ArticleJournal of proteome research2022
In-Depth Mass Spectrometry-Based Proteomics of Formalin-Fixed, Paraffin-Embedded Tissues with a Spatial Resolution of 50-200 μm.
Article in Journal of proteome research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Optimization of trap column properties and loading conditions for proteome profiling of single-cell-level sample inputs.Analytical and bioanalytical chemistry · 2026Article
- Consensus statement on mass spectrometry-based proteomic analysis of cardiac tissue.Nature cardiovascular research · 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
- MR-SPJournal of proteome research · 2026Article
- Comparative proteomic analysis of the zebrafish (Danio rerio) perivitelline fluid; identifying putative cortical alveoli-associated proteins.Biology of reproduction · 2026Article
- Evaluation and application of chemical decrosslinking in the context of histopathological spatial proteomics.bioRxiv : the preprint server for biology · 2026Article
- Article
- Mass spectrometry-based proteomics of FFPE tissues: progress, limitations, and clinical translation barriers.Clinical proteomics · 2025Review
- The $10 proteome: low-cost, deep and quantitative proteome profiling of limited sample amounts using the Orbitrap Astral and timsTOF Ultra 2 mass spectrometers.bioRxiv : the preprint server for biology · 2025Article
- Imaging and spatially resolved mass spectrometry applications in nephrology.Nature reviews. Nephrology · 2025Review
- Trends in Mass Spectrometry-Based Single-Cell Proteomics.Analytical chemistry · 2025Review
- Overlap of Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Matched Tissues for Proteomics and Phosphoproteomics.ACS omega · 2025Article
- Robust collection and processing for label-free single voxel proteomics.Nature communications · 2025Article
- Review
- Single-cell omics: experimental workflow, data analyses and applications.Science China. Life sciences · 2025Review
- A new understanding of tissue biology from MS-based proteomics at single-cell resolution.Nature methods · 2024Article
- Multicolumn Nanoflow Liquid Chromatography with Accelerated Offline Gradient Generation for Robust and Sensitive Single-Cell Proteome Profiling.Analytical chemistry · 2024Article
- Novel FFPE proteomics method suggests prolactin induced protein as hormone induced cytoskeleton remodeling spatial biomarker.Communications biology · 2024Article
- What's new in single-cell proteomics.Current opinion in biotechnology · 2024Review
- Mass spectrometry imaging methods for visualizing tumor heterogeneity.Current opinion in biotechnology · 2024Review
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
Formalin-fixed, paraffin-embedded (FFPE) tissues are banked in large repositories to cost-effectively preserve valuable specimens for later study. With the rapid growth of spatial proteomics, FFPE tissues can serve as a more accessible alternative to more commonly used frozen tissues. However, extracting proteins from FFPE tissues is challenging due to cross-links formed between proteins and formaldehyde. Here, we have adapted the nanoPOTS sample processing workflow, which was previously applied to single cells and fresh-frozen tissues, to profile protein expression from FFPE tissues. Following the optimization of extraction solvents, times, and temperatures, we identified an average of 1312 and 3184 high-confidence master proteins from 10 μm thick FFPE-preserved mouse liver tissue squares having lateral dimensions of 50 and 200 μm, respectively. The observed proteome coverage for FFPE tissues was on average 88% of that achieved for similar fresh-frozen tissues. We also characterized the performance of our fully automated sample preparation and analysis workflow, termed autoPOTS, for FFPE spatial proteomics. This modified nanodroplet processing in one pot for trace samples (nanoPOTS) and fully automated processing in one pot for trace sample (autoPOTS) workflows provides the greatest coverage reported to date for high-resolution spatial proteomics applied to FFPE tissues. Data are available via ProteomeXchange with identifier PXD029729.
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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.