A broad beam proton-induced X-ray emission (PIXE) system was designed in order to emulate and extend the calibration of Curiosity’s Alpha-Particle X-ray Spectrometer (APXS). For calibration of the PIXE system, twenty pure element standards were used to determine the instrumental constant over a range of X-ray energies. The issue of the choice between theoretical mass attenuation coefficient databases, XCOM and FFAST, was addressed. Deviations of light element (sodium, magnesium, aluminum) concentrations previously seen in the APXS were also seen in the accelerator-based PIXE measurements. These deviations arise from the rock structure’s violation of the assumption of sample homogeneity on the atomic scale. Systematically low iron concentrations, which appear unlikely to arise due to the homogeneity assumption, are more likely due to the grain size distribution of iron-bearing minerals in the powdered standards. Corrections for the deviations were determined and extended to Martian analog samples including basaltic trachyandesites, trachyandesites and trachytes.