Aspects of spectrometer secondary reference calibration are described. In one embodiment, a diagnostic measurement for evaluation of an aspect of calibration in spectroscopy is performed. A result of the diagnostic measurement is analyzed to determine a deviation from an expected result. Based on the analysis, a correction algorithm may be applied to the aspect of calibration, in view of the deviation. In some embodiments, a product model diagnostic measurement is also performed for further evaluation of the aspect of calibration. A result of the product model diagnostic measurement is analyzed to determine a product model deviation from an expected result of the product model diagnostic measurement, and a product model correction algorithm is applied, if necessary. According to aspects of the embodiments described herein, using secondary reference standards permits reconstruction of calibration parameters without any need for a master instrument or other forms of calibrated reference instrumentation.