ArticleThe journal of histochemistry and cytochemistry : official journal of the Histochemistry Society2009
Protein extraction of formalin-fixed, paraffin-embedded tissue enables robust proteomic profiles by mass spectrometry.
Article in The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed, 101 citations in OpenAlex.
- Article
- A Fast-Tracking Sample Preparation Protocol for Proteomics of Formalin-Fixed Paraffin-Embedded Tumor Tissues.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Inter-Regional Proteomic Profiling of the Human Brain Using an Optimized Protein Extraction Method from Formalin-Fixed Tissue to Identify Signaling Pathways.International journal of molecular sciences · 2023Article
- Biomarkers in Neurodegenerative Diseases: Proteomics Spotlight on ALS and Parkinson's Disease.International journal of molecular sciences · 2022Review
- Systematic evaluation and optimization of protein extraction parameters in diagnostic FFPE specimens.Clinical proteomics · 2022Article
- Comparative evaluation of two methods for LC-MS/MS proteomic analysis of formalin fixed and paraffin embedded tissues.Journal of proteomics · 2021Review
- Target Score-A Proteomics Data Selection Tool Applied to Esophageal Cancer Identifies GLUT1-Sialyl Tn Glycoforms as Biomarkers of Cancer Aggressiveness.International journal of molecular sciences · 2021Article
- Evaluation of Protein Purification Techniques and Effects of Storage Duration on LC-MS/MS Analysis of Archived FFPE Human CRC Tissues.Pathology oncology research : POR · 2021Article
- Molecular Characterization of Testicular Germ Cell Tumors Using Tissue Microdissection.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Effect of polyethylene glycol 20 000 on protein extraction efficiency of formalin-fixed paraffin-embedded tissues in South Africa.African journal of laboratory medicine · 2021Article
- A Novel Nanoproteomic Approach for the Identification of Molecular Targets Associated with Thyroid Tumors.Nanomaterials (Basel, Switzerland) · 2020Article
- Assessing Autophagy in Archived Tissue or How to Capture Autophagic Flux from a Tissue Snapshot.Biology · 2020Article
- Spatiotemporal Role of Transforming Growth Factor Beta 2 in Developing and Mature Mouse Hindbrain Serotonergic Neurons.Frontiers in cellular neuroscience · 2019Article
- Proteogenomic Analysis of Surgically Resected Lung Adenocarcinoma.Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer · 2018Article
- Lyophilized human cells stored at room temperature preserve multiple RNA species at excellent quality for RNA sequencing.Oncotarget · 2018Article
- Targeted Transcriptional Profiling of Kidney Transplant Biopsies.Kidney international reports · 2018Article
- Potential Value of Qiagen and PrepIT•MAX Kits in Extraction of Mycobacterial DNA From Presumptive Tuberculosis Archived Formalin-Fixed Paraffin-Embedded Tissues.The East African health research journal · 2018Article
- Aptahistochemistry in diagnostic pathology: technical scrutiny and feasibility.Histochemistry and cell biology · 2017Review
- Proteomic analysis of laser capture microdissected focal lesions in a rat model of progenitor marker-positive hepatocellular carcinoma.Oncotarget · 2017Article
- Immune cell profiling in cancer: molecular approaches to cell-specific identification.NPJ precision oncology · 2017Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Global mass spectrometry (MS) profiling and spectral count quantitation are used to identify unique or differentially expressed proteins and can help identify potential biomarkers. MS has rarely been conducted in retrospective studies, because historically, available samples for protein analyses were limited to formalin-fixed, paraffin-embedded (FFPE) archived tissue specimens. Reliable methods for obtaining proteomic profiles from FFPE samples are needed. Proteomic analysis of these samples has been confounded by formalin-induced protein cross-linking. The performance of extracted proteins in a liquid chromatography tandem MS format from FFPE samples and extracts from whole and laser capture microdissected (LCM) FFPE and frozen/optimal cutting temperature (OCT)-embedded matched control rat liver samples were compared. Extracts from FFPE and frozen/OCT-embedded livers from atorvastatin-treated rats were further compared to assess the performance of FFPE samples in identifying atorvastatin-regulated proteins. Comparable molecular mass representation was found in extracts from FFPE and OCT-frozen tissue sections, whereas protein yields were slightly less for the FFPE sample. The numbers of shared proteins identified indicated that robust proteomic representation from FFPE tissue and LCM did not negatively affect the number of identified proteins from either OCT-frozen or FFPE samples. Subcellular representation in FFPE samples was similar to OCT-frozen, with predominantly cytoplasmic proteins identified. Biologically relevant protein changes were detected in atorvastatin-treated FFPE liver samples, and selected atorvastatin-related proteins identified by MS were confirmed by Western blot analysis. These findings demonstrate that formalin fixation, paraffin processing, and LCM do not negatively impact protein quality and quantity as determined by MS and that FFPE samples are amenable to global proteomic analysis.
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