Development of Efficient Protein Extraction Methods for Shotgun Proteome Analysis of Formalin-Fixed Tissues

2007 ◽  
Vol 6 (3) ◽  
pp. 1038-1047 ◽  
Author(s):  
Xiaogang Jiang ◽  
Xinning Jiang ◽  
Shun Feng ◽  
Ruijun Tian ◽  
Mingliang Ye ◽  
...  
Keyword(s):  
Protein Extraction ◽  
Proteome Analysis ◽  
Extraction Methods ◽  
Formalin Fixed

Evaluation of protein extraction methods for in-depth proteome analysis of narrow-leafed lupin (Lupinus angustifolius) seeds

2021 ◽  
pp. 130722
Author(s):  
Arineh Tahmasian ◽  
James A. Broadbent ◽  
Angéla Juhász ◽  
Mitchell Nye-Wood ◽  
Thao T. Le ◽  
...  
Keyword(s):  
Protein Extraction ◽  
Proteome Analysis ◽  
Extraction Methods ◽  
Lupinus Angustifolius

Compatibility of plant protein extraction methods with mass spectrometry for proteome analysis

Plant Science ◽  
2009 ◽  
Vol 176 (1) ◽  
pp. 99-104 ◽  
Author(s):  
Inder S. Sheoran ◽  
Andrew R.S. Ross ◽  
Douglas J.H. Olson ◽  
Vipen K. Sawhney
Keyword(s):  
Mass Spectrometry ◽  
Protein Extraction ◽  
Proteome Analysis ◽  
Extraction Methods ◽  
Plant Protein

scholarly journals Proteome Analysis of Microdissected Formalin-fixed and Paraffin-embedded Tissue Specimens

2007 ◽  
Vol 55 (7) ◽  
pp. 763-772 ◽  
Author(s):  
Tong Guo ◽  
Weijie Wang ◽  
Paul A. Rudnick ◽  
Tao Song ◽  
Jie Li ◽  
...  
Keyword(s):  
Drug Targets ◽  
Protein Extraction ◽  
Proteome Analysis ◽  
Large Degree ◽  
Reversed Phase ◽  
Ffpe Tissue ◽  
Antigen Retrieval ◽  
Fresh Frozen ◽  
Tissue Specimens ◽  
Formalin Fixed

Targeted proteomics research, based on the enrichment of disease-relevant proteins from isolated cell populations selected from high-quality tissue specimens, offers great potential for the identification of diagnostic, prognostic, and predictive biological markers for use in the clinical setting and during preclinical testing and clinical trials, as well as for the discovery and validation of new protein drug targets. Formalin-fixed and paraffin-embedded (FFPE) tissue collections, with attached clinical and outcome information, are invaluable resources for conducting retrospective protein biomarker investigations and performing translational studies of cancer and other diseases. Combined capillary isoelectric focusing/nano-reversed-phase liquid chromatography separations equipped with nano-electrospray ionization-tandem mass spectrometry are employed for the studies of proteins extracted from microdissected FFPE glioblastoma tissues using a heat-induced antigen retrieval (AR) technique. A total of 14,478 distinct peptides are identified, leading to the identification of 2733 non-redundant SwissProt protein entries. Eighty-three percent of identified FFPE tissue proteins overlap with those obtained from the pellet fraction of fresh-frozen tissue of the same patient. This large degree of protein overlapping is attributed to the application of detergent-based protein extraction in both the cell pellet preparation protocol and the AR technique.

Evaluation of three types of protein extraction methods for tetraploid black locust (Robinia pseudoacacia L.) phloem tissue proteome analysis by two-dimensional electrophoresis

2015 ◽  
Vol 7 (3) ◽  
pp. 1008-1017 ◽  
Author(s):  
Sheng Zhang ◽  
Ling-Ling Zhang ◽  
Kai-Kai Zhou ◽  
Yu-Jing Liu ◽  
Zhong Zhao
Keyword(s):  
Protein Extraction ◽  
Robinia Pseudoacacia ◽  
Proteome Analysis ◽  
Extraction Methods ◽  
Two Dimensional ◽  
Phloem Tissue ◽  
Two Dimensional Gel Electrophoresis ◽  
Robinia Pseudoacacia L ◽  
Tetraploid Black Locust ◽  
Tissue Proteome

Sample preparation is a decisive step in a two-dimensional gel electrophoresis (2-DE) proteome approach and is essential for good experimental results.

Proteome Analysis of Formalin-Fixed Paraffin-Embedded Tissues from a Primary Gastric Melanoma and its Meningeal Metastasis: A Case Report

2014 ◽  
Vol 14 (3) ◽  
pp. 382-387 ◽  
Author(s):  
Juliana Fischer ◽  
Nathalie Canedo ◽  
Katia Goncalves ◽  
Leila Chimelli ◽  
Monique Franca ◽  
...  
Keyword(s):  
Case Report ◽  
Proteome Analysis ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

scholarly journals Optimization of Protein Extraction Method for 2DE Proteomics of Goat’s Milk

Molecules ◽  
2020 ◽  
Vol 25 (11) ◽  
pp. 2625
Author(s):  
Muzammeer Mansor ◽  
Jameel R. Al-Obaidi ◽  
Nurain Nadiah Jaafar ◽  
Intan Hakimah Ismail ◽  
Atiqah Farah Zakaria ◽  
...  
Keyword(s):  
Extraction Method ◽  
Protein Extraction ◽  
Chloroform Solution ◽  
Milk Proteins ◽  
Peptide Mass Fingerprinting ◽  
Extraction Methods ◽  
Dairy Goats ◽  
Goat’S Milk ◽  
Peptide Mass ◽  
Goat's Milk

Two-dimensional electrophoretic (2DE)-based proteomics remains a powerful tool for allergenomic analysis of goat’s milk but requires effective extraction of proteins to accurately profile the overall causative allergens. However, there are several current issues with goat’s milk allergenomic analysis, and among these are the absence of established standardized extraction method for goat’s milk proteomes and the complexity of goat’s milk matrix that may hamper the efficacy of protein extraction. This study aimed to evaluate the efficacies of three different protein extraction methods, qualitatively and quantitatively, for the 2DE-proteomics, using milk from two commercial dairy goats in Malaysia, Saanen, and Jamnapari. Goat’s milk samples from both breeds were extracted by using three different methods: a milk dilution in urea/thiourea based buffer (Method A), a triphasic separation protocol in methanol/chloroform solution (Method B), and a dilution in sulfite-based buffer (Method C). The efficacies of the extraction methods were assessed further by performing the protein concentration assay and 1D and 2D SDS-PAGE profiling, as well as identifying proteins by MALDI-TOF/TOF MS/MS. The results showed that method A recovered the highest amount of proteins (72.68% for Saanen and 71.25% for Jamnapari) and produced the highest number of protein spots (199 ± 16.1 and 267 ± 10.6 total spots for Saanen and Jamnapari, respectively) with superior gel resolution and minimal streaking. Six milk protein spots from both breeds were identified based on the positive peptide mass fingerprinting matches with ruminant milk proteins from public databases, using the Mascot software. These results attest to the fitness of the optimized protein extraction protocol, method A, for 2DE proteomic and future allergenomic analysis of the goat’s milk.

Comparison of Two Protein Extraction Methods for Tea Residues

2011 ◽  
Vol 138-139 ◽  
pp. 933-936 ◽  
Author(s):  
Xuan Chen ◽  
Hong Yu Luo ◽  
Jun Yu ◽  
Peng Xiang Yue ◽  
Lin Zhou ◽  
...  
Keyword(s):  
High Temperature ◽  
Protein Extraction ◽  
Ethanol Concentration ◽  
Extraction Methods ◽  
Extraction Yield ◽  
Factorial Experiments ◽  
Extraction Technology ◽  
Digestion Method ◽  
Solid Ratio ◽  
Lower Temperature

Alcohol-alkali method and base digestion method were investigated to extract proteins from tea residues, respectively. According to single factorial experiments, results showed that the optimal extraction technology of alcohol-alkali method were pH 12, temperature of 80 °C, ethanol concentration of 60%, liquid-solid ratio of 40, 60 min, and the protein extraction rate reached 15.0%. And the optimal extract conditions of base digestion were pH 12, temperature of 80 °C, liquid-solid ratio of 50, 80 min, which made the protein yield reached 31.5%. Furthermore, alcohol-alkali method was more beneficial to protein extraction from tea residues under lower temperature and weak alkali condition (40-60 °C, pH 8-10). While base digestion had higher extraction yield under high temperature and strong alkali condition (60-80 °C, pH 11-12).

scholarly journals Evaluation of effective protein extraction procedure to profile petiole of Moringa oleifera

2020 ◽  
Vol 7 (2) ◽  
pp. 214
Author(s):  
Zetty Amirah Zulkifli ◽  
Zaidah Rahmat
Keyword(s):  
Moringa Oleifera ◽  
Protein Extraction ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Extraction Procedure ◽  
Electrophoretic Pattern ◽  
Antioxidant Property ◽  
Extraction Methods ◽  
Protein Profiling ◽  
Sds Page

Moringa oleifera is widely known as multipurpose tree since all of its parts confer multiple functions. The leaf is highly favourable among consumers while the petiole is mostly wasted. There are numerous studies on the flavonoid and antioxidant property of the stem and twig. However, study on the petiole has never been done. There-upon, this study was conducted to develop protein profiling of the petiole. In this study, 6 different protein extraction methods were tested on the fresh petiole before its protein quantity and quality were checked via Bradford assay and Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE) respectively. The in-solution digestion was then done prior to LC-MS/MS analysis. The protein electrophoretic pattern from the SDS-PAGE proves that method 6 using Tris HCl buffer with incorporation of dithiothreitol (DTT) and phenylmethylsulfonyl fluoride (PMSF) confers the best quality of protein. It produced the highest number of visible individual bands compared to other methods. Meanwhile, 93 proteins were successfully identified via LCMS analysis where the protein, signal response and carbohydrate metabolism categories confer the highest percentage. High quality and content of the protein extracted from the petiole including the antioxidant, anticancer and antidiabetic protein identified suggested that consuming this part of the plant could enhance nutrients of human body.

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