Proteomics

Proteomics enables the understanding of cellular phenotypes and function, representing the output of all other levels of cellular regulation, including the genome, epigenome, and transcriptome. With proteomics, scientists are able to obtain actionable insights into biomarkers for important areas of study such as disease mechanisms and the development of new drug targets.

Proteomics can add substantial value to multiomic applications by providing the necessary insights toward validating other omic data for an increased understanding of biology. In addition, proteomics can also identify biomarkers while providing important data on mutations and changes in protein expression as potential drivers of disease. With products such as Illumina Protein Prep, scientists can use existing Illumina NGS systems to comprehensively study biological processes on a single platform, including data analysis.

Mass spectrometry is an essential tool in proteomics, offering advantages in specificity and the ability to quantitatively analyze diverse sample types. In addition, this method can provide qualitative information regarding single point mutations and post-translational modifications. However, its workflow can be labor-intensive and has lower throughput compared to NGS-based proteomics. Illumina Protein Prep provides distinct benefits, including scalability and high-throughput capabilities, enabling the analysis of over 9000 proteins across 96 samples in a single run. This system supports both discovery and screening studies through a fully automated workflow, where the findings can be validated and confirmed using the gold standard method of mass spectrometry. Overall, NGS-based proteomics can increase overall workflow efficiency while saving costs when performing studies for biomarker discovery.

lllumina Protein Prep uses the SomaScan assay to transform the protein epitope into a specific SOMAmer Reagent-based DNA signal. Next, a series of bead capture and wash steps convert relative protein concentrations into SOMAmer Reagent abundancies. These SOMAmer Reagents are converted to barcoded sequencing libraries using a hybridization-based approach. Pairs of probes are hybridized to SOMAmer Reagents before capture onto magnetic beads. Each SOMAmer Reagent has a unique pair of probes, one of which carries a barcode corresponding to a particular SOMAmer Reagent. Unbound probes are washed away and converted to the abundance of the barcoded probe. Index PCR primers are added to append sample indexes for sequencing and amplified to create individually indexed-barcode libraries. These indexed-barcode libraries are sequenced and the output of the assay is a relative quantitative measurement of the protein abundance in the sample. The entire Illumina Protein Prep assay is automated on a single platform, the Illumina Protein Prep Automation System. Download the data sheet to learn more.

Illumina Protein Prep is compatible with NovaSeq 6000, NovaSeq X, and NovaSeq X Plus Systems.