Waters Alliance 2695 Separations Module is coupled with a Waters 2996 PDA detector and a Waters 3100 Mass Detector.

The system records fine UV chromatograms.

The Waters 3100 Mass Detector also acquires nice looking mass spectra when operated in direct infusion mode.

The problem is when the LC/MS/PDA are used in combination to collect UV and mass chromatograms. Again the UV chromatograms look great, but the mass chromatograms are extremely noisy, even after rigorous tuning. Even after doing an extracted ion the chromatogram remains extremely noisy, with noise even on the extracted peak. Reducing infusion rate to ESI source from 1.0mL/min. all the way down to 0.05mL/min. makes no improvement on noise. We are using +ESI to ionize substances such as stable carbamates where ion intensity and peak shape are excellent when tuned in direction infusion mode.

This problem appears to be some sort of software problem.

LC/MS operates on Empower 2 software.

Anyone have advice on how to correct this problem as all the instrumentation appears to be in good working order?

This entire Waters system was installed new 10 years ago and has always had this problem. It was serviced for years by Waters, but they never addressed it or corrected it. They have since been replaced by a third party service company, which also does not know how to remedy the problem.