Chromatography Forum

We have recently completed the analysis of a set of samples using ion-pair chromatography. Although I was quite pleased with the results, the mobile phases we used, (nonafluoro pentanoic acid on one instrument, and pentafluoroheptanoic acid on another instrument - both are Aquity UPLCs), are proving extremely difficult to get rid of; both show quite clear IPR parent ion contamination even after exhaustive flushing sequences. We've tried all the recommended flushing mixes (acid, base, strong solvent, weak solvent) and have also changed a number of different filters (solvent frits, in-line filters, mixer) and tubing (of course there is no column). In 15 years of working with LCs I have really never seen anything quite like this problem; I'm not sure what to do next. I was wondering if anybody had experienced a similar problem and could perhaps advise us on how to proceed.

Kind Regards

Ion paring is the last resort to seek only if any other option fails. However, because there are so many LC phases available on the market, you always have the chance to find one suiting you application without using ion-paring.

My experience with ion paring is to dedicate every removeable component, if possible, a full system to this application only. The only viable suggestion I have is to keep flushing the systen over an extended period of time, you may eventually get ride of it.

What type of compounds are you trying to separate (besides being bases).

The application was profiling small molecules (mainly amino acids) in culture media; although it's no excuse, I'm particularly disapointed since the solution was published as an instrument manufacturer application note. Well, we've certainly learnt our lesson, and certainly won't be going back to this particular system.....but my main concern for the moment is getting rid of the problem so that we can work on other things.

Besides replacing ALL tubing, have you tried replacing the LC degasser?

Have you tried THF?

The UPLC instrument requires a special kit for THF use.....I've ordered the kit.

I'm not sure if it is a good idea to order such a kit for cleanig only. Nobody can be sure if THF would be good enough although it should be better than methanol.