Mass spectrometry explained…

Identification and quantification of chemical compounds

Mass spectrometry (MS) is a very versatile and powerful analytical method. In addition to identifying and quantifying chemical compounds, it is also used to determine various chemical properties. Mass spectrometry is not one of the spectroscopic methods, such as FTIR or RAMAN, because no electromagnetic radiation is detected.

MS can be used to determine the ratio of mass to charge (m/z) of one or more substances from a sample. To uniquely identify a substance, the molecules are split into smaller ions – this is called fragmentation. The splitting is characteristic for each molecule and thus enables identification. First, the molecules of the sample are transferred to the gas phase and ionized. Then the ions are separated from each other according to mass and charge and the respective quantities are recorded. Many mass spectrometers therefore essentially consist of an ion source for ionization, an ion trap for separation, and a detector for detecting the individual ions.

Many different variations are available for each component of a mass spectrometer, so that application-specific mass spectrometers can be constructed by combining different components. This makes MS an extremely versatile yet very powerful analytical method with high relevance.


For mass spectrometric analyses it is necessary to generate ions, i.e. to convert the substances of a sample into electrically charged atoms or molecules. This is done in the ion source. If an electron is removed from an atom or molecule, it is positively charged and called a cation. Negatively charged ions are named anions.


Once the ions are created, they are held in a stable orbit by a static or dynamic electric or magnetic field. As long as this field exists, the ions are trapped in this orbit, hence this component is also called an ion trap. The frequency with which the ions circulate in the ion trap depends on the mass to charge ratio. To prevent the ions from being deflected from their trajectory by collisions with air molecules, the ion trap usually operates with greatly reduced pressure (vacuum up to 10-7 mbar). The strength of the vacuum required depends on the volume of the ion trap: The larger the volume the lower the required pressure and vice versa. For large ion traps, the vacuum system pumps the air down to the working pressure. Powerful turbopumps with 10,000 to 90,000 revolutions per minute are used for this purpose. Thus, many MS units are very large and heavy, requiring maintenance and servicing.


Once the ions are captured in the ion trap, they can be detected in a variety of ways. Usually, the frequency of their circulation path is controlled. On one hand this depends on their mass and charge and on the other on the applied field. By changing the field, the orbit of ions with a certain mass to charge ratio can be destabilized so that they leave the ion trap and are detected at the detector. Since the change at the applied field is known, the mass to charge ratio of the ions can be determined and their frequency measured at the detector.


Different molecules with the same mass are called isomers. If isomers are fragmented, they break down in a molecule-specific manner into smaller molecules or atoms that differ in their mass and charge. This makes it possible to identify substances unambiguously.