Overview
Illumina Protein Prep enables discovery and quantification of human proteins across more than 200 biological pathways using a SOMAmer-based proteomics assay with an NGS readout.
Key features
9.5K unique human protein targets in a single plasma or serum sample with NGS readout on NovaSeq Systems
Sample to results in under 2.5 days with just 4 hours of hands-on time
Integrated analysis with DRAGEN secondary analysis and Illumina Connected Multiomics
SOMAmer Reagents used in the Illumina Protein Prep assay are rigorously characterized by shape specificity and polyionic competition and orthogonally confirmed by methods such as mass spectrometry and ELISA (enzyme-linked immunosorbent assay).
SOMAmer Reagents provide market-leading reproducibility with ~5.5%* CV and femtomolar sensitivity with over a 10-log dynamic range.
*Expected median CV calculated using samples from healthy donors.
The entire workflow is automated on a single platform, providing an end-to-end solution for processing up to 340 samples and 44 controls per week, with seamlessly integrated secondary analysis pipelines and comprehensive tertiary analysis solutions.
Applications
Illumina Protein Prep enables sequence-ready libraries for the detection of ~9500 unique human proteins for proteomic discovery and quantification applications, including biomarker discovery and population genetics studies.
Example workflow
Illumina Protein Prep
Illumina Protein Prep combines sequencing by synthesis chemistry with SOMAmer Reagents for a comprehensive NGS-based assay. The entire workflow is automated on the Illumina Protein Prep Automation System.
NovaSeq X Series
Gain unprecedented scalability and sequencing depth for comprehensive multiomic projects.
NovaSeq 6000 System
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
Unlock deeper biological insights with a powerful omics analysis software featuring interactive visualization and statistical analysis.
Project recommendations
Instrument: Recommended number of samples
NovaSeq 6000 System: 192 reactions per flow cell on S4 35c
192 reactions per flow cell on S4 35c
40M reads, 1 × 15
NovaSeq X System: 192 reactions per flow cell on 10B 100c 384 reactions per flow cell on 25B 100c
192 reactions per flow cell on 10B 100c 384 reactions per flow cell on 25B 100c
Related applications and methods
Proteomics
Explore the entire set of proteins in an organism, also known as the proteome, with next-generation sequencing.
Multiomics
Use multiomics profiling to multiply discovery power and better connect genotype to phenotype.
Overview of the Illumina Protein Prep solution
Human serum or plasma samples are used as input to the SomaScan assay, followed by Illumina library prep, automated on Illumina Protein Prep Automation System, and sequenced on a NovaSeq System.
Protein capture using the SOMAScan assay
SOMAmer Reagents (blue) contain a photocleavable linker and biotin. Bound to streptavidin beads, they capture specific proteins and tag with biotin (yellow). UV light breaks the linker, releasing SOMAmer-protein complexes, which are captured on new beads and eluted for quantification using NGS.
lllumina Protein Prep NGS conversion chemistry
Following the SomaScan assay, SOMAmer Reagent abundances are converted to barcoded sequencing-ready libraries using a hybridization-based approach.
Resources
Illumina Protein Prep solution: the new standard in proteomics
Launch the next era of proteomics with the NGS-based Illumina Protein Prep 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 Protein Prep
Illumina Protein Prep 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, even those that are nearly identical, to accelerate biomarker and drug discovery.
The Evolving Landscape of Proteomics
At the HUPO World Congress, 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.
Proteomics workflows: affinity and mass spectrometry
Presented at the HUPO World Congress, Stuart Cordwell, PhD, University of Sydney, examines how mass spectrometry and affinity proteomics complement one another to advance clinical proteomics. He shares clinical insights and introduces Illumina Protein Prep, an NGS-based approach designed to support scalable, reproducible biomarker discovery.
Scalable NGS‑based proteomics
At the HUPO World Congress, 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 Protein Prep, an end‑to‑end NGS‑based platform designed to enable high‑confidence, large‑scale biomarker discovery in workflows complementary to mass spectrometry.
Illumina Protein Prep 9.5K, Plasma, 96-Reactions
20137827
Illumina Protein Prep 9.5K, Plasma, 96-Reactions View less
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Illumina Protein Prep 9.5K, Serum, 96-Reactions
20137828
Illumina Protein Prep 9.5K, Serum, 96-Reactions View less
Illumina Protein Prep Automation System
20116818
This package supports customers who wants to automate their Illumina Protein Prep Assay. It includes a Tecan Fluent OEM automation system equipped to run Illumina Protein Prep Assay protocols, robotic accessories, and the control software to run the assay. View less
Illumina® DNA/RNA UD Indexes v3, Set A, Auto (96 Indexes 96 samples)
20141196
Includes one box of 96 Illumina DNA/RNA UD v3 Indexes Set A for labeling 96 samples sufficient for automation View less
Illumina® DNA/RNA UD Indexes v3, Set B, Auto (96 Indexes 96 samples)
20141197
Includes one box of 96 Illumina DNA/RNA UD v3 Indexes Set B for labeling 96 samples sufficient for automation View less
Illumina® DNA/RNA UD Indexes v3, Set C, Auto (96 Indexes 96 samples)
20141198
Includes one box of 96 Illumina DNA/RNA UD v3 Indexes Set C for labeling 96 samples sufficient for automation View less
Illumina® DNA/RNA UD Indexes v3, Set D, Auto (96 Indexes 96 samples)
20141199
Includes one box of 96 Illumina DNA/RNA UD v3 Indexes Set D for labeling 96 samples sufficient for automation View less
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What method of protein capture is used in Illumina Protein Prep?
SOMAmer technology (aptamer-based) is used for protein capture. See Protein capture using the SOMAScan assay in the Figures tab on this page.
What sample types are compatible with Illumina Protein Prep?
Human plasma and serum samples.
How large is the protein panel in Illumina Protein Prep? What types of pathways can be identified with this panel?
The Illumina Protein Prep 9.5K assay detects ~9500 unique human proteins. This panel can be used to detect proteins in major biological pathways, including those implicated in oncology, neurology, inflammation, and cardiology.
What are the output files associated with Illumina Protein Prep for secondary analysis?
Secondary analysis generates a protein quantification file (ADAT) and DRAGEN QC report.
Read the data normalization technical note for more information on secondary analysis.
Is automation required?
Yes, the assay must be automated using the Illumina Protein Prep Automation System.
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