What is proteomics and why do we study the proteome?

Proteomics is the study of all the proteins inside a biological sample, for example a cell, tissue or organism. Together, these proteins, known collectively as the proteome, carry out the basic functions of cells, and are foundational to most all of biology.

Researchers have understood the importance of proteins to biology for many years. Thus, they have developed many tools and techniques to study how proteins function. Their research has taught us much about the composition, structure, and function of many individual proteins. However, a single cell contains billions of proteins, and it is the dynamic make-up and interactions of all these proteins that determine cellular behavior. Instead of studying individual proteins in isolation, proteomics research aims to study all of these proteins and the interactions between them, at the same time.

Studying the proteome at high resolution

Recognizing the potential insights that can come from studying the proteome, many researchers have made forays into studying it at scale. They’ve developed proteomics techniques and technologies aiming to provide a comprehensive view of the proteome in any sample of interest. Unfortunately, traditional proteomics technologies have only been able to scratch the surface of the full proteome and have not delivered on the promise of this exciting field.  

Proteomic profiling platforms are finally poised to deliver on the promise of the proteome thanks to advances in a variety of enabling technologies. We’re moving beyond the scale of protein microarrays and into a platform that can capture billions of proteins, identify them, and measure their abundance across a wide dynamic range. With advances in nanofabrication, machine learning, data storage, and more, we’re designing technologies with the potential to analyze nearly all the proteins in the human proteome at once. These proteomics technologies will drive great advances in healthcare, basic research, and much more.

Applications of proteomics

Novel technologies, like the Nautilus proteome analysis platform, are designed to measure the majority of the proteome and provide information-rich but easy-to-understand protein analysis. Nautilus’ platform aims to provide researchers with information on >95% of the proteome of any sample. Having access to this depth of proteomic information will enable scientists to explore new horizons in their research. We discuss some of the many exciting applications of proteomics data below.

Monitoring and forecasting changes in health and disease

Prior to observing signs of disease at the whole-organism level, it is likely that the proteome of affected tissues will begin to change. Fluctuations in the proteome can act as biomarkers that predict how patients’ health will change or how they will respond to a treatment. Thus, to forecast changes in health, physicians can analyze the proteomes of patient samples to see if anything is going awry. They can then prevent health issues, or lower their severity, by prescribing preventative measures.  

For instance, a physician might begin to see proteins associated with heart disease increase in a patient during a routine check-up. To prevent heart issues, the physician might put this patient on drugs that lower cholesterol.

Similarly, farmers could use proteomics to forecast changes in crop health. Before entire crops begin to die off, farmers might be able to check them for changes in protein biomarkers associated with viral or bacterial infections. They could then apply protective chemicals throughout the farm and prevent the spread of the disease, improving crop yields.

Using proteomics to understand cellular identity and function 

The genome of an organism is – with some exceptions – the same in every cell,  but the proteome of different cells within an individual varies widely. By profiling the protein composition of different cell types, proteomics researchers can learn what proteins give cells their functions. 

Eventually, they may even be able to manipulate the proteome of one cell to turn it into another kind of cell. For instance, using insights from proteomics physicians may one day be able to generate replacement cells to heal damaged tissues or organs.   

Proteome-level information on cellular identity will also be useful in work with other species. For example, humanity currently spends a vast amount of energy and money creating nitrogen-based fertilizers for crops. Interestingly, there are plants that naturally cooperate with bacteria in the soil that create nitrogenous nutrients from the abundant nitrogen in the air, converting it into a form plants can use. Researchers could measure the proteomes of these nitrogen-fixing bacteria and the plant cells that interact with them to better understand how they cooperate to facilitate this transfer of nutrients. 

With a better understanding of how the proteome enables this process, researchers may be able to give other plants the ability to create their own nitrogenous nutrients and thereby make it possible to grow more food for a growing global population using less fertilizer.

Proteomics applications in disease research

Although researchers know the symptoms of many diseases and may know what genes or pathogens drive them, they do not necessarily have a good understanding of the underlying molecular mechanisms. That is, they don’t always know how diseases alter proteins to change cellular function. Proteomics can reveal how the composition and abundance of proteins change when cells are diseased or stressed, enabling researchers to create treatments that counter such changes.  

For example, in a disease like COVID-19, researchers might see that patient samples have an overabundance of immune system proteins. They could then prescribe these patients drugs that tamp down the effects of the immune-activating proteins to protect patients from autoimmune damage.  

This kind of proteomic profiling will not only be useful for tackling human disease but could also be used to improve environmental health as the planet faces threats like climate change. For instance, scientists will be able to use proteomics to study how various plants’ proteomes respond to climatic stresses like drought. If they find plants that fare well in droughts, they can compare their proteomes to those of plants that die off during drought. They may find proteins or sets of proteins that make plants particularly drought resistant. Researchers might then increase the levels of these resistance proteins in drought-susceptible plants, helping them to survive. This could help preserve ecosystem health as the climate changes.

New horizons in proteomics research

We are only barely skimming the surface of what proteomics can do for applied and basic research across many different fields. Nonetheless, we hope you are convinced that the potential of novel proteomics technologies is vast and largely untapped. In future posts, we will dive into a little more detail on how scientists study the proteome and take a look at the types of biological information they can uncover using various proteomics methods.