FFPE Quantitative Proteomics Service
- High Accuracy: QC CV as low as 25% for large projects
- High Throughput: More than 9000 proteins can be identified at once
- High Repeatability: Up to 90%
- Comprehensive Quantification: Quantitatively identify nearly all detectable molecules, covering low-abundance proteins/peptides
- Low Cost: Reduce the cost by more than 3 times
In contemporary clinical proteomics, the majority of studies utilize fresh or frozen tissue samples, which often provide limited long-term follow-up data, restricting their practical application in patient care. In contrast, Formalin Fixed Paraffin Embedded (FFPE) tissues represent the gold standard for sample preservation in clinical histopathology. This method not only ensures the long-term integrity of samples, allowing for storage at room temperature for years, but also supports dense archiving of tissues—an estimated 500 million FFPE cancer specimens are currently preserved, with this number growing rapidly. These archived samples are a valuable resource for exploring the molecular mechanisms of diseases and for both testing and discovering new biomarkers. Harnessing these samples for proteomic analysis could significantly enhance their clinical utility. Recent advancements in mass spectrometry (MS)-based proteomic techniques have made it possible to conduct large-scale, unbiased investigations of proteomes with unprecedented depth.
The process of formaldehyde fixation and paraffin embedding results in significant molecular cross-linking among proteins, nucleic acids, and other biomolecules within tissue cells, presenting challenges in proteomic extraction from FFPE samples. Fixation can diminish protein extraction efficiency and immune reactivity, complicating protein identification via mass spectrometry. Therefore, an effective extraction method is crucial. At MtoZ Biolabs, we have developed a robust protein extraction protocol, grounded in extensive literature review and rigorous R&D testing, to ensure the recovery of high-quality proteins from FFPE samples.
Services at MtoZ Biolabs
At MtoZ Biolabs, we employ cutting-edge data-independent acquisition (DIA) proteomics technology to analyze protein extracts from FFPE tissues. This approach uncovers extensive functional information relevant to disease processes, facilitating the identification of critical biomarkers associated with diagnosis, prognosis, monitoring, and treatment strategies for specific diseases. In addition, we provide highly multiplexed targeted proteomics that offer absolute quantification for tailored panels of proteins, meeting the specific needs of your research.
Barnabas, G. D. et al. Anal. Chem. 2023.
Figure 1. The Workflow of FFPE Quantitative Proteomics
Service Advantages
Sample Submission Requirements
1. FFPE Slices: Thickness of 5-10 μm, size of 50 mm², with a minimum of 10 slices, to be transported at room temperature.
2. Formalin-Fixed Tissue: Recommended sample weight is 30 mg, with long-term transport temperature maintained at 4°C, and not below 0°C.
At MtoZ Biolabs, we are committed to delivering high-quality FFPE Quantitative Proteomics Service, empowering researchers to unlock the potential of archived tissues and contribute to groundbreaking advancements in clinical proteomics.
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