scholarly journals Improved protein extraction and protein identification from archival formalin-fixed paraffin-embedded human aortas

2013 ◽  
Vol 7 (3-4) ◽  
pp. 217-224 ◽  
Author(s):  
Zongming Fu ◽  
Kun Yan ◽  
Avraham Rosenberg ◽  
Zhicheng Jin ◽  
Barbara Crain ◽  
...  
Keyword(s):  
Protein Identification ◽  
Protein Extraction ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

LysargiNase enhances protein identification on the basis of trypsin on formalin‐fixed paraffin‐embedded samples

2019 ◽  
Vol 33 (17) ◽  
pp. 1381-1389 ◽  
Author(s):  
Shu Liu ◽  
Feng Xu ◽  
Yanan Yin ◽  
Junling Zhang ◽  
Fuqiang Wang ◽  
...  
Keyword(s):  
Protein Identification ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

scholarly journals Extraction and Analysis of Diagnostically Useful Proteins from Formalin-fixed, Paraffin-embedded Tissue Sections

1998 ◽  
Vol 46 (3) ◽  
pp. 397-403 ◽  
Author(s):  
Kimimasa Ikeda ◽  
Takushi Monden ◽  
Toshiyuki Kanoh ◽  
Masaki Tsujie ◽  
Hikaru Izawa ◽  
...  
Keyword(s):  
Western Blot ◽  
Cyclin D1 ◽  
Blot Analysis ◽  
Western Blot Analysis ◽  
Protein Extraction ◽  
Simple Method ◽  
Tissue Sections ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

We describe and discuss a method of protein extraction for Western blot analysis from formalin-fixed, paraffin-embedded tissue sections. From 5-mm2 50-μm-thick tissue sections, an abundance of proteins could be extracted by incubating the sections in lysis buffer containing 2% sodium dodecyl sulfate (SDS) at 100C for 20 min followed by incubation at 60C for 2 hr. Extracts yielded discernible protein bands ranging from 10 kD to 120 kD as identified by SDS-polyacrylamide gel electrophoresis (PAGE). Western blot analysis successfully detected membrane-bound protein such as E-cadherin, cytosolic protein such as β-catenin, and nuclear proteins including proliferating cell nuclear antigen (PCNA), mutant-type p53, cyclin D1, cyclin E, and cyclin-dependent kinases (CDKs). With this technique, we could examine cyclin D1 and CDK2 expression in small adenomas compared with cancer tissues and normal mucosa. The simple method of protein extraction described here should make it possible to use large-scale archives of formalin-fixed, paraffin-embedded samples for Western blot analysis, and its application could lead to detailed analysis of protein expression. This new technique should yield valuable information for molecular biology.

scholarly journals HYPERsol: flash-frozen results from archival FFPE tissue for clinical proteomics

2019 ◽  
Author(s):  
Dylan M. Marchione ◽  
Ilyana Ilieva ◽  
Benjamin A. Garcia ◽  
Darryl J. Pappin ◽  
John P. Wilson ◽  
...  
Keyword(s):  
Protein Extraction ◽  
Ffpe Tissue ◽  
Clinical Proteomics ◽  
High Yield ◽  
Proteome Coverage ◽  
Formalin Fixed Paraffin ◽  
Ffpe Samples ◽  
Formalin Fixed Paraffin Embedded ◽  
Proteomics Research ◽  
Formalin Fixed

Massive formalin-fixed, paraffin-embedded (FFPE) tissue archives exist worldwide, representing a potential gold mine for clinical proteomics research. However, current protocols for FFPE proteomics lack standardization, efficiency, reproducibility, and scalability. Here we present High-Yield Protein Extraction and Recovery by direct SOLubilization (HYPERsol), an optimized workflow using adaptive-focused acoustics (AFA) ultrasonication and S-Trap sample processing that enables proteome coverage and quantification from FFPE samples comparable to that achieved from flash-frozen tissue (average R = 0.936).

Antibody validation by combining immunohistochemistry and protein extraction from formalin-fixed paraffin-embedded tissues

2012 ◽  
Vol 60 (6B) ◽  
pp. E37-E50 ◽  
Author(s):  
Claudia Schuster ◽  
Katharina Malinowsky ◽  
Sibylle Liebmann ◽  
Daniela Berg ◽  
Claudia Wolff ◽  
...  
Keyword(s):  
Protein Extraction ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Antibody Validation ◽  
Formalin Fixed

scholarly journals A novel procedure for protein extraction from formalin-fixed paraffin-embedded tissues

PROTEOMICS ◽  
2011 ◽  
Vol 11 (12) ◽  
pp. 2555-2559 ◽  
Author(s):  
Teresa Rodríguez-Rigueiro ◽  
Manuel Valladares-Ayerbes ◽  
Mar Haz-Conde ◽  
Moisés Blanco ◽  
Guadalupe Aparicio ◽  
...  
Keyword(s):  
Protein Extraction ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

scholarly journals Optimization of Urea Based Protein Extraction from Formalin-Fixed Paraffin-Embedded Tissue for Shotgun Proteomics

2016 ◽  
Vol 2016 ◽  
pp. 1-6 ◽  
Author(s):  
Stephen A. Luebker ◽  
Scott A. Koepsell
Keyword(s):  
Proteomic Analysis ◽  
Protein Extraction ◽  
Protein Detection ◽  
Ffpe Tissue ◽  
Extraction Temperature ◽  
Esi Ms ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Buffer Composition ◽  
Formalin Fixed

Urea based protein extraction of formalin-fixed paraffin-embedded (FFPE) tissue provides the most efficient workflow for proteomics due to its compatibility with liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). This study optimizes the use of urea for proteomic analysis of clinical FFPE tissue. A series of protein extraction conditions manipulating temperature and buffer composition were compared to reduce carbamylation introduced by urea and increase protein detection. Each extraction was performed on a randomized pair of serial sections of homogenous FFPE tissue and analyzed with LC-ESI-MS/MS. Results were compared in terms of yield, missed cleavages, and peptide carbamylation. Lowering extraction temperature to 60°C decreased carbamylation at the cost of decreased protein detection and yield. Protein extraction for at least 20 minutes at 95°C followed by 60°C for 2 hours maximized total protein yield while maintaining protein detection and reducing carbamylation by 7.9%. When accounting for carbamylation during analysis, this modified extraction temperature provides equivalent peptide and protein detection relative to the commercially available Qproteome® FFPE Tissue Kit. No changes to buffer composition containing 7 M urea, 2 M thiourea, and 1 M ammonium bicarbonate resulted in improvements to control conditions. Optimized urea in-solution digestion provides an efficient workflow with maximized yields for proteomic analysis of clinically relevant FFPE tissue.

scholarly journals A novel procedure for protein extraction from formalin-fixed paraffin-embedded tissues

2011 ◽  
Vol 5 (9-10) ◽  
pp. 570-570
Author(s):  
Teresa Rodríguez-Rigueiro ◽  
Manuel Valladares-Ayerbes ◽  
Mar Haz-Conde ◽  
Moisés Blanco ◽  
Guadalupe Aparicio ◽  
...  
Keyword(s):  
Protein Extraction ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed
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