A method and system for evaluating a colored gem stone which has been cooled to below a designated temperature are provided. The system includes a cooling unit configured to support and cool a gem stone to below a desired temperature, an electromagnetic radiation source, a spectrometer, an integrating sphere, and a processing unit. The method includes receiving a spectral response of the colored gem stone and sampling a noise component within a range of wavelengths in the spectral response so as to make a baseline determination. The method further includes ascertaining a presence of at least one designated peak within the range of wavelengths as a function of the baseline determination, and evaluating the presence of each of the at least one designated peaks so as to provide an indication of whether the colored gem stone requires further evaluation.