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A mass spectrometer performs three essential functions: ionization of molecules or atoms to create charged species, separation of ion fragments based on their mass-to-charge ratio using magnetic or electrical fields, and detection of ions to record their relative abundance. Together, these functions produce a mass spectrum showing the fragment distribution of the analyzed sample.

In electron ionization, a vaporized sample in the ionization chamber is bombarded with a high-energy electron beam, typically around 70 eV. These electrons strip electrons from analyte molecules, producing radical cations. The radical cation quickly fragments into neutral molecules, radicals, and cations, which are then directed toward the analyzing chamber for separation and detection.

Mass spectrometers record only charged species because the electric or magnetic fields in the analyzing chamber control and manipulate ions based on their charge and mass. Neutral molecules lack charge and cannot be deflected by these fields, making them impossible to separate or detect. Only charged fragments reach the detector and contribute to the mass spectrum.

A magnetic field applied in the analyzing chamber bends the trajectories of accelerated ions based on their mass-to-charge ratio. At a constant magnetic field strength, ions with different masses follow different curved paths with varying radii of curvature. A narrow slit positioned before the detector allows only ions of a specific mass to pass through, enabling selective detection of individual ion masses.

Accelerator plates, positioned after the ionization chamber, accelerate the generated ions toward the analyzing chamber using a series of negatively charged plates. This acceleration gives the ions kinetic energy, which is essential for their subsequent separation by magnetic or electrical fields. The accelerated ions then enter the mass analyzer where they are separated based on mass-to-charge ratio.

By varying the magnetic field strength, the mass spectrometer can selectively allow ions of different masses to pass through the detector slit one at a time. As the field is scanned through a range of values, each mass-to-charge ratio reaches the detector sequentially. The relative abundance of each ion type is recorded, creating a complete mass spectrum showing all charged species present in the sample.

After formation, the molecular ion is unstable and quickly undergoes mass spectrometry molecular fragmentation, breaking into smaller charged fragments, neutral molecules, and radicals. Only the charged fragments are accelerated by the accelerator plates and separated in the analyzing chamber. This fragmentation pattern is characteristic of each molecule and provides structural information in the resulting mass spectrum.