Molecular ions, addition ions and fragment ions

A single compound may appear in several different ionic forms in mass spectrometry. Understanding their origins and relationships is fundamental to interpreting the spectrum correctly and avoiding the mistake of ‘counting one substance as several’. Based on their origin, ions are broadly classified into three categories: molecular ions, addition ions and fragment ions.

A molecular ion is an ion formed when the compound as a whole loses or gains a single electron (or proton). When it carries a single charge, its m/z is approximately equal to the molecular mass; consequently, it directly provides the most crucial molecular mass information and serves as the starting point for structural identification. Soft ionisation methods generally preserve molecular ions well, allowing one to see at a glance ‘how heavy this molecule is’.

Adduct ions are formed when a molecule combines with other ions in the system. In electrospray/DESI positive mode, [M+H]⁺, [M+Na]⁺ and [M+K]⁺ are commonly observed, whilst in negative mode, [M−H]⁻ and [M+Cl]⁻ are common. Addition ions do not alter the elemental composition of the molecule itself, but only its apparent mass; therefore, when identifying them, one must remember to subtract the mass of the additive (e.g. Na is approximately 22 heavier than H), otherwise the m/z reading may be incorrect and the identification mistaken. The simultaneous appearance of multiple addition peaks from the same molecule can, in fact, serve to corroborate one another.

Fragment ions refer to smaller ions produced when the molecular ion breaks apart during ionisation or subsequent processes; their m/z values are lower than that of the molecular ion. Although fragments are ‘incomplete’, they carry structural information—different compounds exhibit distinct fragmentation patterns, which can be used to distinguish isomers with the same molecular weight but different structures; this forms the basis for structural identification via tandem mass spectrometry.

In ambient-pressure open-system imaging techniques (such as DESI, MALDI and laser desorption), soft ionisation primarily produces molecular ions and addition ions, with few fragments, resulting in relatively clean spectra; hard ionisation, on the other hand, generates a large number of fragments, providing rich information but potentially yielding very weak molecular ions. Neo Source INSTRUMENT’s two imaging ion sources utilise a back-photodissociation pathway to perform single-photon ionisation of neutral molecules, producing virtually no fragments. They primarily yield molecular ions and a small number of addition peaks—resulting in clean, easily recognisable spectra that minimise the risk of error when identifying lipids and metabolites in complex biological tissues. The MSI DPI and MSI LDPI can be fitted to mass spectrometers from Agilent, AB SCIEX and Thermo.