In the running of our Waters 2690 HPLC there are peaks appearing between 30-35 minutes when samples or standards are run. However, when we run THF (which is our mobile phase) with a 20% solution of acetone or a zero volume injection, the interference peaks in this area disappear. My first instinct was that the peaks were from slightly oxidized THF, but the same bottle was used to make the standards as was used to make the THF/20% Acetone Solution. I was wondering if any could help me troubleshoot this problem we are running into?

Is it possible that your injector was contaminated? In other words, pure THF could whash out some of your contaminations in the injector but the THF/20%-acetone could not do that.