Mass analyzers can be quadrupole, magnetic sector, time-of-flight, ion trap or ion cyclotron resonance type. Most benchtop GC/MS systems designed for routine, high throughput analysis of organic compounds utilize a quadrupole analyzer, and newer models are quite compact.
In most benchtop instruments designed for routine analysis, the GC is the only sample inlet to the mass spectrometer. Containers for gaseous samples may be plumbed directly to the high vacuum chamber of the mass spectrometer, but a needle valve should be used to regulate gas effusion rate. In addition, solid samples of known high purity can be analyzed using a direct insertion probe. This technique is generally much quicker than using a GC as the inlet, but lacks the separating capability provided by the GC.
Mass spectrometers typically use either oil diffusion pumps or turbomolecular pumps to achieve the high vacuum required to operate the instrument. Diffusion pumps run quieter and are cheaper, but take longer to reach maximum pumping speed and may lead to instrument contamination in the event of a vacuum breach. Turbo pumps, on the other hand, produce a turbo whine (which can contribute to operator fatigue) and are more expensive, but are quicker with regard to venting and reaching ultimate pumping speed.
Regardless of the choice of high vacuum pump, foreline or roughing pump(s) will also be needed. For a small, benchtop instrument, one mechanical pump may serve double duty as both the roughing and foreline pump; in more versatile instruments, dedicated roughing pumps may be present to allow pumping of inlet ports while the instrument is pumped to high vacuum.
There are several choices for ionization methods as well. Most laboratories utilize electron impact ionization, but a laboratory tasked with identification of unknowns may benefit from having chemical ionization capability as well. In general, this will require an instrument specifically designed to allow chemical ionization since there are differences in the ionization volume design, a means of injecting reagent gas and adequate pumping speed to dispose of the excess gas load. The trade-off for this increased complexity is the ability to more reliably measure molecular masses.
There is another additional benefit for having chemical ionization capability if the instrument 'polarity' can be changed. Negative ion chemical ionization is a powerful, specific technique for compounds with large electron capture cross sections. Often, negative ion mass spectra are highly specific for compounds that have electron impact positive ion spectra that appear very similar (such as some isomers).