What is proteomics?

Proteomics is the study of all proteins contained in an organism or other biological entity. By understanding the composition of and interaction between all these important macromolecules at once, scientists can gather insights far beyond those obtained from studying individual proteins. 

Proteomics research has vast applications. The list includes finding new biomarkers for disease, discovering and testing drug targets, designing better crops to address food security, and unlocking the secrets of biology itself.  But current technologies for studying proteins aren’t advanced enough to truly cover the breadth and depth – the scale – of the proteome. Soon, new technologies may finally unlock proteomics at a scale large enough to truly deliver on its promise.

What is proteomics research used for?

While an organism’s genome stays almost entirely the same throughout its life, its proteome is always changing. Cells make different proteins to respond to different situations — a healthy person’s proteome will look different than a sick person’s, for example, and different types of cells produce and use different sets of proteins. So, while it’s relatively easy to study someone’s genome from a single sample, it’s much harder to fully sample their proteome.  

Furthermore, proteomics research doesn’t just mean figuring out which proteins are in a sample. It also means understanding how much of each protein is there, how each protein has been modified, and the ways these proteins interact. This kind of work is fundamental to biological research and clinical development. For example, with proteomics, researchers can determine the roles protein modifications play in cellular communication, while drug developers can see if inhibiting a particular signaling pathway actually reduces the expression of genes normally induced by that pathway.
 

In addition, cells produce different proteins when they’re infected with a pathogen, or otherwise unwell, so researchers studying human disease often use proteins as biomarkers that can diagnose diseases or show if a treatment is working. Currently, researchers use proteomics to find biomarkers for cardiovascular disease, diabetes, COVID-19, renal diseases, and much more. Scientists have also found many proteomics biomarkers for specific cancers, making proteomics an ideal way to diagnose particular malignancies. 

This is just the tip of the iceberg when it comes to the many potential applications of proteomics. Check out our white paper series on the “proteomics revolution,” to dive into more ways comprehensive proteomics technologies can change the world. 

Proteomics techniques

Currently, scientists can only peer into the proteome in a limited way. Existing proteomic analysis technologies cannot fully reveal all the proteins in a sample, or their abundance, modifications, and interactions. That means the true scope of the proteome remains hidden; a biological ‘black hole’ of sorts. 

Part of the reason is that the tools scientists use for proteomics research weren’t made with the scale and complexity of the proteome in mind. They contain fundamental tradeoffs that limit the type of proteomics research we can carry out. Some of these traditional methods include: 

• Mass spectrometry – This involves breaking proteins into small molecular fragments that are run through a mass spectrometer. The device determines the mass of each fragment, which scientists use to infer their identity.

• Antibodies and other affinity reagents – These bind to certain specific proteins. Using fluorescent labeling or additional reagents lets scientists visualize binding and tells them whether these specific proteins are in a sample, where these proteins are, and how abundant they are. 

• Edman degradation – This is a form of protein sequencing that involves binding a chemical to the amino acid at the end of a protein and then stripping it off. Doing this repeatedly lets scientists see what molecules the protein is made of, which gives them information about its structure and function. 

All these proteomics technologies have pros and cons, but none truly check all the boxes for an ideal proteome analysis platform. To truly interrogate the proteome in a way that’s accessible to most researchers, we need technologies that are:
 

• Comprehensive
• Sensitive 
• Able to cover a broad dynamic range 
• Reproducible 
• Rapid throughput 
• Designed with an integrated workflow 

Mass spectrometry has difficulty seeing low abundance proteins, for example, while many antibody-based technologies are targeted to a small subset of the proteome. Most proteomic analysis technologies today can identify less than 10-30 percent of the proteins in a sample, leaving much of the proteome in the dark. 

Next-generation proteomics technologies like the Nautilus Proteome Analysis Platform seek to resolve many of these issues. Using multi-affinity probes and hyper-dense single-molecule arrays that can hold billions of proteins, the Nautilus platform is designed to be sensitive while also having a large dynamic range that can match the enormous scale of the proteome. The platform is predicted to be capable of measuring more than 95 percent of the proteome. That breadth and sensitivity will enable researchers to ask far more nuanced questions and uncover new knowledge about the proteome. 

Future proteomics applications

Though proteomics research is already fundamental to medicine and biology,  much of its true potential has yet to be tapped. Better proteomics technologies could supercharge the process of drug discovery and development by giving researchers insights into far more proteins and revealing previously unknown nuances of drug-protein interactions. Similarly, finding better protein biomarkers for Alzheimer’s disease would both enable doctors to diagnose it earlier and enable more precise insights into how the disease progresses. 

Proteomics research isn’t limited to the human body, either. Just as in humans, proteins drive plant biology, meaning better proteomics technologies could revolutionize the agricultural industry. Watching how a plant’s proteome responds when water or nutrient levels are low might show scientists how to design better means of protecting crops in harsh conditions. And studying how plant proteins function could reveal better ways to help plants adapt to a changing climate. 

Ultimately, the study of proteomics is the study of life itself: How it functions, grows, and changes on a fundamental level. In-depth knowledge of proteins benefits our understanding of medicine, biology, agriculture, and even entire ecosystems. Right now we’re only scratching the surface of the proteome, but, with the right proteomics tools, we’ll be able to dive far deeper, and enable revolutionary new capabilities.