Sapient FFPE Proteomics enables quantification of target expression, pathway activation, post-translational signaling, and drug response in FFPE tissues with coverage comparable to fresh-frozen tissue, revealing functional insights that were previously hidden in these archival samples.
Our mass spectrometry method enables peptide-level analysis to capture phospho-, glyco-, and non-canonical protein variants which may represent key or novel biomarkers and targets.
Proteins measured by our FFPE Proteomics method include 200+ oncogenes and 500+ approved drug targets, with comprehensive detection of hundreds of oncogenic and immune signaling pathways.
Sapient enables pharma oncology teams to extract quantitative pathway activation and target discovery and validation data from FFPE tissues – whether new collections or from samples already used for genomics or IHC – turning archived tissue into functional translational data for both retrospective and prospective analyses.
Discovery oncology scientists are under pressure to identify and validate novel drug targets, but with limited protein-level insights, programs often advance targets with incomplete functional validation, leading to high failure rates in translation.
What if you could turn FFPE tissue into a discovery engine to identify and functionally validate protein targets for higher confidence – without waiting for new sample collections?
Why not de-risk and accelerate your path from target nomination to functional validation in weeks, not months, with Sapient?
Translational oncology teams must show that a therapeutic engages its target and modulates downstream pathways in patient tissue, but lack of protein-level insights means uncertainty around proof-of-mechanism, delaying or obscuring go/no-go decisions.
What if you could confirm target engagement and pathway modulation in FFPE tissue, retrospectively, before committing to costly Phase 2 trials?
Why not accelerate proof-of-mechanism with quantitative pathway and TE data in your FFPE samples or ours?
Clinical oncology programs require robust biomarkers for patient stratification and PK/PD data to guide enrollment, dosing, and patient response. A lack of protein-level insights slows identification of target engagement, and can lead to missed responder subgroups.
What if you could unlock new biomarker insights and responder profiles from archived trial samples – without adding new patient burden?
Why not optimize patient stratification and dosing through rapid, deep protein analysis of existing FFPE trial samples with Sapient?
Precision oncology leaders have revolutionized genomic and transcriptomic profiling of FFPE tumors, yet they face the same strategic limitations: a lack of robust protein-level data means incomplete molecular insight for pharma partners and clinicians, and unrealized value from existing datasets and biobanks.
What if you could extend genomics insights already generated from your FFPE biorepositories by adding functional measures of tumor biology and drug response?
Why not extract new value from under-leveraged FFPE archives with Sapient?
Our FFPE proteomics seamlessly integrates with other omics offerings available through Sapient, including:
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.
FFPE proteomics enables the direct measurement of proteins in formalin-fixed, paraffin-embedded (FFPE) tissue. Recently, next-generation mass spectrometry-based approaches have transformed the ability to measure proteins in FFPE samples at scale, quantifying over 10,000 proteins and their isoforms in a single 5µm FFPE section.
While FFPE tumor tissue represents the largest, most clinically annotated oncology resource available, the proteome has remained largely inaccessible due to the effects of fixation on protein structures. Previously profiling was largely limited to DNA and RNA sequencing or low-plex immunohistochemistry (IHC) which cannot quantify important functional tumor biology, assay specific protein isoforms, or uncover novel protein targets for therapeutic development.
Next-generation FFPE proteomics represents a critical unlock in cancer research because it turns the hundreds of millions of FFPE tumor blocks that are already archived worldwide into new discovery engines – directly measuring previously inaccessible functional biology in FFPE samples to enable novel biomarker discovery, faster target identification and validation, and mechanistic context for accelerating drug development.
Sapient’s next-generation FFPE proteomics method has been demonstrated in oncology studies to deliver protein- and pathway-level resolution across 200+ oncogenic pathways from a single FFPE tumor section, uncovering novel targets that would otherwise require fresh-frozen tissue.
See our poster on discovery of novel oncogenic targets in FFPE tissue and our white paper, Mass Spectrometry-Based FFPE Proteomics as a Transformational Platform for Modern Oncology R&D, for the underlying data.
Traditionally, due to formalin fixation causing protein crosslinking, proteomics in FFPE tissue would yield considerably fewer detectable proteins compared to in fresh-frozen tissue. These percentages have changed significantly, however, with modern sample processing techniques and mass spectrometry instrumentation used as part of Sapient’s next-generation FFPE proteomics.
Our FFPE proteomics data shows exceptional protein-level concordance with fresh-frozen tissue, with >90% protein matching and correlation of >0.8. This means we can achieve close reproducibility in proteins assayed and quantitation in FFPE tissues relative to matched fresh-frozen tissue samples. See our data sheet for more details.
Yes. IHC measures one to several proteins at a time and depends on an antibody existing for the target(s), while mass spectrometry-based FFPE proteomics measures thousands of proteins simultaneously and quantitatively, with no antibody required. FFPE proteomics also directly measures protein isoforms, PTMs, protein complexes, and pathway activation states – key elements of biology that determine therapeutic success but remain inaccessible to IHC and genomics or transcriptomics.
This makes it possible to survey the tumor proteome broadly before narrowing in on specific markers, rather than testing candidates one at a time. Researchers can observe entire signaling networks, resistance pathways, immune cell states, microenvironmental phenotypes, and metabolic programs in a single experiment.
This scale and depth provide mechanistic insights that are immediately relevant to pharmaceutical drug development decisions, including asset prioritization, indication expansion opportunities, clinical trial design, and competitive differentiation.
Sapient’s next-generation FFPE proteomics workflow detects 10,000+ proteins from a single 5 µm FFPE section – comparable to the tissue used for a single IHC stain – delivering pathway-level resolution across 200+ oncogenic pathways.
Importantly, our workflow achieves exceptional reproducibility across technical replicates and across sequential samples from a given FFPE block, with a technical median coefficient of variation (CV) of less than 5% for repeat samples and less than 8% across serial FFPE sections. See our data sheet for more details.
Yes. Archived FFPE blocks from completed trials or biobanks can be reanalyzed for proteomic biomarkers years after collection, letting you mine retrospective cohorts for target validation, resistance mechanisms, or patient stratification without launching a new prospective study.
Sapient also offers streamlined access to thousands of annotated FFPE tumor and normal tissue samples through our DynamiQ™ Tumor-Tissue virtual biobank.
Connect with our scientists to discuss your project and how we can help you turn archived FFPE samples into new discovery engines – unlocking previously hidden protein-level insights that add the critical layer of functional biology to existing genomics datasets.
