The formation of adducts resulting from interactions between protein ions and residual gases in an electrospray ionization ion trap/time-of-flight mass spectrometer is reported. This instrument utilizes diffusion pumps to achieve high vacuum, and we found that when silicon based diffusion pump fluids were used, characteristic adduct peaks appeared in the mass spectra. These adduct peaks were not detected, however, when a polyphenyl ether (Santovac 5) was used as the diffusion pump fluid. In switching the diffusion pump fluid to Santovac 5, a rigorous cleaning procedure capable of removing residual silicon pump fluid from the instrument was a critical step. This cleaning procedure can also be used for routine cleaning of the ion trap and other source components. ©1997 American Institute of Physics.