June 14, 2026
As part of our “Multiomics Explained” series, we’re unpacking one ome at a time. To get an overall picture, read our first piece, “What is multiomics? A simple guide to the future of biology.” You’ll learn how the omes work together to help solve some of the toughest questions in human health and see how researchers are already putting multiomic pipelines to use.
Now, let’s focus on how proteomics provides a more complete view of biology.
What is proteomics?
If genomics tells us what could happen in a cell, proteomics shows us what is happening right now.
Proteomics is the large-scale study of proteins, the molecules that carry out nearly all functions in living organisms. While genes provide the blueprint and RNA conveys instructions, proteins are the functional end products that regulate biological processes.
Unlike the genome, which is relatively static, the proteome is highly dynamic. It changes across cell types, developmental stages, and environmental conditions. At any given moment, different proteins are being expressed, modified, activated, or degraded, creating a constantly shifting picture of cellular activity.
This dynamic nature is exactly what makes proteomics so powerful. By measuring proteins directly, researchers gain insights into real-time biology that cannot be fully captured through DNA or RNA analysis alone.
What proteomics can tell us
Proteomics provides a deeper layer of biological insight by answering questions that genomics and transcriptomics cannot fully address:
1. Which proteins are present and in what quantity
Gene expression does not always correlate with protein abundance. Proteomics directly measures which proteins are present in a sample and at what levels, revealing the true functional state of a cell or tissue.
2. Protein structure and function
Protein function is determined not only by the amino acid sequence but also by how the protein folds into a three-dimensional structure. Even small structural changes can dramatically alter function.
3. Post-translational modifications (PTMs)
After proteins are synthesized, they often undergo chemical modifications—such as phosphorylation, glycosylation, or ubiquitination—that regulate activity, localization, and stability. These modifications are critical for processes like signal transduction and immune response, and they are only detectable through proteomic analysis.
4. Biological pathways and networks
Proteins rarely act alone. Proteomics helps map complex interaction networks and signaling pathways, providing insight into how biological systems respond to disease, treatment, or environmental stimuli.
Together, these capabilities make proteomics essential for understanding disease mechanisms, identifying biomarkers, and discovering potential therapeutic targets.
Illumina’s approach to proteomics
Recent innovations are transforming proteomics from a targeted, low-throughput discipline into a scalable, high-throughput science that can be integrated with sequencing workflows. Illumina proteomic solutions enable proteomics at scale by offering protein analysis in next-generation sequencing (NGS)-compatible and microarray slide workflows.
Illumina SomaSeq™ Discovery, formerly known as Illumina Protein Prep, brings protein analysis into a sequencing-compatible workflow. This technology allows researchers to convert protein measurements into NGS readouts.
Illumina SomaScan™ Discovery, formerly known as SomaLogic SomaScan® 11K Assay, converts protein measurements into microarray readouts.
Key advantages include:
- High-throughput protein measurements (~11,000) across large cohorts
- Seamless integration with existing sequencing infrastructure
- Compatibility with multiomic study designs
- Minimal sample input requirements
- Suitability for large-scale population studies
Learn more about Illumina SOMAmer proteomics
Applications of proteomics
Proteomics is already playing a critical role across many areas of research:
- Disease research and biomarker discovery: Proteomics helps identify protein signatures associated with diseases such as cancer, neurodegenerative disorders, and cardiovascular conditions. These signatures can provide early indicators of disease or help stratify patient populations in research settings.
- Drug discovery and development: Most drug targets are proteins. By mapping protein pathways and interactions, proteomics enables researchers to identify potential drug targets and evaluate how compounds affect biological systems. It can also reveal off-target effects earlier in development.
- Immunology and infectious disease: Proteins govern immune responses. Proteomic analysis can uncover how immune systems respond to pathogens, vaccines, or therapies, offering insights into mechanisms of protection and disease progression.
- Population-scale studies: With high-throughput platforms like Illumina SomaScan Discovery assay and Illumina SomaSeq assay, researchers can now analyze protein data across thousands of samples—opening new possibilities for large-scale, data-driven discovery.
How researchers use proteomics
Researchers use proteomics to understand what proteins are present, how much of each is there, and how those proteins change across conditions. Proteins provide a direct view of how biology is functioning in health and disease.
- Researchers at Cleveland Clinic used the SomaScan Discovery assay to identify protein biomarkers for COPD, learning more about how to better classify emphysema severity and progression. The research team combined genomics and proteomics to give them insight and improve prediction models for these diseases.
- The SomaScan Discovery assay measures proteins in cerebrospinal fluid (CSF), a crucial site of neurological disease pathogenesis. In a 2023 Nature Parkinson’s Disease paper, researchers used the SomaScan Discovery assay to perform the largest affinity-based CSF proteomics study to date.
- Harnessing the combined power of the SomaScan Discovery assay and AI, researchers developed a 26-protein model to predict the age of the eye. Of the 26 model proteins, five proteins had no prior known associations to aging and were reported for the first time in this study.
The future of proteomics in precision medicine
Proteomics is poised to play a central role in the future of precision medicine and systems biology. As technologies scale and integrate more seamlessly with genomic platforms, researchers will be able to:
- Link genetic variation directly to functional protein outcomes
- Identify more precise disease subtypes
- Predict responses to therapies with greater accuracy
- Discover novel therapeutic targets
In many ways, proteomics completes the story that begins with DNA. It provides the functional context needed to understand how biological systems operate in health and disease.
By combining multiomic data, researchers can move from isolated observations to a holistic understanding of life’s complexity. With innovations like the SomaSeq Discovery and SomaScan Discovery platforms, proteomics is becoming more scalable, accessible, and integrative than ever before.
The result is a clearer, more connected picture of biology—one that brings us closer to unlocking the full potential of precision medicine.
Visit our online resources to learn more about SomaSeq Discovery
Read publications using the SomaScan Discovery Platform
To read about unveiling the function with multiomics, follow this link
