ArticleThe EMBO journal2025
Towards routine proteome profiling of FFPE tissue: insights from a 1,220-case pan-cancer study.
Article in The EMBO journal, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Scalable clinical proteomics from DNA/RNA extraction flowthroughs enables integrated proteogenomic profiling from a single cancer biopsy.Clinical proteomics · 2026Article
- MLMarker: a machine learning framework for tissue inference and biomarker discovery.Genome biology · 2026Article
- A Micro-Quantitative and FFPE-Compatible Workflow for Immunohistochemistry-Guided Spatial Proteomic Analysis of Cellular Subpopulations Within the Tumor Microenvironment.Bioengineering (Basel, Switzerland) · 2026Article
- Mass spectrometry-based proteomics delivers in-depth proteome profiling of FFPE lung cancer biopsies from single glass slides.NPJ precision oncology · 2026Article
- [Proteomics and glycomics in pathology : Potential of autopsy and FFPE tissue for diagnostics and research].Pathologie (Heidelberg, Germany) · 2026Review
- 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
- Evaluation and application of chemical decrosslinking in the context of histopathological spatial proteomics.bioRxiv : the preprint server for biology · 2026Article
- Mass spectrometry-based proteomics of FFPE tissues: progress, limitations, and clinical translation barriers.Clinical proteomics · 2025Review
- Proteomic Analysis of FFPE Tissue Samples Identifies Potential Molecular Mechanisms Mediating Resistance to Radiotherapy in Rectal Cancer.Journal of proteome research · 2025Article
- MSFragger-DDA+ enhances peptide identification sensitivity with full isolation window search.Nature communications · 2025Article
- Molecular Phenotyping With Proteomics.JAMA · 2025Article
- MSFragger-DDA+ Enhances Peptide Identification Sensitivity with Full Isolation Window Search.bioRxiv : the preprint server for biology · 2024Article
- Proteomics in IDH-mutated diffuse lower-grade glioma: a scoping review.Neuro-oncology advancesReview
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Authors and funding
23 authors.
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Abstract
Proteome profiling of formalin-fixed paraffin-embedded (FFPE) specimens has gained traction for the analysis of cancer tissue for the discovery of molecular biomarkers. However, reports so far focused on single cancer entities, comprised relatively few cases and did not assess the long-term performance of experimental workflows. In this study, we analyze 1220 tumors from six cancer entities processed over the course of three years. Key findings include the need for a new normalization method ensuring equal and reproducible sample loading for LC-MS/MS analysis across cohorts, showing that tumors can, on average, be profiled to a depth of >4000 proteins and discovering that current software fails to process such large ion mobility-based online fractionated datasets. We report the first comprehensive pan-cancer proteome expression resource for FFPE material comprising 11,000 proteins which is of immediate utility to the scientific community, and can be explored via a web resource. It enables a range of analyses including quantitative comparisons of proteins between patients and cohorts, the discovery of protein fingerprints representing the tissue of origin or proteins enriched in certain cancer entities.
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