Automated high-plex proteomics solution using SOMAmer technology for accurate, reproducible protein quantification and biological insight.
Illumina SomaSeq Discovery is a high-content proteomics assay using synthetic monoclonal SOMAmer Reagents which bind proteins with high affinity and specificity, eliminating the tradeoff between assay breadth and detection sensitivity.
Apply 11K protein measurements across 200+ biological pathways in a single assay, detecting more proteins across every major biological process than any other NGS-based proteomics assay, to reveal novel biomarker and pathway-level changes pathway-level changes.
Achieve femtomolar sensitivity across proteins spanning more than 10 orders of magnitude in concentration—yielding a rich dataset from rare to abundant proteins.
Maintain reproducibility from pilot to population-scale studies. SomaSeq Discovery pairs a high-plex, automated workflow—processing up to 340 samples and 44 controls per week. With SOMAmer Reagents engineered for accuracy using shape complementarity and poly-ionic competition to block off-target binding, producing ~5.5% CVs*.
*CVs calculated using pooled healthy donor plasma and serum samples.
The SomaSeq Discovery Multi Matrix Kit supports flexible study design through analysis of cell lysates and tissue homogenates within the same run. Built-in Advanced Normalization software enables normalization against proprietary cell lines or study-specific reference samples.
| Assay time | ~2.5 days |
|---|---|
| Automation capability | Liquid handling robot(s) |
| Automation details | The Illumina SomaSeq Discovery Automation System powered by a Tecan Fluent 780 enables an automated workflow for our growing portfolio of SomaSeq Discovery assays |
| Content specifications | The SomaSeq Discovery assay is the largest NGS-based proteomics panel with ~9500 unique human protein targets with over 11K protein measurements |
| Description | An NGS-based proteomics assay using SOMAmer Reagents for the analysis of proteins spanning diverse biological functions, including cytokines, chemokines, receptors, kinases, growth factors, and hormones |
| Hands-on time | ~4 hr |
| Input quantity | 55 μl of human plasma or serum, 35 μl at 400 μg/mL cell lysate or tissue homogenate |
| Instruments | NovaSeq X System, NovaSeq 6000 System, NovaSeq X Plus System |
| Method | NGS-based proteomics |
| Multiplexing | SomaSeq Discovery Automation system: Processes 96 reactions per batch, NovaSeq X: 10B flow cell up to 192 reactions/run, NovaSeq 6000: S4 flow cell up to 192 reactions/run, NovaSeq X: 25B flow cell up to 384 reactions/run |
| Sample type details | Human plasma, serum, cell lysate, tissue homogenate |
| Species category | Human |
| Technology | Sequencing |
Option 1: Run in your own lab
To run the Illumina SomaSeq Discovery assay in-house, you will need the following:
Required instrumentation
• Illumina SomaSeq Discovery Automation System (Cat. No. 20116818), a Tecan Fluent 780, with the required parts to completely automate the assay on deck
• Compatible sequencing system: NovaSeq X System, NovaSeq X Plus System, or NovaSeq 6000 System
Assay kits (choose based on sample type)
• Illumina SomaSeq Discovery Plasma, 96 reactions (Cat. No. 20137827)
• Illumina SomaSeq Discovery Serum, 96 reactions (Cat. No. 20137828)
• Illumina SomaSeq Discovery, Multi Matrix Kit
Indexing
• Illumina DNA/RNA UD Indexes (96 indexes, 96 samples)
• Set A (Cat. No. 20141196)
• Set B (Cat. No. 20141197)
• Set C (Cat. No. 20141198)
• Set D (Cat. No. 20141199)
Option 2: Work with a service provider if you prefer not to run the assay in-house. Illumina-certified service providers can perform the workflow for you.
• Send your samples to a service provider for processing and analysis (Sample Shipment)
• Matrix™ tubes (0.5 mL screw top, Catalog number: 3744)
• Contact Service Provider for site-specific requirements
Visit our Service Provider page to find a partner and get started.
Illumina SomaSeq Discovery enables sequence-ready libraries for ~11,000 protein measurements to support proteomic profiling and quantification applications across biomarker research, translational science, and population genetics studies.
Illumina SomaSeq Discovery
Illumina SomaSeq Discovery combines sequencing by synthesis (SBS) chemistry with SOMAmer Reagents for a comprehensive NGS-based assay. New preplated kits streamline assay setup, while the entire workflow is automated on the Illumina SomaSeq Automation System.
Gain unprecedented scalability and sequencing depth for comprehensive multiomic projects.
Access robust, scalable sequencing for high-throughput applications.
DRAGEN Protein Quantification
Integrated secondary analysis pipeline auto-launches after sequencing for complete normalization and protein expression quantification.
Illumina Connected Multiomics
Uncover significant protein changes and biological insights with a powerful omics analysis software featuring interactive visualization and statistical analysis.
| Instrument | Recommended number of samples | Read length |
|---|---|---|
| NovaSeq 6000 System | Plasma, Serum kit: 170 samples and 22 controls per run on the S4 35c flow cell Multi Matrix kit: 180 samples and 12 controls per run on the S4 35c flow cell |
40M reads, 1 × 15 |
| NovaSeq X System | Plasma or Serum Kit: 85 samples and 11 controls per run on 5B 100c flow cell 170 samples and 22 controls per run on 10B 100c flow cell 340 samples and 44 controls per run on 25B 100c flow cell Multi Matrix kit: 180 samples and 12 controls per run on the 10B 100c flow cell 360 samples and 24 controls per run on the 25B 100c flow cell 90 samples and 6 controls per run on the 5B 100c flow cell |
40M reads, 1 × 15 |
Explore the entire set of proteins in an organism, also known as the proteome, with next-generation sequencing.
Use multiomics profiling to multiply discovery power and better connect genotype to phenotype.
Proteins from biological samples are captured by SOMAmer Reagents followed by Illumina SomaSeq Discovery, automated on Illumina SomaSeq Automation System, and sequenced on a NovaSeq System.
This double-capture approach enables high specificity and low background noise. SOMAmers target proteins by their 3D shape, ensuring precise measurements by discarding non-specific bindings with a competitor step.
Following the double-capture approach with SOMAmer Reagents, reagent abundances are converted into barcoded, sequencing-ready libraries using a hybridization-based method, enabling protein quantification.
Illumina SomaSeq Discovery: the new standard in proteomics
Launch the next era of proteomics with the NGS-based SomaSeq Discovery solution. Unlock high-throughput discovery power, market-leading performance, and integrated analysis to accelerate your next proteomics breakthrough on NovaSeq 6000 and NovaSeq X Systems.
Precision proteomics with Illumina SomaSeq Discovery
SomaSeq Discovery delivers high-throughput proteomic insights with exceptional specificity, enabling accurate detection of over 9500 unique human proteins from a single sample. Powered by rigorously validated SOMAmer Reagents, this solution helps researchers confidently identify and quantify proteins, to accelerate biomarker and drug discovery.
The Evolving Landscape of Proteomics
At HUPO World Congress 2025, join Stuart Cordwell, PhD, University of Sydney Mass Spectrometry director to explore where proteomics is headed and why reproducibility, wide dynamic range, and SOMAmer-based tools support more effective biomarker discovery for precision medicine research.
Proteomics workflows: affinity and mass spectrometry
Presented at HUPO World Congress 2025, Stuart Cordwell, PhD, University of Sydney, examines how mass spectrometry and affinity proteomics complement one another to advance clinical proteomics research. He shares clinical research insights and introduces Illumina SomaSeq Discovery, an NGS-based approach designed to support scalable, reproducible biomarker discovery.
Scalable NGS‑based proteomics
At HUPO World Congress 2025, Fiona Kaper, PhD, VP and Head of Assay Research and Development at Illumina, shares a vision for scalable, reliable proteomics as a core pillar of multiomics. She introduces Illumina SomaSeq Discovery, a NGS‑based platform designed to enable high‑confidence, large‑scale biomarker discovery in workflows complementary to mass spectrometry.
María Bueno Álvez, a postdoctoral researcher in the Human Protein Atlas group at SciLifeLab, KTH, discusses how plasma proteomics reveals disease biology, how dynamic the proteome is across the lifespan, and how high-throughput proteomics offers an accessible path toward precision medicine, from screening tools to understanding drug effects.
Illumina SomaSeq Discovery v2, Plasma, 96-reactions
20167042
ILMN SomaSeq Discovery v2, Plasma, 96 Rxns
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Illumina SomaSeq Discovery v2, Serum, 96-reactions
20167043
ILMN SomaSeq Discovery v2, Serum, 96 Rxns
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Illumina SomaSeq Discovery v2, Multi Matrix, 96-reactions
20167045
ILMN SomaSeq Discovery v2, Multi Matrix, 96 Rxns
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Illumina SomaSeq Discovery Plasma (96-Reactions)
20137827
Illumina SomaSeq Discovery Plasma reagents for 96-Reactions.
Illumina SomaSeq Discovery Serum (96-Reactions)
20137828
Illumina SomaSeq Discovery Serum reagents for 96-Reactions.
Illumina SomaSeq Automation System
20116818
This package supports customers who want to automate their Illumina SomaSeq Discovery assay. It includes a Tecan Fluent OEM automation system equipped to run SomaSeq Discovery assay protocols, robotic accessories, and the control software to run the assay
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SOMAmer Reagents are small, chemically modified aptamers (8—20 kDa) that bind to three‑dimensional protein structures. Because they are fully synthetic, they provide consistent batch‑to‑batch performance. Their distinct chemistry also allows them to bind non‑immunogenic and epitopes currently not targeted by antibodies. Learn more about SOMAmer technology.
SOMAmer technology (aptamer-based) is used for protein capture. See Protein capture using SOMAmer proteomics in the Figures tab on this page.
Compatible sample types include human plasma, serum, cell lysates and tissue homogenates. Additional sample types have been analyzed but are not yet validated for use in the current workflow. Please contact an Illumina specialist for questions about alternative sample types.
Illumina SomaSeq Discovery provides 11K protein measurements. This panel can be used to detect proteins over 200 biological pathways, including those implicated in oncology, neurology, inflammation, and cardiology research.
Secondary analysis generates a protein quantification file (ADAT) and DRAGEN QC report.
Read the data normalization technical note for more information on secondary analysis.
Yes, the assay must be automated using the Illumina SomaSeq Automation System.
Advanced chemistry, optics, and informatics combine to deliver exceptional sequencing speed and data quality, outstanding throughput, and scalability.
Reagent kits for the NovaSeq X Series include a reagent cartridge, buffer cartridge, flow cell, lyo insert, pre-load buffer, and library tube strip.
Perform powerful high-throughput sequencing studies with the NovaSeq 6000 System. Match data output and time to results to project needs.
Reagent kits for the NovaSeq 6000 System consisting of ready-to-use pre-filled reagent cartridges and flow cells.
Illumina Connected Multiomics is a powerful and intuitive cloud-based solution that enables multiomic data analysis and visualization at scale.
Explore genomic and multiomic software for the world's most ambitious science with award-winning accuracy, peer-reviewed AI, and purpose-built cloud solutions
A rapid, cost-effective workflow for accurate, unbiased detection of the protein-coding transcriptome with precise measurement of strand information.
A fast, integrated workflow for preparing libraries for use in a wide range of sequencing applications.
Reach out for information about our products and services, or get answers to questions about our technology.
