Next-Generation FFPE Proteomics

While genomic profiling and RNA sequencing have transformed oncology, they reveal potential—not function. The proteome, which defines target expression, pathway activation, post-translational signaling, and drug response, has remained largely inaccessible in formalin-fixed, paraffin-embedded (FFPE) tissues, as extracting protein insights from these biospecimens is challenging. The effects of fixation, such as formalin-induced cross-linking, can distort the structure of proteins and reduce the binding efficiency of antibody-based proteomic methods – which are also typically low-plex.

Because FFPE tissue is one of the most accessible sample types available, there is significant opportunity to transform vast existing biorepositories into new discovery engines for functional biology through large-scale, robust protein- and pathway-level analyses in FFPE samples.

That is where Sapient’s next-generation FFPE Proteomics comes in. Our mass spectrometry-based workflows overcome both fixation and coverage limitations via the direct measure of proteins in FFPE tissue.

In fact, from a 5 µm FFPE section, Sapient’s FFPE tissue proteomics quantifies >10,000 protein groups, including phospho- and glyco-proteins and isoforms – revealing insights into tumor signaling, immune activation, and pharmacodynamic effects with single protein and pathway-level resolution.

What’s more, our FFPE tissue proteomics seamlessly integrates with other omics offerings available through Sapient, including DNA sequencing for mutation and CNV mapping; single-cell sequencing for cell-type specific expression; and spatial profiling for tissue contextualization.

This multi-omic integration enables reconstruction of tumor biology from mutation to pathway activation, cell-type, and spatial localization, creating a unified molecular map of each tumor.