The problems that often arise during the X-ray analysis of light elements are caused by the physics of the X-ray spectrum process and the mathematical algorithms (correction systems) used to calculate the concentration of elements. Therefore, the solution to these problems is determined by the hardware implementation of the analysis methods and its functionality. The most difficult situations arise in the qualitative and quantitative analysis of rocks that contain carbon in their composition. This is due to the fact that in the zone of generation of the X-ray signal, the polymerization of residual oil vapors and the appearance of a carbon film on the surface of the sample under study occurs. Therefore, with the standard method of studying a sample of unknown composition using an energy dispersive spectrometer, the peak of carbon is usually excluded from the scheme for calculating the concentrations of elements, which is unacceptable for carbon-containing samples. Using the example of the study of calcium and strontium carbonates, we have developed a method for measuring elemental chemical composition using the INCA Energy+ X-ray analysis system, which includes energy dispersive and wave dispersive spectrometers. The X-ray spectrum analysis system was applied in the study of carbon-containing unstable samples under the electron probe – unique remnants of paleoflora in the impact-melted rocks of the impact crater Elgygytgyn.Ref