Overcoming reproducibility and cost barriers in proteomics for biomedical research

A new proteomics platform will make high-precision protein analysis faster and more affordable—accelerating drug discovery and disease research across Canada. 

Proteomics, which is the study of the complement of proteins expressed in tissue samples, offers a better picture of disease phenotypes than genomics. Current technical limitations, however, prevent its use in large-scale preclinical and clinical studies.

Most proteomics labs focus on identifying differences in proteins between samples. However, batch effects and limited robustness mean that all samples should be processed and analyzed together, on the same instrument, in the same lab, to ensure reliable results.

Absolute quantitation (AbsQuan) is more precise and allows researchers to measure the exact concentrations of proteins. This makes data consistent across labs, studies and using different instruments. The problem is that AbsQuan relies on individually synthesized, purified and characterized stable isotope-labeled (SIL) peptide standards, driving the cost per protein over $1,500, and thus limiting its use. What is needed is a solution to reproducibility at an affordable cost.

Researchers at McGill University and the University of Manitoba have teamed up with industry partners MRM Proteomics (MRMP), a Canadian CRO in protein quantitation, as well as Agilent, Bruker, and Evosep to develop SysQuan, an affordable, ready-to-use platform to measure thousands of human proteins. SysQuan kits leverage the biological similarity between humans and mice, replacing expensive SIL peptides with SIL mouse tissues at proteome-wide standards. This reduces the cost of AbsQuan 100 fold.

SysQuan allows labs to measure thousands of proteins in up to thousands of samples to generate comparable data between labs, independent of the user or when the analysis was performed. Data from the lab predicts that two-thirds of the human proteome is quantifiable using SysQuan, including more than 7,000 proteins in human liver and 1,400 in plasma. For select metabolic proteins, the team demonstrated that SysQuan allows reverse absolute quantitation in human tissue, demonstrating the feasibility of the technique for thousands of human samples. SysQuan is superior to current commercial platforms that rely on affinity binding of whole protein structures (e.g. SomaLogic and Olink) due to its unmatched specificity, precision, accuracy and cost-effectiveness.

Genome Canada is contributing funds to the development of SysQuan. Initially for research use only, SysQuan targets growing markets for research reagents and biomarkers—expected to be worth $130 billion USD by 2028. MRMP is poised to grow significantly, given co-marketing agreements with major industry partners and a ring trial with global leaders in proteomics. SysQuan will transform MRMP’s portfolio, allow it to address new markets, and bring in revenues in the first five years ($4–5 million) to support ongoing operations and hire new skilled talent in the increasingly important proteomics space.

SysQuan will accelerate the impact of proteomics studies and increase the return-on-investment of Canadian biomedical research, with MRMP providing the technology free for Canadian clinical trials and early adopters.