Desalting can be achieved using a PD-10 gel filtration column, or dialysis, or by concentrating the sample by ultrafiltration and rediluting it with low-salt buffer.

If the pI of your protein is acidic and you intend to do the ion exchange chromatography at approximately neutral pH, the protein will have a net negative charge, so you should use an anion exchange column, such as a QAE column.

I think the easiest way of desalting is via buffer exchange using the ultrafiltration method stated above. We use Amicon Ultra units (from emdmillipore) and they are extremely simple to use. It's a bit more heavy handed (especially if done too rapidly), though, as compared to dialysis or gel filtration. If you want to be really delicate with your protein, the latter choices might be better for you.

Thank you, Adam and Jesse.