ArticleNature protocols2020
Spatially resolved analysis of FFPE tissue proteomes by quantitative mass spectrometry.
Article in Nature protocols, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- Article
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- Proteogenomics: decoding cancer in multiple dimensions.MedScience · 2026Review
- Evaluation and application of chemical decrosslinking in the context of histopathological spatial proteomics.bioRxiv : the preprint server for biology · 2026Article
- Identification of MFN2 and NCL as cardiac biomarkers for post-mortem diagnosis of atypical electrocution death.International journal of legal medicine · 2026Article
- Polyamines sustain epithelial regeneration in aged intestines by modulating protein homeostasis.Nature cell biology · 2025Article
- Mass spectrometry-based proteomics of FFPE tissues: progress, limitations, and clinical translation barriers.Clinical proteomics · 2025Review
- MUC1 drives ferroptosis resistance in ICC via Src-mediated FSP1 deubiquitination and myristoylation.Clinical and translational medicine · 2025Article
- Quantitative proteomics of formalin-fixed, paraffin-embedded cardiac specimens uncovers protein signatures of specialized regions and patient groups.Nature cardiovascular research · 2025Article
- The Neurolipid Atlas: a lipidomics resource for neurodegenerative diseases.Nature metabolism · 2025Article
- Screening of Protein Related to Wool Development and Fineness in Gansu Alpine Fine-Wool Sheep.Animals : an open access journal from MDPI · 2025Article
- Proteome analysis of preserved formalin-fixed and paraffin-embedded specimens to explore the pathogenesis of infantile hypertrophic pyloric stenosis.Pediatric surgery international · 2025Article
- Altered translation elongation contributes to key hallmarks of aging in the killifish brain.Science (New York, N.Y.) · 2025Article
- Spatially resolved proteomics surveys the chemo-refractory proteins related to high-grade serous ovarian cancer.Clinical and translational medicine · 2025Article
- Aging and diet alter the protein ubiquitylation landscape in the mouse brain.Nature communications · 2025Article
- Impact of lymph node metastasis on immune microenvironment and prognosis in colorectal cancer liver metastasis: insights from multiomics profiling.British journal of cancer · 2025Article
- An AI-assisted morphoproteomic approach is a supportive tool in esophagitis-related precision medicine.EMBO molecular medicine · 2025Article
- Robust collection and processing for label-free single voxel proteomics.Nature communications · 2025Article
- Towards routine proteome profiling of FFPE tissue: insights from a 1,220-case pan-cancer study.The EMBO journal · 2025Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bottom-up mass spectrometry-based proteomics relies on protein digestion and peptide purification. The application of such methods to broadly available clinical samples such as formalin-fixed and paraffin-embedded (FFPE) tissues requires reversal of chemical crosslinking and the removal of reagents that are incompatible with mass spectrometry. Here, we describe in detail a protocol that combines tissue disruption by ultrasonication, heat-induced antigen retrieval and two alternative methods for efficient detergent removal to enable quantitative proteomic analysis of limited amounts of FFPE material. To show the applicability of our approach, we used hepatocellular carcinoma (HCC) as a model system. By combining the described protocol with laser-capture microdissection, we were able to quantify the intra-tumor heterogeneity of a tumor specimen on the proteome level using a single slide with tissue of 10-µm thickness. We also demonstrate broader applicability to other tissues, including human gallbladder and heart. The procedure described in this protocol can be completed within 8 d.
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