How Sapient’s Next-Gen Proteomics Platform Helps Quantify Proteins at Scale

Sapient Bioanalytics, based in San Diego, has announced the launch of a next-generation platform to quantify proteins, at scale, in formalin-fixed, paraffin-embedded (FFPE) tissue and tumor samples. Using a robust mass spectrometry-based method, Sapient said its FFPE Proteomics platform can enable direct measurement of more than 10,000 protein groups in a single, 5-µm slide, in addition to phospho-proteins, glyco-proteins, and non-canonical protein variants (1).

In a press release, Sapient said that the platform allows for deep profiling of functional biology from proteins in FFPE tissue not traditionally captured by DNA or RNA sequencing, or immunohistochemistry (IHC) approaches (1). Among the characteristics the company said the platform could reveal are quantification of protein expression, pathway activation, post-translational signaling, and drug distribution in tissue.

So far, the method has been applied across diverse tumor samples, including a variety of cancers, demonstrating high precision and reproducibility.

Why is it difficult to obtain deep insights in protein analysis?

“FFPE tissue is one of the most accessible sample types available, but extracting protein insights from these biospecimens has traditionally been challenging due to the effects of fixation on protein structures,” Jeramie Watrous, PhD, co-founder and head of Analytical R&D at Sapient, said in the release (1). “Using mass spectrometry, we perform peptide-level analysis which bypasses the need to fully restore native protein structures and additionally captures protein isoforms and post-translational modifications that are inaccessible via DNA and RNA sequencing. It also addresses the low-plex constraints of IHC, allowing us to measure thousands of proteins—a depth comparable to what is possible in fresh-frozen tissue—across thousands of samples per study.”

“What’s most exciting is that we can now go back to the vast biorepositories of FFPE tissue samples already collected, and using our method, essentially turn them into new discovery engines—unlocking previously hidden protein-level insights that add the critical layer of functional biology to existing genomics datasets,” Mo Jain, MD, PhD, Sapient founder and chief scientific officer, said (1).

“By providing access to actionable FFPE tissue samples, we can support rapid retrospective studies to identify disease biomarkers, patient responders, and drug mechanism of action insights that can optimize prospective studies and de-risk drug development efforts,” Jonathan Usuka, PhD, MBA, CEO of Sapient, said (1).

How do FFPE advances reshape drug discovery?

Recent advancements such as Sapient’s platform offer biopharma researchers an opportunity to leverage vast archival tissue repositories (1). For the industry at large, this technology promises to support rapid retrospective studies for identifying disease biomarkers, defining patient responders, and clarifying drug mechanisms of action, thereby optimizing prospective trials and de-risking drug development efforts.

This progress in proteomics stands in contrast to the persistent, critical challenges associated with extracting reliable genomic data from the same FFPE samples. Formalin fixation chemically modifies and fragments DNA, potentially leading to incorrect sequences and misinterpretations in downstream data analysis, necessitating extensive mitigation strategies like enzymatic repair and complex bioinformatic filtering (2). By complementing complex DNA sequencing workflows with high-depth protein analysis, pharmaceutical teams can now utilize integrated, multi-omic molecular mapping to trace tumor biology from mutation to pathway activation and spatial localization, providing a more complete picture of targets and drug efficacy (1).

References

1. Sapient. Sapient Launches Next-Generation FFPE Proteomics Platform to Unlock New Functional Insights from Archived Tissue. Press Release. Nov. 19, 2025.
2. Steiert, T.A.; Parra, G.; Gut, M.; et al. A Critical Spotlight on the Paradigms of FFPE-DNA Sequencing. Nucleic Acids Res. 2023, 51 (14) 7143–7162. DOI: 10.1093/nar/gkad519