by
danko » Fri Aug 29, 2008 12:45 pm
I must admit: I’d rather optimize various conditions than add a second column in addition to the analytical one (the SEC).
Mattias, are there any aromatic amino acids in your protein? It’s almost difficult to imagine this large protein without aromatic AAs. For instance, I have a protein containing a single tryptophan and its fluorescence is huge. But one has to determine the excitation and the emission spectra accurately and adjust the detector in accordance to their maxima. I’m sure the excitation wavelength for many proteins is 280 nm, but did you confirm that by actual scan? Even more important is the emission wavelength it varies tremendously with pH, temperature and other conditions in the analyte’s environment.
You don’t describe your mobile phase, so it’s difficult to point at a potential optimization possibility but anyway here are some suggestions you might like to examine closer:
1. Determine the working wavelengths by scanning the spectra and make sure the solute (protein) is dissolved in mobile phase.
2. Degas the mobile phase by sparkling with He, because oxygen quenches fluorescence.
3. If your mobile phase is purely aqueous, try and add ca. 10% isopropanol. It should facilitate the fluorescence and maybe it could disperse the micelles – if that’s what you’re dealing with.
4. Finally, make sure the temperature isn’t too high. High temperature is another known florescence quenching factor.
I’m assuming you’ve chosen the right SEC column for the protein you’re dealing with (i.e. it’s not excluded together with these potential micelles etc.) If it shows that your protein is excluded, then you’ll need to find a column with larger pores and then you wouldn’t even need the fluorescence detector.
Good luck with your troubleshooting/optimization.
Best Regards