11 December 2025
Last month marked a major milestone for Illumina: our first-ever presentation at The Human Proteome Organization (HUPO) World Congress, a flagship event for the proteomics community, with a strong mass spectrometry (MS) presence and a shared mission to advance human health. It was the perfect stage to reinforce our vision for multiomics and celebrate the full launch of Illumina Protein Prep.
The next chapter in proteomics
Mass spectrometry has long been considered the key technology enabling multiomics research of which proteomics is a cornerstone. Now, for many applications—especially large-scale strategies for various proteome- and genome-matched projects for discovery research—integrating next-generation sequencing (NGS)-based proteomics and mass spectrometry is creating a more holistic view for biomarker and drug target discovery and analysis. Illumina Protein Prep's throughput, sensitivity, broad dynamic range and large discovery panel of over 9,500 protein targets allows researchers to screen the plasma proteome at scale. Discovery power can then be amplified when using mass spectrometry to confirm and validate identified candidates.
Our vision is simple: to make next-generation proteomic research accessible and interoperable—empowering seamless multiomic data integration for every lab. Today, many researchers face hard tradeoffs between content and performance, depth and throughput, or cost and study size. By introducing proteomics to the Illumina ecosystem, we seek to remove those barriers—delivering consistent, high-quality results across expanded panel content, automating complex workflows, and enabling cost-effective discovery at scale.
The goal is to empower scientists to explore biology with both depth and breadth, without compromise.
Today, researchers are expanding what’s possible. There’s a growing shift from a genomics-only mindset to a broader embrace of proteomics. And Illumina is helping lead that shift by making proteomics scalable, accessible, and integrated.
The solution built for scale and designed for discovery: Illumina Protein Prep
Illumina Protein Prep offers broad coverage of the blood proteome available through an NGS platform. The workflow is fast—delivering results in just 2.5 days—and precise, with industry-leading performance.
Since launching our early access program for Illumina Protein Prep, we’ve seen remarkable traction: 40,000+ samples processed across 16 global sites and 40+ customers. Our workflow is enabling labs of all sizes to overcome the discovery bottleneck.
Illumina Protein Prep and mass spectrometry are advancing proteomics
The University of Sydney Mass Spectrometry Core recently completed their first real-world study using Illumina Protein Prep to analyze blood plasma samples from a clinical trial focused on dietary interventions in individuals with metabolic disease. At HUPO, we had the pleasure of hearing the early results from Professor Stuart Cordwell, PhD, academic director at the facility. The assay revealed significant cohort-level differences, guiding researchers toward the validation of several promising novel protein candidates.
One of the most powerful aspects of this approach is how it meets researchers where they are—leveraging the familiarity of NGS readouts to make proteomics accessible without requiring deep technical training. For teams historically focused on mass spectrometry, it opens the door for them to engage with NGS-based proteomics assays more meaningfully and at scale.
Proteomics is enabling discovery around the world
Adding proteomics to genomic studies can elevate disease classification and accelerate discovery—especially in previously undiagnosed patients.
Genomics England is one of our early access partners leading the way, integrating proteomics into large-scale genomic studies. As part of their expanded multiomics initiative within the 100,000 Genomes Project, they used Illumina Protein Prep to profile disease-specific proteomic signatures across rare disease categories. The data revealed a 7.5% increase in disease classification when genomics and proteomics were integrated in previously undiagnosed patients. Their expanded study aims to validate the initial findings and discoveries of differentially abundant proteins in specific disease categories.
We’re also seeing the power of proteomics come to life in population-scale studies like Singapore’s PRECISE-SG100K. As part of their mission to better understand disease mechanisms in historically underrepresented populations, the team is using Illumina Protein Prep to analyze 10,000 plasma samples—building on an earlier proteomic profiling project to drive more equitable precision medicine. It’s a compelling example of how proteomics bridges the gap between genetic variation and protein expression in diverse communities.
Technical differentiators that matter
What sets Illumina Protein Prep apart is its simplicity and power. Integrating SOMAmer reagents into the Illumina ecosystem offers multiplexing capability and reproducibility for reliable protein detection at scale. NovaSeq systems deliver cost-effective, high-throughput sequencing. And Illumina Connected Multiomics (ICM) integrates proteomic data with other ‘omes’—genomics, transcriptomics—unifying insights.
Later this year, we’re releasing an RNA-proteome paired analysis pipeline, with support for cis and trans pQTL detection. These innovations are designed to help researchers ask bigger questions and get clearer answers.
The future of multiomics starts here
Illumina is building the infrastructure to fully realize the vision of proteomic analysis and the future for integrated multiomic data insights. By integrating Illumina Protein Prep into our multiomics ecosystem, we’re helping researchers uncover transformative insights—without compromise.
To learn more about Illumina’s multiomics innovation roadmap, explore our latest updates.
