6: Mass spectrometry

Mass spectrometry – colloquially called mass spec – gives us information about a sample molecule’s mass. Since we should know our target molecule’s chemical formula, and from that can calculate its molecular mass, mass spec is a very useful technique for quickly verifying that we have managed to make our target compound!

But before we can interpret data from a mass spectrometer, we need to look more closely at what makes up a molecule: its atoms!

What makes up an atom?

All matter is made up of tiny building blocks called atoms. And atoms are themselves made up of subatomic particles: protons, neutrons, and electrons. Protons are positive, and carry a +1 charge. Neutrons are neutral, or carry 0 charge. Electrons are negatively charged with a -1 charge. When the number of protons and electrons are balanced, the overall charge on the atom is 0. 

Protons and neutrons exist in the nucleus of an atom. The number of protons found inside an atom corresponds to its atomic number on the periodic table. If I change the number of protons, I change the element. But what about the number of neutrons?

Well, unlike protons, atoms of the same element can contain different numbers of neutrons. That means that I can have a carbon atom (6 on the periodic table, so 6 protons) with 6 neutrons (mass of 12 amu), 7 neutrons (mass of 13 amu), or 8 neutrons (mass of 14 amu). These are called isotopes.

For carbon, carbon-12, carbon-13, and carbon-14 occur naturally in different amounts. Carbon-12 is the most common isotope, and accounts for almost 99% of all existing carbon atoms – this is why the atomic mass for carbon on the periodic table is closest to 12 amu! The reason it is not exactly 12 is because it is an average, and includes the masses of carbon-13 and carbon-14 as well. The amount at which each isotope exists in nature is called its natural abundance. 

What does this have to do with mass spectrometry? It will become more clear, but for now, remember that each isotope of each atom has a different mass. And what does mass spectrometry measure? Mass!

So how does mass spectrometry work?

Theory and instrumentation of mass spectrometry

First a solution containing our target compound is injected into the mass spectrometer, where it is heated up and vaporised. The sample is ionised – which means electrons have been knocked off atoms in the sample, creating positively-charged ions (less electrons means less negative charge – so positively charged). The diagram below shows ionisation by electron impact – literally bombarding the sample with high-energy electrons! – though there are many different ways to ionise a sample. 

The positively-charged ions are then accelerated towards a magnetic field, where they are deflected. The amount of deflection depends on both their mass – heavier ions are deflected less – and their charge – ions with higher charges are deflected more. This ratio, between an ion’s mass and its charge, is referred to as m/z, where m is the ion’s mass, and z is its charge.

The ions impact the detector in the mass spectrometer, and the detector collects information on both the mass:charge (m/z) ratio of each ion, and how abundant they are in the sample. The data is plotted in a mass spectrum, as “intensity” (abundance of ions of a particular m/z ratio) vs m/z.

The following video gives a useful analogy to explain the deflection of ions by the magnetic field:

How to read a mass spectrum

As mentioned, a mass spectrum measures the abundance of ions at each m/z detected. Therefore, our spectrum will measure abundance on the y-axis, and the m/z on the x-axis. Some experiments will only generate ions with a charge of +1. This simplifies our analysis, because then the m/z of the ion is equal to its mass m.

The right-most significant peak of a mass spectrum – the highest m/z – corresponds to the molecular ion, or parent ion, of the compound of interest. During the ionisation process, the ion can fragment, or break-apart, which gives rise to the peaks at lower m/z. The distance between the fragment peaks and the parent ion peak corresponds to the mass of the part that has broken off.

The parent ion peak does not always have the highest intensity! It is very common for a fragment to be the most abundant ion detected (i.e. the highest intensity peak). The highest intensity peak is called the base peak.

Both the m/z of the parent ion and the fragmentation pattern are used to characterise a sample.

Isotopic distribution patterns

Now, as well as our significant peaks, with high abundance, we have smaller peaks to the right and left of them, differing only by a few mass units. What do these correspond to? 

These are due to atomic isotopes. Remember isotopes from the beginning of this lesson?

We can see that our parent ion (M) has a small peak to the right of it, which is equal to the mass of the ion plus 1 (M+1). This peak comes from an ion of our target compound which contains one carbon-13 atom. It is so much smaller than the parent ion peak because carbon-13 is much less naturally abundant than carbon-12 – so there are much fewer ions striking the detector which contain a carbon-13 atom. This pattern – two peaks in a ratio of 99:1, 1 atomic mass unit apart – is diagnostic for carbon. We call this an isotopic distribution pattern.

There are other elements which have naturally occurring isotopes, and characteristic isotopic distribution patterns. In the next exercise, you will investigate two others which are relevant to mass spectrometry: chlorine and bromine.