ArticleMolecular oncology2019
High-throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification.
Article in Molecular oncology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
85 citing papers in PubMed, 1 synthesis or guideline pooled it, 169 citations in OpenAlex.
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- Multiomics analyses revealed the roles of the epithelial-mesenchymal transition and novel early candidate diagnostic biomarkers in neonatal necrotising enterocolitis.Clinical and translational medicine · 2026Article
- SPINK1-driven cellular heterogeneity and interaction networks in intrahepatic cholangiocarcinoma revealed by integrated multi-omics analysis.Journal of advanced research · 2026Article
- Proteomic analysis reveals modulation of key proteins in follicular thyroid cancer progression.Chinese medical journal · 2026Article
- A 1-year forensic evaluation of DNA degradation and STR typing in embalmed human tissues: Muscle, brain, liver, and bone marrow.Journal of forensic sciences · 2026Article
- Proteomic Analysis of Paired FFPE Tissue and Extracellular Vesicles Reveals Proteins Associated with Recurrence in Stage II Colorectal Cancer.Journal of proteome research · 2026Article
- Mass spectrometry analysis of young and aged mice and human Alzheimer's disease with Lewy body pathology using on-slide tissue digestion.Analytical and bioanalytical chemistry · 2026Article
- Proteomic profiling identifies prognostic signature for Krukenberg tumor of gastrointestinal origin.iScience · 2026Article
- Region-resolved proteomic map of the human brain: functional interconnections and neurological implications.Signal transduction and targeted therapy · 2026Article
- Multiomics Reveals Mitochondrial and Metabolic Perturbations Underlying Cyclotriphosphazene-Induced Lung Injury.Environment & health (Washington, D.C.) · 2026Article
- Multi-center multi-omics integration predicts individualized prognosis in medullary thyroid carcinoma.Nature communications · 2026Article
- Mass spectrometry-based proteomics of FFPE tissues: progress, limitations, and clinical translation barriers.Clinical proteomics · 2025Review
- Proteomic insights into the macaque insular parcellation based on structural connectivity gradients.Cerebral cortex (New York, N.Y. : 1991) · 2025Article
- Spatial proteomics to discover aging-associated alterations in the renal tubulointerstitium.Clinical proteomics · 2025Article
- Quantitative proteomics of formalin-fixed, paraffin-embedded cardiac specimens uncovers protein signatures of specialized regions and patient groups.Nature cardiovascular research · 2025Article
- Advances in lymphoma biomarkers research based on proteomics technology (Review).Oncology reports · 2025Review
- Article
- Region- and Cell-type-Resolved Multiomic Atlas of the Heart.Molecular & cellular proteomics : MCP · 2025Article
- Role of multi‑omics in advancing the understanding and treatment of prostate cancer (Review).Molecular medicine reports · 2025Review
25 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
39 authors at 13 institutions in 4 countries.
Funding
Abstract
Formalin-fixed, paraffin-embedded (FFPE), biobanked tissue samples offer an invaluable resource for clinical and biomarker research. Here, we developed a pressure cycling technology (PCT)-SWATH mass spectrometry workflow to analyze FFPE tissue proteomes and applied it to the stratification of prostate cancer (PCa) and diffuse large B-cell lymphoma (DLBCL) samples. We show that the proteome patterns of FFPE PCa tissue samples and their analogous fresh-frozen (FF) counterparts have a high degree of similarity and we confirmed multiple proteins consistently regulated in PCa tissues in an independent sample cohort. We further demonstrate temporal stability of proteome patterns from FFPE samples that were stored between 1 and 15 years in a biobank and show a high degree of the proteome pattern similarity between two types of histological regions in small FFPE samples, that is, punched tissue biopsies and thin tissue sections of micrometer thickness, despite the existence of a certain degree of biological variations. Applying the method to two independent DLBCL cohorts, we identified myeloperoxidase, a peroxidase enzyme, as a novel prognostic marker. In summary, this study presents a robust proteomic method to analyze bulk and biopsy FFPE tissues and reports the first systematic comparison of proteome maps generated from FFPE and FF samples. Our data demonstrate the practicality and superiority of FFPE over FF samples for proteome in biomarker discovery. Promising biomarker candidates for PCa and DLBCL have been discovered.
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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.