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?