An inlet and vacuum system for a portable, or handheld, mass spectrometer. The mass spectrometer comprises three vacuum chambers, which includes two ion funnels connected in series in the first two vacuum chambers, followed by a mass spectrometer analyzer and ion detector in the third vacuum chamber. The ion funnels are arranged with their central axes aligned in a linear fashion. The sample inlet to the portable mass spectrometer is from an external ion source, typically operating at atmospheric, or near atmospheric, pressure. An improvement in desolvation, and a reduction in the injection of neutrals, excited state molecules, and particulates into the analyzer is achieved by incorporating a lateral offset for the inlet capillary used to transfer ions into the first injection funnel. Additional efficiency for ion focusing is achieved by replacing the ion guide, typically used with atmospheric pressure ionization sources, with an additional ion funnel.