Hmmh... I am not sure that a column contamination can explain a partial (!) breakthrough of an analyte. Also, if I want to clean a WCX column, I would go to strongly acidic conditions to eliminate the charge on the ion exchanger. At alkaline conditions, you are still left with analytes with a permanent positive charge that still stick to the packing. To me, partial breakthrough does not sound like a problem with the column, but like something that has to do with the sample - age, preparation etc. This is why I asked the questions about the sample, but I am still missing something since the problem seems to remain unresolved.
That may be good advice if one is dealing mainly with small, permanently charged molecules, but it is well off the mark with a complex mix of proteins. The surface of a typical monoclonal antibody is a complex patchwork of hydrophobic surface, negatively charged (mostly carboxyl) groups and positively charged nitrogen groups. These groups are all titratable. While it is true that at very acidic pH you will greatly reduce the charge of the column, you will also make it and the protein more hydrophobic and reduce greatly reduce the powerful electrostatic forces that could push the protein off the column by making the protein ever more positive, and thus still attracted to any residual negative charge on the column. In contrast, at high pH the net charge on most contaminting proteins would become highly negative while the column is highly negative also and the resulting repulsive electrostatic free energy term would become very large. That is why Dionex recommends removing really stubborn protein contaminants with NaOH. That said, following such a protocol with a low pH elution in the presence of a compatible organic such as ACN is certainly a good idea
