What is Proteomics?

Proteomics is the study of proteins. More specifically, proteomics aims to identify and catalogue all of the proteins found in human cells, as well as the cells of other species. This is a massive task – there are at least 20,000 different human proteins and the largest protein databases now contain information on more than 5 million different proteins. To make the task even more challenging, proteins can be chemically modified inside our cells in order to change their behaviour. These changes also need to be studied and understood. Ultimately proteomics aims to understand how the thousands of different proteins in our cells behave and interact to produce cells and organisms. This information will have a significant impact on the future of medicine and agriculture.

Why study proteins?

We all know that protein is an important part of our diet, but proteins are much more than just a part of the healthy eating pyramid. inside our cells are millions of tiny molecular machines that generate energy, build and repair our cells, and regulate every aspect of our biology. These molecular machines are proteins. Understanding how these proteins work and interact with each other is critical if we are going to find the cure to human disease or increase the efficiency of our agriculture.
Every protein is deceptively simple and incredibly complex all at the same time. A protein is just a polymer chain made from 20 different kinds of building blocks, known as amino acids. Each different protein is identified by the unique order in which these amino acids are assembled. The specific order or sequence of amino acids in a protein is encoded in our genes. In fact, every gene is just the instructions for building a specific protein. When we say someone has the gene for blue eyes, we are really saying that their gene encodes a protein that is responsible for making their eyes appear blue.
While the sequence of amino acids in every protein is simple, this chain of amino acids then folds to form a complex shape. This shape is determined by the sequence of amino acids but the folding process is so complex we are yet to understand the rules that determine how a protein chooses the correct shape. Fortunately, we can calculate the folded structures of proteins using x-ray crystallography.

A video explaining how a protein chain made of amino acids folds into a specific 3 dimensional shape.

Protein structure is important as the shape of a protein determines its function. Some proteins are structural, building the cytoskeleton that holds our cells together. Other proteins, known as enzymes, catalyse chemical reactions that are essential for cellular and biochemical processes. Another class of proteins regulate the functions of other proteins, ensuring that all biological processes occur at the right time and in the right place. When you put these thousands of tiny molecular machines together, they can achieve the incredible complexity that we see in living things.

This movie from the Walter and Eliza Hall Institute shows how proteins are synthesized from RNA code. The amino acids are assembled into a protein chain by a large protein complex known as a ribosome. The ribosome is a perfect example of how proteins can act as tiny molecular machines.

Proteomics is a global scientific enterprise

Some great scientific projects, such as putting a man on the moon, capture the imagination of the world. Other projects, equally as ambitious, continue outside of the public’s gaze.
We are in the midst of an incredible international effort to understand the secrets of life. Proteomics is an integral part of this process of discovery. The Human Genome Organisation (HUGO) was responsible for sequencing the first human genome. Similarly, the Human Proteome Organisation (HUPO) is coordinating the efforts of thousands of scientists to catalogue all the proteins that make up a human being. When completed, understanding how all of these proteins add up to make a man or a woman, will have a transformational effect on modern medicine.
One of the remarkable things about modern proteomics (and genomics) is the incredible amounts of information being collected by scientists. All of this information is accumulated into massive databases and is being searched for insights into human health. Most of this information is freely accessible by anyone with an internet connection. When you visit central repositories of research data such as the National Centre for Biotechnological Information or the European Bioinformatics Institute, it is easy to see that this great project to solve the mysteries of life is every bit as grand and important as the first moon landing.

Technology Driven Science

Like many fields of science, proteomics is driven by advances in analytical technology. One of the key advances in the last 10 years is the development of efficient mass spectrometers capable of identifying thousands of different proteins in a single analysis. Mass spectrometers are incredible instruments that literally measure the mass of atoms. By measuring the mass of proteins, and the patterns formed when the protein molecules are broken up in the instrument (known as fragmentation), it is possible to determine the order of amino acids that make up a specific protein. This process is called peptide sequencing. Modern mass spectrometers can sequence up to 20 different peptides every second. It is these mass spectrometers, that make proteomics such a productive and rewarding field of science to work in.