The Omics Brief | Next-Gen FFPE Proteomics: Turning yesterday’s tissue into tomorrow’s breakthroughs

How can mass spectrometry FFPE proteomics reveal new biomarkers and drug targets in existing tissue and tumor samples?

FFPE biosamples are a mainstay of oncology-based diagnostics, with over 400 million FFPE tissues collected and stored globally in biobanks, hospitals, and clinical trial sites. The traditional approaches to analyze these samples include immunohistochemistry (IHC), which provide insight into protein presence and localization for one to dozens of proteins at a time, or DNA sequencing which can capture 500 or more different oncogenic mutations.

While both of these technologies and approaches have been instrumental in cancer diagnostics, they provide limited information regarding functional tumor biology. Precision oncology increasingly requires measurements of functional markers that read out not only underlying tumor biology, but tumor microenvironment interactions, pathway activation, and drug response and resistance.

In this Omics Brief, we introduce Sapient’s next-generation approaches for mass spectrometry FFPE proteomics, providing the ability to quantitate up to 10,000 proteins simultaneously in a single FFPE section or curl. This allows for peptide-level resolution, not only measuring whole proteins but specific protein isoforms, including post-translational modifications (PTMs) such as phospho- and glyco-proteins that are hidden to genomics profiling and difficult to measure via IHC.