The application of X-ray spectro-microscopy to image changes in the chemical state in application areas such as catalysis, environmental science, or biological samples can be limited by factors such as the speed of measurement, the presence of dilute concentrations, radiation damage, and thermal drift during the measurement. We have adapted a reduced-order model approach, known as the discrete empirical interpolation method, which identifies how to optimally subsample the spectroscopic information, accounting for background variations in the signal, to provide an accurate approximation of an equivalent full spectroscopic measurement from the sampled material. This approach uses readily available prior information to guide and significantly reduce the sampling requirements impacting both the total X-ray dose and the acquisition time. The reduced-order model approach can be adapted more broadly to any spectral or spectro-microscopy measurement where a low-rank approximation can be made from prior information on the possible states of a system, and examples of the approach are presented.