A new method is presented for removing the effect of the gain variation of parallel detectors used for the quantitation of trace elements with electron energy loss spectroscopy (EELS). Use of the ratio of two first-difference spectra eliminates the effect of gain variation of the detector, therefore eliminating the need for gain normalization and dark current subtraction. This method is particularly suitable for revealing small signals superimposed on a large background, a typical scenario for trace element quantitation of both biological and inorganic materials. This method has been tested on a system with a cooled CCD camera as the parallel detector and illustrated by the analysis of low concentration Ca in an organic matrix. The method is expected to be generally applicable to spectral analysis affected by gain variations of parallel detectors.