Illumina Protein Prep: New Era of Proteomics

Introduction

Proteins are fundamental biomolecules that mediate nearly all biological processes. Unlike genomic data, which remains largely static, the proteome is highly dynamic, reflecting real-time physiological and pathological states. However, proteomics research has been constrained by several technical challenges, including the vast dynamic range of protein concentrations in blood, the dominance of high-abundance proteins such as albumin and globulins, and the difficulty in detecting low-abundance proteins that are often the most biologically relevant. Traditional methods such as mass spectrometry and affinity-based assays struggle with limited throughput, sensitivity, and reproducibility, making large-scale proteomic studies difficult.

At GeneTiCA Group, we have fully implemented and validated the Illumina Protein Prep (IPP) workflow, providing a high-throughput, NGS-based solution for proteomics. This technology enables the simultaneous measurement of 9,500 protein targets from a single plasma or serum sample, delivering deep proteomic insights with high accuracy and scalability. Our fully equipped laboratory, validated protocols, and expert team are ready to provide end-to-end proteomics services, including sample processing, sequencing, and bioinformatics analysis.

Workflow

From Sample to High-Quality Data in Under 2.5 Days.

Illumina Protein Prep integrates SOMAmer® reagents with Illumina Next-Generation Sequencing (NGS), enabling highly multiplexed protein quantification through a scalable workflow. The entire workflow is automated on the Illumina Protein Prep Automation System, reducing hands-on time to approximately 4 hours per batch while ensuring high reproducibility and minimal technical variability.

The process consists of the following key steps:

• Sample Input – Plasma or serum samples are prepared, requiring only 55 µL of input material per sample.
• Protein Capture – SOMAmer reagents selectively bind to 9,500 unique protein targets, ensuring high specificity even in the presence of abundant proteins such as albumin and globulins.
• Library Preparation – Captured proteins are converted into barcoded DNA libraries using a hybridization-based approach.
• NGS Sequencing – The barcoded protein libraries are sequenced on the NovaSeq™ 6000 or NovaSeq X System, generating highly accurate quantitative readouts with a 10-log dynamic range.

Data Analysis and Results

Precision Insights at Scale

The strength of Illumina Protein Prep lies in its advanced bioinformatics capabilities, enabling high-confidence protein quantification and multiomics integration.

• Ultra-Sensitive Detection – Detects low-abundance proteins with femtomolar sensitivity, enhancing the discovery of early-stage biomarkers and subtle protein expression changes.
• Automated Data Analysis – The DRAGEN™ Protein Quantification pipeline performs automated normalization and protein quantification, ensuring high accuracy and reproducibility with CV values consistently below 10 percent.
• Seamless Multiomics Integration – Results are processed using Illumina Connected Analytics, allowing researchers to correlate proteomic, genomic, and transcriptomic data for a more comprehensive understanding of biological processes.
• High-Throughput Capability – The workflow supports up to 170 samples per sequencing run, making it ideal for large-scale population studies and biomarker discovery efforts.

At GeneTiCA Group, we provide comprehensive data analysis services, ensuring that researchers receive high-quality, ready-to-use proteomic datasets tailored to their study requirements.

Applications

Advancing Biomedical and Translational Research

The ability to quantify 9,500 protein targets with high specificity and scalability opens new opportunities for research and clinical applications.

• Biomarker Discovery & Disease Research
  • Identification of novel protein biomarkers in oncology, neurodegeneration, cardiovascular disease, and inflammatory disorders
  • Detection of low-abundance regulatory proteins linked to early disease progression
• Clinical & Translational Research:
  • Stratification of patients based on proteomic signatures
  • Evaluation of therapeutic responses in precision medicine studies
  • Integration with genomics and transcriptomics for a systems biology approach
• Pharmaceutical & Drug Development
  • Identification of novel drug targets based on large-scale protein expression profiles
  • Optimization of biologic therapeutics through comprehensive protein quantification
  • Validation of therapeutic mechanisms via proteomic screening
• Population & Epidemiological Studies
  • Large-scale proteomic profiling for precision medicine initiatives
  • Longitudinal studies tracking protein expression changes over time

At GeneTiCA Group, our fully operational laboratory and expert team provide comprehensive support from sample processing to data interpretation, helping researchers achieve more accurate and biologically meaningful results.

Conclusion

GeneTiCA Group has fully implemented and validated the Illumina Protein Prep workflow, making high-throughput, NGS-based proteomics accessible to researchers across multiple disciplines. Our fully equipped laboratory, automated workflows, and expert bioinformatics support ensure high-quality, reproducible data at scale. Whether you are conducting biomarker discovery, clinical research, or large-cohort studies, our end-to-end proteomics services will provide the insights you need.

For further information or to discuss collaboration opportunities, contact GeneTiCA Group today.