ArticleClinical proteomics2022
Systematic evaluation and optimization of protein extraction parameters in diagnostic FFPE specimens.
Article in Clinical proteomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Post‑translational modification‑governed immune states in cancer immunity: Biomarker implications for checkpoint competence, tumor visibility and immunotherapy resistance (Review).International journal of oncology · 2026Review
- Mass spectrometry-based proteomics of FFPE tissues: progress, limitations, and clinical translation barriers.Clinical proteomics · 2025Review
- Quantifying Protein Acetylation in Diabetic Nephropathy from Formalin-Fixed Paraffin-Embedded Tissue.Proteomics. Clinical applications · 2024Article
- Proteomic analysis of the urothelial cancer landscape.Nature communications · 2024Article
- A Fast-Tracking Sample Preparation Protocol for Proteomics of Formalin-Fixed Paraffin-Embedded Tumor Tissues.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Proteomic analyses identify HK1 and ATP5A to be overexpressed in distant metastases of lung adenocarcinomas compared to matched primary tumors.Scientific reports · 2023Article
- EpCAM tumor specificity and proteoform patterns in urothelial cancer.Journal of cancer research and clinical oncology · 2023Article
- Disease-Specific α-Synuclein Seeding in Lewy Body Disease and Multiple System Atrophy Are Preserved in Formaldehyde-Fixed Paraffin-Embedded Human Brain.Biomolecules · 2023Article
- ASAP─Automated Sonication-Free Acid-Assisted Proteomes─from Cells and FFPE Tissues.Analytical chemistry · 2023Article
- Highly Accurate and Robust Absolute Quantification of Target Proteins in Formalin-Fixed Paraffin-Embedded (FFPE) Tissues by LC-MS.Analytical chemistry · 2023Article
- Mass Spectrometry-Based Proteomics Workflows in Cancer Research: The Relevance of Choosing the Right Steps.Cancers · 2023Review
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
objectivesFormalin-fixed paraffin-embedded (FFPE) tissue is the standard material for diagnostic pathology but poses relevant hurdles to accurate protein extraction due to cross-linking and chemical alterations. While numerous extraction protocols and chemicals have been described, systematic comparative analyses are limited. Various parameters were thus investigated in their qualitative and quantitative effects on protein extraction (PE) efficacy. Special emphasis was put on preservation of membrane proteins (MP) as key subgroup of functionally relevant proteins.
methodsUsing the example of urothelial carcinoma, FFPE tissue sections were subjected to various deparaffinization, protein extraction and antigen retrieval protocols and buffers as well as different extraction techniques. Performance was measured by protein concentration and western blot analysis of cellular compartment markers as well as liquid chromatography-coupled mass spectrometry (LC-MS).
resultsCommercially available extraction buffers showed reduced extraction of MPs and came at considerably increased costs. On-slide extraction did not improve PE whereas several other preanalytical steps could be simplified. Systematic variation of temperature and exposure duration demonstrated a quantitatively relevant corridor of optimal antigen retrieval.
conclusionsPreanalytical protein extraction can be optimized at various levels to improve unbiased protein extraction and to reduce time and costs.
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