I am using a Xterra coloumn for reverse phase chromatography. The mobile phase consists of MEOH and Ammonium acetate buffer. The method I am using is 5080 gradient. The ghost peak I get when I run a blank is around 7.4. I have used 100% Methonol washes so many times but it has no effect on its intensity. Neither does a acetonitrile wash. I have cleaned the needle, the injector, changed the guard coloumn and frit but still the peak is there.

You should probably look at your sample diluent. What is in it? Could it have become contaminated? Try making it up fresh with different lot numbers of modifiers and see if that helps. What kind of system are you running it on? How large are your injections, and does the peak area/height change with different injection volumes? Ammonium acetate seems to be an inherently dirty modifier, try a new lot number of that also.

We use Methanol as the sample diluent and have tried many different lot numbers of this so are confident that this is not where the problem lies. Our operating system is TotalChrom Navigator. We use a Perkin Elmer (PE) DAD, PE series 200 autosampler, PE series 200 lc pump. We have tried various injection volumes from 10 mirolitre to 150 microlitre but the peak area/height does not appear to change. The ammonium acetate is from the same jar as we have been using for months and we haven`t had a problem with it before. Any other suggestions?

9 times out of 10, it's the water that is causing the problem in these cases.

What is the wavelength?

Have you tried running the gradient without making an injection? If the ghost peak is there, try waiting a longer period of time before running the gradient again without making an injection. Does the ghost peak increase in size? If so, as Anon 10:12 suggested, it could be the water you are using.