For a through treatment of your problem, we will need the information Babcock_Hall: asked for. However, your underlying premise may very well be flawed. If you're doing ion exchange chromatography, you might get two peaks. But if you're doing reverse phase or other column chemistry, the protonated vs non-protonated won't resolve from each other at all. Instead, you'll get mis-shapen peaks. We try to minimize ionization, or maximize, if that gives us better results. We don't try to get two species for one analyate. Otherwise, you will get horrible reproducibility.