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Effects of low energy electron irradiation (5-30 keV) on some of the optical properties of CdSe nanocrystals are examined. Degradation in luminescence intensities are measured and compared for inorganic nanocrystals coated in trioctylphosphine oxide (TOPO) and biologically compatible CdSe nanocrystals coated in mercaptoacetic acid (MAA), as well as CdSe-MAA nanocrystals conjugated with the protein Streptavidin. Electron beam effects are investigated using the technique of cathodoluminescence, which is seen to induce significant degradation in nanocrystal related fluorescence in all nanocrystals. Varying beam energy and sample temperatures showed faster degradation at cryogenic temperatures and a higher susceptibility to low beam energies in protein conjugated nanocrystals.