Rick1112, you are looking for a simple answer to a complex question.
The true answer is that you have no way of knowing the best pH ahead of time (that's why chromatography is an experiment-based technique). To the extent that there is a "cookbook", it would go something like this:
1. (per danko's advice) decide if you want to do anion or cation exchange chromatography.
2. Start with a pH 2 or more units away from the pI on the appropriate side (below for cation exchange, above for anion exchange). That will ensure that your protein has a net charge appropriate for retention. Select an appropriate buffer for that pH. Usually the buffer will be in the 25mM or so range.
3. Run a gradient from 0 - 1N NaCl and see what happens. Trim the gradient range as appropriate.
4. If you need different selectivity, move the pH closer to the pI and try again. (note that a selectivity change may make the separation worse!).
5. Other ways of changing selectivity:
- changing the salt (either the driving ion or the counterion)
- using a different ion exchange packing
- changing the temperature
- adding small amounts of organic modifier.
The above assumes that you are using strong anion or cation exchange. If you are using weak exchangers, then you have to take the pKa of the stationary phase into account, and the situation gets even more complex.
