Martin Humphries

What is mass spectrometry?

Written by Jon Humphries

How do scientists perform proteomics? There are a number of ways to perform proteomics, which is the study of all of the proteins in a system. We use a method called mass spectrometry.

Essentially, mass spectrometry measures how heavy molecules are. A popular way of doing proteomics with mass spectrometry involves chopping up the proteins in your sample into smaller bits using enzymes. (Enzymes are a type of protein that cut up other proteins; they are very selective molecular scissors.) The smaller bits of proteins that are left are called peptides, and they are fired into a machine called a mass spectrometer. There are many different types of mass spectrometers, but in one version the peptides fly down a tube within the machine. The heavier peptides take longer to get to the end of the tube compared to the faster, lighter peptides. So you can tell how heavy a particular peptide is by how fast it flys through the mass spectrometer. You can also ask the machine to break the peptides into even smaller fragments. This gives you extra information about what atoms make up the peptides (called the “peptide sequence”). We know the peptide sequence of virtually every protein in the human body, so knowing the peptide sequence lets you work out from which protein the peptide came. This means you can find out which proteins were in your sample at the beginning of the experiment.

Why do scientists use proteomics? Traditionally, studies of cells have looked at the way one or two proteins behave at a time. This requires you to decide which proteins you want to study at the start of the experiment. One of the advantages of performing a proteomic study is that you can look at many hundreds or even thousands of proteins at once. You don't need to know exactly what the proteins are before you start the study, either, so you can find new proteins linked with a certain disease or a certain cell in the body. Also, modern mass spectrometers are very sensitive machines, so you can find proteins that only exist in very small amounts in a sample.

We use proteomics to study integrins, which are molecules that let cells of the body move and stick to each other. Integrins do this by collecting helper molecules, which cluster around the feet of integrins. The protein clusters fall apart easily, but we have found a way to fix them in place with a type of molecular glue. We can then use mass spectrometry to look at all the proteins within these protein clusters, find out how they are different for one type of integrin compared to another, and also find new proteins in these clusters that were not known to be important before. As the ability of cells to move and stick is very important for diseases like cancer, arthritis and asthma, we hope to find out more about how these diseases occur and find new ways to treat them.