The mass analyzer is a crucial component of the mass spectrometer. In the ionization chamber, the vaporized sample is bombarded with a high-energy electron beam to generate a radical cation and further fragment into neutral molecules, radicals, and cations. A series of negatively charged accelerator plates accelerate the cations into the mass analyzer. The mass analyzer separates ions according to their mass-to-charge (m/z) ratios and then directs them to the detector. The common types of mass analyzers include magnetic sector, double-focusing, quadrupole, time-of-flight, and ion trap.

A magnetic field is applied in the magnetic sector analyzer, and the moving charges deflect to a curved path. For a given magnetic field, the radius of curvature depends on the m/z value, and the ions of a particular m/z value pass to the detector. As a result, the magnetic field of the instrument is continuously varied to sequentially pass ions in a broader m/z range to the detector.

A double-focusing mass analyzer uses a combination of the electrostatic sector and magnetic sector. As the ions exit the source, the electrostatic field focuses the ionic beam to minimize the kinetic energy spread and then leads the ions to the magnetic sector. The magnetic sector sorts the ions based on the deflection. This double-focusing of the beam helps in achieving high resolution.

The resolution of the mass spectrometer is defined as its ability to differentiate between two closely spaced mass spectra. A unit resolution indicates the ability of the instrument to differentiate the masses with a difference of one integer unit. For example, an instrument with unit resolution can distinguish m/z 50 from m/z 51, or m/z 100 from m/z 101, or m/z 500 from m/z 501. Generally, the resolution for commercial spectrometers is in the range of 500 to 500,000.