Why did the dialysis cause protein concentration to skyrocket? Doesn't it just remove the salt reagent and some other small molecules?
Yes, dialysis does just remove salt and other small inorganic/organic molecules; the protein is too large to pass through the pores of the membrane. The amount of protein in the closed dialysis bag does not change; since the system tries to reach equal concentration of protein on both sides of the membrane (but the protein cannot escape) you might expect, if anything, the liquid volume inside the dialysis bag to increase slightly. Protein concn. might therefore be expected to be lower, not higher. I have assumed that the protein is in a purely aqueous medium.
This makes sense to me, but have I missed something ?