Many of the methods run in our lab are run with an ion-pairing reagent in an 80% aqueous mobile phase. The organic is generally ACN. It is generally necessary to clean the columns after 200 injections because of highly retained compounds will eventually begin to elute and interfere with the chromatographic purity or other analysis that is being performed. The method requires the column clean up to be performed with 50/50 water/acetonitrile. It is our experience that by doing this we will spend a significant amount of time re-equilabrating the column and after cleaning the performance with regards to retention time is no longer the same. We have found that if we alter the cleaning procedure to use the same 50/50 mix, but to add the ion pairing agent to the same concentration as it is found in the mobile phase we accomplish the required cleaning, but also do not have that disadvantages mentioned above. I understand why this occurs, but I need a reference to help convince my client that this is a proper and a more correct method for cleaning the columns when an ion-pairing reagent is used. Please let me know.

Hi Tihs,
I would say your best approach would be to stop the late eluters getting on the column, as you are hinting at. This would be the normal approach. Ion-pairing is a dynamic thing and can be easy to upset, as you have found. Dedicated columns would be my choice, together with solid phase extraction of the interferences.
The problem you have, as you point out, is convincing a third party, may be the only way is to demonstrate it, (at cost to them for the development work if/when it works). So often third party methods are 'quick and dirty', to save time/money, but we all end up losing in the end!
Hope that gives you some help, you are not alone!
Cheers
Bryan Wallwork

You have the references you need right in your data system. You have documented the problems with the present clean-up method, and you have demonstrated that your proposed alternate method is superior. Present the data to your client, along with a cost estimate for each method. Show them the time/money saved, it should be a no brainer for them. If they insist on the current protocol, bill them for the time. It may be time wasted for you, but at least it's paid time.