Sapient launches next-generation FFPE Proteomics platform
Platform enables direct measure of more than 10,000 proteins in diverse FFPE tissue and tumor samples, integrated multi-omic molecular mapping of tumors
10 Dec 2025
Sapient has launched its next-generation FFPE Proteomics platform offering a robust mass spectrometry-based method to quantify proteins at scale in formalin-fixed, paraffin-embedded (FFPE) tissue and tumor samples.
The workflow enables direct measurement of more than 10,000 protein groups in a single 5-µm FFPE slide, as well as phospho-proteins, glyco-proteins, and non-canonical protein variants, with exceptional reproducibility across replicates, FFPE sections, and in relation to fresh-frozen tissue samples.
Sapient’s FFPE Proteomics allows for deep profiling of functional biology from proteins in FFPE tissue not captured by traditional DNA sequencing, RNA sequencing, or immunohistochemistry (IHC) approaches, including quantification of protein expression, pathway activation, post-translational signaling, and drug distribution in tissue.
Sapient’s FFPE Proteomics workflow integrates with other omics offerings available through Sapient, including single-cell sequencing and spatial profiling, to enable comprehensive multi-omic molecular mapping of tumor biology.
“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,” said Jeramie Watrous, PhD, Co-Founder and Head of Analytical R&D at Sapient.
“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,” he added.
Mo Jain, MD, PhD, Founder and Chief Scientific Officer at Sapient, commented, “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.”
“We can then go even further using our FFPE Multi-Omics platform, not only combining FFPE proteomics and DNA-seq but also single-cell sequencing and spatial profiling data to map tumor biology from mutation to pathway activation, cell-type, and spatial localization,” he concluded.
As part of its FFPE Proteomics platform, Sapient offers its DynamIQ™ virtual biobank for streamlined access to thousands of annotated FFPE tumors and tissues, enabling biophama clients to tap into the diverse global inventory of existing archival tissue samples for their studies.
“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,” noted Jonathan Usuka, PhD, MBA, Chief Executive Officer at Sapient.