The PureJet system uses electrospray injection to generate a stream of molecular ions. These ions travel through several differential pumping stages, where pressure-appropriate ion beam shaping elements ensure high transmission. The first pumping stage utilizes an ion funnel to drive the ions to the exit aperture, while the second pumping stags is a quadrupole collision cell design. A gate valve separates the pumping stages from the deposition chamber. A three stage pumping system enables depositions in the 1E-9 torr range at the sample position. This enables clean depositions for sensitive surface science experiments such as scanning probe microscopy.