ArticleJournal of proteome research2011
Initial development and validation of a novel extraction method for quantitative mining of the formalin-fixed, paraffin-embedded tissue proteome for biomarker investigations.
Article in Journal of proteome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
27 citing papers in PubMed, 82 citations in OpenAlex.
- Probe-dependent Proximity Profiling (ProPPr) Uncovers Similarities and Differences in Phospho-Tau-Associated Proteomes Between Tauopathies.Molecular neurodegeneration · 2025Article
- The effect of storage time and temperature on the proteomic analysis of FFPE tissue sections.Clinical proteomics · 2025Article
- Inter-Regional Proteomic Profiling of the Human Brain Using an Optimized Protein Extraction Method from Formalin-Fixed Tissue to Identify Signaling Pathways.International journal of molecular sciences · 2023Article
- Comparative evaluation of two methods for LC-MS/MS proteomic analysis of formalin fixed and paraffin embedded tissues.Journal of proteomics · 2021Review
- Protein Extraction From FFPE Kidney Tissue Samples: A Review of the Literature and Characterization of Techniques.Frontiers in medicine · 2021Article
- HYPERsol: High-Quality Data from Archival FFPE Tissue for Clinical Proteomics.Journal of proteome research · 2020Article
- Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization.Clinical proteomics · 2018Article
- Fast and Simple Protocols for Mass Spectrometry-Based Proteomics of Small Fresh Frozen Uterine Tissue Sections.Analytical chemistry · 2017Article
- Laser Capture Microdissection of Pancreatic Acinar Cells to Identify Proteomic Alterations in a Murine Model of Caerulein-Induced Pancreatitis.Clinical and translational gastroenterology · 2017Article
- "Omics"-Informed Drug and Biomarker Discovery: Opportunities, Challenges and Future Perspectives.Proteomes · 2016Review
- Optimized Protocol for Quantitative Multiple Reaction Monitoring-Based Proteomic Analysis of Formalin-Fixed, Paraffin-Embedded Tissues.Journal of proteome research · 2016Article
- Formalin-Fixed, Paraffin-Embedded Tissues (FFPE) as a Robust Source for the Profiling of Native and Protease-Generated Protein Amino Termini.Molecular & cellular proteomics : MCP · 2016Article
- Elucidating the Molecular Composition of Cartilage by Proteomics.Journal of proteome research · 2016Article
- Proteomic analysis of neurons microdissected from formalin-fixed, paraffin-embedded Alzheimer's disease brain tissue.Scientific reports · 2015Article
- Tissue proteomics using chemical immobilization and mass spectrometry.Analytical biochemistry · 2015Article
- Comparison of Different Buffers for Protein Extraction from Formalin-Fixed and Paraffin-Embedded Tissue Specimens.PloS one · 2015Article
- Proteomic and metabolic prediction of response to therapy in gastric cancer.World journal of gastroenterology · 2014Review
- Assessment of the 2-d gel-based proteomics application of clinically archived formalin-fixed paraffin embedded tissues.The protein journal · 2014Article
- Sorbin and SH3 domain-containing protein 2 is released from infarcted heart in the very early phase: proteomic analysis of cardiac tissues from patients.Journal of the American Heart Association · 2013Article
- Improved protein extraction and protein identification from archival formalin-fixed paraffin-embedded human aortas.Proteomics. Clinical applications · 2013Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
Abstract
Annotated formalin-fixed, paraffin-embedded (FFPE) tissue archives constitute a valuable resource for retrospective biomarker discovery. However, proteomic exploration of archival tissue is impeded by extensive formalin-induced covalent cross-linking. Robust methodology enabling proteomic profiling of archival resources is urgently needed. Recent work is beginning to support the feasibility of biomarker discovery in archival tissues, but further developments in extraction methods which are compatible with quantitative approaches are urgently needed. We report a cost-effective extraction methodology permitting quantitative proteomic analyses of small amounts of FFPE tissue for biomarker investigation. This surfactant/heat-based approach results in effective and reproducible protein extraction in FFPE tissue blocks. In combination with a liquid chromatography-mass spectrometry-based label-free quantitative proteomics methodology, the protocol enables the robust representative and quantitative analyses of the archival proteome. Preliminary validation studies in renal cancer tissues have identified typically 250-300 proteins per 500 ng of tissue with 1D LC-MS/MS with comparable extraction in FFPE and fresh frozen tissue blocks and preservation of tumor/normal differential expression patterns (205 proteins, r = 0.682; p < 10(-15)). The initial methodology presented here provides a quantitative approach for assessing the potential suitability of the vast FFPE tissue archives as an alternate resource for biomarker discovery and will allow exploration of methods to increase depth of coverage and investigate the impact of preanalytical factors.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.