What is mass spectrometry?

When you have been doing something for a long time, it is sometimes good to go back to basics. And I have been around mass spectrometry for a long time, well not as long as some - but still feels like ages. 

So what is mass spectrometry?

Mass spectrometry (or MS) is an analytical technique based on measuring the mass to charge ratio of ions, or simply said charged particles. A mass spectrometer in turn, is an instrument used to produce those particles. It then uses electric and magnetic fields to measure their mass to charge ratio. Plenty of examples here; Orbitrap, Quadrupole, Time of Flight.

You’d be surprised how old MS actually is. The first mass spectrometer was built by J.J. Thompson back in 1911. Today, there are many variations of this technique, each with a different application and the instruments can have very different designs. All of those techniques however are fundamentally based on the ionization of molecules or atoms and then detecting the ions based on their mass to charge ratio (m/z). The resulting information is usually presented in the form of so-called mass spectra. Here’s an example of one.

Example MS/MS spectrum

 

In this picture, the horizontal axis is the mass (m) to charge (z) ratio of the ion and the vertical axis is the number of counts by the ion detector.

In a classical MS experiment a pure chemical compound is placed in the ionization chamber and then fragmented using techniques like Fast Atom Bombardment (FAB) or Electron Ionization. Spectra of pure compounds obtained by FAB or EI at similar experimental conditions (for example same fragmentation energies) always lead to the same, or very similar, fragmentation pattern. At the same time it is extremely rare that two different chemical compounds fragment in the exact same way. MS can therefore be successfully used for the identification of compounds, but of course not always with a 100% certainty. The fact that certain groups of chemical compounds fragment in a certain way also allows determination of the probable structure of unknown compounds. Analyzing mass spectra in this way is rather cumbersome and does not always lead to clear conclusions. For that reason MS is often used as a complementary technique to NMR spectroscopy and IR spectroscopy. 

A popular application of MS is in proteomics. In proteomics mass spectra of peptide mixtures are created using ESI (Electrospray Ionization) and result in much more complex fragmentation patterns.

But MS can also be used for other purposes apart from identification of chemical compounds and determination of their structure. It can, for example, be used to investigate compounds' elemental composition or to specify their source of origin.

Overall, MS is a very versatile analytical technique.