If, as part of your observing programme, you take spectra of standard stars then you will be able to attempt to flux calibrate your data.
The flux-calibration process is simple: you compare the extracted standard-star spectrum to a published spectrum of the same star. At each `wavelength' (I use the term very loosely here - see below for a proper explanation) you find the ratio of the observed to published spectrum. The result is a conversion factor at each `wavelength'. To flux calibrate your target objects you multiply the spectra by these per-wavelength conversion factors. The effect of this is to remove instrumental-response wavelength-dependency. At least that's the idea... in practice, you must be careful to understand how the published standards are tabulated, and how this might relate to your data.
Simple Spectroscopy Reductions