I am measuring the activity of my promoters in response to different sugar substrates. I placed the reporter gene downstream of the promoter. FACS is not available in our laboratory, so we used fluorescence spectrometer instead.
Depending on how many cells and how strong your fluorescent label this should be feasible. Also the contrast of your response will need to be within the LOD of your spec. Give it a shot, all you have to lose is some cells (assuming you have a stable line).
If you know the excitation wavelengths of your cellular samples (from UV-Visible absorbance spectroscopy), then you should be able to measure and collect the fluorescence spectra at the fixed excitation wavelengths. I'm assuming that these proteins absorb strongly in the UV (lambda 200-400 nm)? If so, then you will need to find out the lower detection limit wavelength on the fluorescence spectrometer. Chris