Mass spectrometry is a technique by which the molecular mass of a compound may be determined. A small sample of the compound is vaporised in a mass spectrometer under high vacuum and then subjected to bombardment by a beam of high-energy electrons. The impact of the electrons on the molecule (M) causes the ejection of an electron from the molecule to form a positively charged ion called the molecular ion or parent ion (M^+⋅).

In principle, more than one electron can be removed from a molecule, so that the ion is characterised by its mass-to-charge ratio, m/z (or m/e). In practice multiply charged ions are rare in mass spectrometry.

M + e^- → M^+⋅ + 2e^-

The positively charged ions are accelerated through an electric field before passing into a magnetic field. This causes the ions to travel a curved path whose curvature is dependent upon the m/z ratio and the speed at which the ions enter the magnetic field. Lighter ions have less momentum and are deflected more strongly than are heavier ions. The m/z ratio is calibrated in atomic mass units. Molecular ions arriving at the detector produce a peak in the mass spectrum at the molecular mass. The peak height is proportional to the number of ions arriving in a given time. The symbol for the molecular ion (also called the parent ion) is M^+⋅ (since it also has an unpaired electron) but M⁺ is also commonly used.

During the ionisation process, molecular ions with high energy may break up to produce fragment ions or daughter ions (m⁺):

M^+⋅ → m⁺ + neutral fragment

Such ions also appear in the mass spectrum at the relevant masses. The height of the peak due to the fragment depends on the amount formed.

The pattern of fragment peaks is characteristic of the original molecular constitution, because different kinds of bonds vary in strength; the weaker bonds break first during fragmentation. Different molecules have different weak spots, and so the molecular weight and fragmentation pattern give a lot of information on the structure of an unknown organic compound.

The peak with the highest m / z value usually (but not always) corresponds to the parent ion and so can usually be used to measure the molar mass of the molecule. Sometimes, a fragment ion is the most abundant ion and so produces the tallest peak in the spectrum. Whether the tallest peak is due to the parent or a fragment, it is called the base peak and is arbitrarily assigned a relative height of 100%. Heights of all of the other peaks are then expressed as percentages of the base peak.