Ultra-Deep FFPE Proteomics Service
Formalin-fixed paraffin-embedded (FFPE) tissue is the standard preservation method in clinical practice today. Among the vast collection of tissue samples stored in hospitals and biobanks worldwide, the vast majority are preserved in FFPE format. For certain rare tumor types and diseases, FFPE specimens are often the only available source material, making them invaluable for research on some of the rarest cancers and other disease conditions. With advances in sample preparation techniques and the development of mass spectrometry instrumentation, the scientific value of FFPE samples has been fully unlocked. By combining cutting-edge proteomics methods, researchers can now extract deep protein-level insights from these long-term archived clinical specimens, providing critical support for disease mechanism studies, biomarker discovery, and precision medicine applications.
Our Services
- Comprehensive Protein Quantification from FFPE Samples
We employ label-free quantitative proteomics technology to analyze the complete protein profile from FFPE specimens. Through optimized sample preparation protocols—including paraffin removal, rehydration, protein extraction, peptide digestion, and purification—we recover the full complement of proteins from FFPE samples for in-depth analysis. Following high-resolution LC-MS/MS mass spectrometry detection, we perform reliable database searching and rigorous statistical analysis, making our approach ideal for large-scale studies with multiple sample comparisons. - In-Depth Bioinformatic Analysis
Building on quantitative protein detection results, we provide comprehensive bioinformatic interpretation services, including:- Differential protein identification and enrichment analysis
- Protein-protein interaction network construction
- Pathway analysis and functional annotation
- Clinical relevance assessment
Application
- Disease Mechanism Studies: By comparing protein profiles between diseased and normal tissues, we illuminate the molecular mechanisms underlying disease pathogenesis, particularly valuable for cancer and neurodegenerative disease research.
- Biomarker Discovery: We systematically identify protein biomarkers from FFPE samples that correlate with disease diagnosis, classification, and prognosis, supporting the development of precision diagnostic and therapeutic approaches.
- Therapeutic Target Validation: Our comprehensive analysis of protein expression changes before and after drug intervention supports mechanistic studies and the discovery of novel drug targets.
- Tumor Microenvironment Analysis: We provide deep characterization of immune infiltration-related protein signatures in tumor tissues, establishing molecular foundations for immunotherapy research.
- Translational Medicine Research: Leveraging large cohorts of FFPE specimens, we enable cohort studies that translate basic discoveries into clinical applications.
Workflow
Upon receiving FFPE samples from clients, we conduct preliminary quality evaluation, assessing sample integrity, preservation status, and identifier verification to ensure samples meet analysis standards.
We perform paraffin removal and rehydration of tissue sections using appropriate reagents to effectively eliminate paraffin components, followed by gentle tissue digestion to prepare for subsequent protein extraction.
We employ optimized protein extraction methods to recover proteins from processed samples, then quantify protein concentration, providing the quantitative basis for downstream analysis.
Proteins undergo specific enzymatic digestion (typically with trypsin) to generate peptide mixtures, followed by purification steps such as solid-phase extraction or chromatography to remove non-protein contaminants.
Using high-resolution liquid chromatography-mass spectrometry instrumentation, we perform peptide separation and detection to acquire high-quality mass spectrometry data, establishing the foundation for accurate protein identification and quantification.
We process and analyze mass spectrometry raw data, performing comprehensive database searches and comparisons to accurately identify the protein constituents present in FFPE specimens.
We consolidate all analytical results into professional data analysis reports, including data visualization, key findings summary, and scientific interpretation, providing comprehensive support for clients' subsequent research.
If you have any questions about our ultra-deep FFPE proteomics service, please don't hesitate to reach out to our technical team. We're here to provide expert consultation and support.
