Method and system are disclosed for determining sample composition from spectral data acquired by a charged particle microscopy system. Chemical elements in a sample are identified by processing the spectral data with a trained neural network (NN). If the identified chemical elements not matching with a known elemental composition of the sample, the trained NN is retrained with the spectral data and the known elemental composition of the sample. The retrained NN can then be used to identify chemical elements within other samples.