The identification of atoms, anions and cations in proteinstructure electron density is often inferred from the tem-perature factor of the atom and from its coordination dis-tances to surrounding amino acids. In many casesunambiguous identification is not possible without the useof additional techniques. Mass spectrometry analysismethods [1] have advanced significantly over the past fewyears and precise total mass measurements are nowachievable. There is often ambiguity in the identificationof bound atoms, however, because extra mass can arisefrom a combination of sources; for example, from covalentmodification such as that of cysteine residues or glycosyla-tion, and from partially occupied metal atom sites asopposed to totally occupied lighter atom sites. One unique signature of an element that can be used inunambiguous identification is the energy of an X-rayemitted when an atomic electron undergoes an energytransition between its shell and a vacant electron site in alower energy shell (e.g. for an M to L shell transition,sulphur gives a 2.3 keV X-ray). The energy resolution ofmodern single crystal solid-state X-ray detectors allowsassignment of characteristic X-ray peaks in an energyspectrum to the various elements of the periodic table. Emission of the characteristic X-rays from a sample can beinduced by an incident beam of higher energy X-rays(X-ray fluorescence, XRF), electrons (electron probe X-raymicroanalysis, EPMA) or by protons (proton-inducedX-ray emission, PIXE). All three techniques have beenused on a wide variety of biological specimens [2]. None ofthem has a clear cut advantage for all experimental cases,and in fact the various advantages and disadvantages makethem complementary rather than competitive techniques. Synchrotrons produce beams intense enough to make amicroscopic probe for XRF, and the natural horizontalpolarisation of the X-ray beam results in increased signal-to-noise ratios over non-polarised X-ray beams. Thephotoionisation cross-sections for K and L series X-rays inXRF are very low for the lightest elements (below atomicnumber