I am purifying a protein on a SP-Sepharose FF (strong cation exchanger) at pH 5.0. The EQ consists of 50mM NaAcetate, wash is 50mM NaAcetate, 30mM NaCl, and elution is 50mM NaAcetate, 500 mM NaCl. There appears to be a transient pH dip (from pH 5 to 4.5) during the start of elution according to the online pH meter. The pH recovers fairly quickly. The only reason this is a concern is because my protein appears to have some n-terminal degradation post column which may have to do with localized pH drops on the column. I charge the column prior to EQ with elution buffer, but this doesn't correct the problem. I can eliminate the pH drop with a stronger buffer (100mM NaCitrate), but my protein won't bind under those conditions. Ideas on how to correct the pH problem?

Your problem is due to the fact that your buffer system only buffers the mobile phase not the stationary phase pH. A SCX phase excludes the acetate anion at that pH so the buffer effect of this anion doesn't extend to the stationary phase (this detail is often overlooked in buffer selection). Ideally you should add a buffering cation to your system to overcome this problem but at this pH there are relatively few options at such a pH that are UV transparent. MES might work if you add it to your buffer system (being zwitterionic at this pH it has access to your stationary phase) but this is a bit outside it's buffering range so I'm not sure how much it will help. I did find one refernce to it's use at pH 5.2, though, so it might work.