Mass spectrometry

Mass spectrometry (MS) is an analytical technique used to measure small molecules. The small molecules may be either directly injected into the mass spectrometer (direct infusion) or through a coupled chromatographic system. The analytes are ionised at an ion source before they can be detected in a coupled mass detector. The resulting data typically consists of mass-to-charge (m/z), time, and intensity triplets that describe – for every detected ion mass – the strength of the ion beam and the time it is detected by the spectrometer.

Find out more about mass spectrometry, including an interactive animation of how a mass spectrometer works (5).

The sections below detail the different modules that comprise a simple mass spectrometer.

Sample inlet

The port through which samples enter the mass spectrometer. A mass spectrometer can be combined with a chromatographic technique or used via direct infusion without prior separation of analytes.

Ion source

Ionisation techniques are grouped into hard and soft. Hard ionisation, such as electron impact ionisation (EI), heavily fragments a compound by creating high energy electrons that interact with an analyte. In contrast, soft ionisation, such as electron spray ionisation (ESI), ionises a compound but creates only a few fragments.

Mass analyser

Generated ions are separated by their m/z ratio in the mass analyser where – for simplicity – charge is often assumed to be equal to one. Consequently a m/z ratio approximately equals the molecular mass of an ion. All mass analysers exploit the mass and electrical charge properties of ions but use different separation methods 

Detector and recorder

Separated ions are detected by a mass detector that scans a pre-defined mass range at close intervals. The chromatographic profile of an ion, i.e. the generated continuous ion beam, is recorded across multiple scans at discrete time intervals.