(August 2004)

Development of mass spectrometry began with J.J. Thomson’s vacuum tube, with which, in the early part of the 20th century, he demonstrated the existence of electrons and “positive rays.” Thomson observed that the new technique could also be used by chemists to analyze chemicals. Despite this far-sighted observation, the primary application of mass spectrometry remained in the realm of physics for nearly thirty years. It was used to discover a number of isotopes, to determine the relative abundance of isotopes, and to measure isotope masses. These important fundamental measurements laid the foundation for later developments in diverse fields ranging from geochronology to biochemical research.

A mass spectrometer produces charged particles (ions) from the chemical substance that is to be analyzed. The mass spectrometer then uses electric and magnetic fields to measure the mass of the charged particles. There are many different kinds of mass spectrometers, but all use magnetic and/or electric fields to exert forces on the charged particles produced from the chemical to be analyzed. A basic mass spectrometer consists of three parts: A source in which ions are produced from the chemical substance, an analyzer in which ions are separated according to mass,and a detector, which produces a signal from the separated ions.

Figure 1. Schematic diagram of a Mass Spectrometer. Samples are introduced and are bombarded with electrons resulting in the acquisition of a positive charge. The samples are then accelerated and subjected to a magnetic field. Samples will interact with the receptor based on their mass. The masses are then interpreted to infer the amino acid sequence.

The magnetic or electric field separates ions according to their momentum (the product of their mass times their velocity). To understand how the force exerted by a magnetic field can be used to separate ions according to their mass, let us imagine that we have a bowling ball and a feather moving by us (both move at the same velocity). If we blow on the two objects in a direction perpendicular to the path of the objects, the feather will be deflected away from its path because it has a smaller mass (momentum), but the bowling ball, with its larger mass (momentum) will continue to move in its original path.

The atom is ionized by the loss of one or more electrons yielding a positive ion. This is true even for things that you would normally expect to form negative ions (chlorine, for example) or never form ions at all (argon, for example). Mass spectrometers always work with positive ions (with the exception of electrospray MS, which uses negative ions*). The ions are accelerated so that they all have the same kinetic energy. The ions are then deflected by a magnetic field according to their masses. The lighter they are, the more they are deflected. The amount of deflection also depends on the number of positive charges on the ion — in other words, on how many electrons were knocked off in the first stage. The more the ion is charged, the more it gets deflected. The beam of ions passing through the machine is detected electrically.

Mass spectrometers are used for all kinds of chemical analyses, ranging from environmental analysis (e.g. detection of poisons such as dioxin) to the analysis of petroleum products, trace metals and biological materials (including the products of genetic engineering).

Let’s suppose that we put some water vapour into the mass spectrometer. A very small amount of water is all that is needed — the water is introduced into a vacuum chamber (the “ion source”) of the mass spectrometer. If we shoot a beam of electrons through the water vapour, some of the electrons will hit water molecules and knock an electron loose. If we lose a (negatively charged) electron from the (neutral) water molecule, the water will be left with a net positive charge. In other words, we have produced charged particles, or “ions” from the water: Some of the collisions between the water molecules and the electrons will be so hard that the water molecules will be broken into smaller pieces, or “fragments “. For water, the only possible fragments will be [OH]+, O+, and H+.

A mass spectrometrist is someone who figures out what something is by smashing it with a hammer and looking at the pieces. A trained mass spectrometrist can interpret the masses and relative abundances of the ions in a mass spectrum and determine the structure and elemental composition of the molecule. Computer programs can also be used to interpret a mass spectrum.

Mass spectrometry plays a role in proteomics mainly through identifying proteins. Mass spectrometry allows even tiny amounts of a protein to be identified both by its sequence and through database searches of protein fingerprints. Protein fingerprints are discrete masses that individual proteins form upon mass spectrometrical analysis. And it is through the development of modern mass spectrometry that proteomics is becoming such a hot bed of scientific research today.


1. Pandey A., Mann M. (2000). Proteomics to study genes and genomes. Nature 405: 837-846.
2. Glish G.L., Vachet R.W. (2003). The Basics Of Mass Spectrometry In The Twenty-First Century. Nature Reviews Drug Discovery 2: 140-150.

*Thanks to Peter Findeis from Bucknell University for bringing this to our attention

(Art by Jiang Long – note that a slightly higer res version of this image file is available here)