A mass spectrometer system includes a pulsed ion source configured to generate ionized molecules and neutral molecules. The system also includes a first enclosure coupled in flow communication with the pulsed ion source. The first enclosure defines a first vacuum chamber and an ion inlet aperture. The system further includes a detector positioned within said first enclosure and a plurality of ion transmission devices positioned within the first vacuum chamber and aligned with the ion inlet aperture. The plurality of ion transmission devices is configured to channel and accelerate ionized molecules through a first transmission path such that the ionized molecules and the neutral molecules are physically separated in space and temporally separated.