detector is used to record and measure these X-rays.
Only elements heavier than fluorine can be detected. The lower detection limit for a PIXE beam is given by the ability of the X-rays to pass through the window between the chamber and the X-ray detector. The upper limit is given by the ionisation cross section, the probability of the K electron shell ionisation, this is maximal when the velocity of the proton matches the velocity of the electron (10% of the speed of light), therefore 3 MeV proton beams are optimal.