Evaluation of sample extraction methods for proteomic analysis of coniferous seeds

Zhen, Yan; Shi, Jisen

doi:10.1007/s11738-010-0697-1

Cited by 13 publications

(13 citation statements)

References 20 publications

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“…Then, TCA-acetone was used for protein precipitation, and ice-cold acetone was used to wash the protein pellet. This nding is similar to those of previous reports on coniferous seeds, 36 although it is not exactly the same compared with reports on banana 8 and tomato pollen. The proper extension of the extraction time and increase in the volume of leaching solution will help to enhance the output of proteins.…”

Section: Resultssupporting

confidence: 90%

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

Zhang

Zhou

et al. 2015

Anal. Methods

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Sample preparation is a decisive step in a two-dimensional gel electrophoresis (2-DE) proteome approach and is essential for good experimental results. For recalcitrant plant tissues, choosing a suitable protein extraction method is very important for follow-up research. Many articles about protein extraction methods have been published that have mainly focused on plant leaves, fruits, and seeds, whereas few of them have evaluated protein extraction methods using phloem tissue. This study was performed to compare three precipitation protocols for protein extraction for 2-DE proteomics analysis of tetraploid black locust phloem tissue as follows: TCA/acetone precipitation, Tris-HCl extraction, and phenol extraction-ammonium acetate/methanol precipitation. The results showed that classic TCA/acetone precipitation was the most effective method for protein extraction. Compared to the Tris-HCl and phenol extraction methods, TCA/acetone precipitation had the highest total protein yield and the greatest number of protein spots on the 2-DE gels. To verify the quality of the 2-DE analysis, several gel spots were identified by MALDI TOF/TOF MS/MS. These data demonstrated the characteristic features of each extraction protocol. In conclusion, the TCA/acetone precipitation extraction method is suitable for proteomic analyses of recalcitrant tissues from woody plants.

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Section: Resultssupporting

confidence: 90%

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

Zhang

Zhou

et al. 2015

Anal. Methods

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“…Over the last few decades, rapid advancements in high-resolution protein separation, mass spectrometry techniques and bioinformatics knowledge have led to an increasing application of proteomics to elucidate the underlying biology mechanisms [1]. Now, proteomics approaches 3 integrated two-dimensional electrophoresis (2-DE) with mass spectrometry (MS) has still proved to be the predominant technique [2][3][4][5][6][7][8], which was widely used in comparative proteomics studies, posttranslational modifications and protein interaction network analysis [9][10][11].…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…The perfect protocol of protein extraction should reproducibly capture all most unprejudiced and comprehensive proteins from various tissues of different species while reducing contamination and minimizing degradation and modification. However, considering the diversity and specificity of sample tissues or species, no general and high-efficiency extraction protocol can capture the full proteome [1,10,11]. To date, tremendous efforts are more devoted to developing sample preparation protocols that could enhance plant proteomic analysis [14][15][16][17].Nevertheless, plant proteomics analysis remains to be more troublesome challenges that are associated with large amounts of co-extraction of non-protein constituents, and comprehensive proteins are notoriously difficult to extract from plants, mostly due to having relatively low protein content and interfering compounds such as phenolic compounds, lipids, polysaccharides, proteolytic enzymes, oxidative enzymes and other secondary materials [18][19][20][21][22].Currently, several reviews related to protein sample preparation have been published [23,24].…”

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confidence: 99%

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Evaluation of six different protocols for protein extraction from rice young panicles by two-dimensional electrophoresis

Huang

Zhou

2020

Preprint

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Background: For most reported proteomics approaches, protein extraction are of crucial importance for optimal results. However, extraction of protein from plant tissues still exist great challenges due to low protein content and many secondary metabolites that prominently interfering with isoelectric focusing. Up to now, no attempts are focused on comparison of protein extraction from rice young panicles.Methods: To establish a higher efficiency protein extraction protocol suited for two-dimensional electrophoresis in rice young panicles, six protocols for protein preparation were evaluated in terms of protein concentration, the molecular weight range of protein, gel image resolution, the number of protein spots: 1) Phenol extraction; 2) Mg/Nonidet P-40 (NP-40) extraction; 3) Tris-Base/acetone extraction; 4) SDS extraction; 5) trichloroacetic acid (TCA)/acetone/phenol extraction; 6) TCA/acetone precipitation.Results: The result explicitly demonstrated that TCA/acetone/phenol method provided a high-enhanced protein extraction efficacy from rice young panicles than other protocols in terms of the protein concentration (9.79±0.23 SD), the most comprehensive proteins (10 KDa to 150 KDa), the maximum number of protein spots (450±53 SD), the greater gel image resolution and spot abundance. In addition, these methods also generated remarkably differential 2-DE protein patterns. Twenty-nine of 30 visible differentially extracted proteins were identified by MS analysis and were divided into eight categories. Prediction for protein subcellular localization and grand average of hydropathy (GRAVY) analysis showed that certain special proteins respectively necessitate different extraction methods due to different physicochemical properties of each protocol.Conclusions: Overall, this paper will facilitate to provide a cornerstone of comparative proteomic analysis from rice young panicles, including other complicated plant tissues.

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“…Some researchers also demonstrated that trichloroacetic acid−acetone (TCA−acetone) precipitation gave the highest yield of total protein and the greatest number of protein spots for the following two-dimensional gel electrophoresis (2-DE) analysis. 10 However, protein functional properties are greatly dependent upon their preparation processes, which may affect protein structure along with amino acid composition. For example, protein three-dimensional (3D) structures as well as protein functionalities undergo a significant change during isoelectric precipitation.…”

Section: ■ Introductionmentioning

confidence: 99%

Functional Properties of Protein Isolates from Caragana korshinskii Kom. Extracted by Three Different Methods

Zhong

Rui²,

Zhou³

et al. 2012

J. Agric. Food Chem.

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Seeking cheap, sustainable protein sources greatly facilitates in alleviating the dependence upon expensive animal-based protein in many developing countries. Caragana korshinskii Kom. offers a good alternative feedstock because of its high-content of protein, low fertilizer and pesticide requirements, excellent stress (high salty and less water) tolerance, wide adaptability, etc. The functional properties of C. korshinskii Kom. protein isolates by three different extraction methods were investigated. The extraction processes greatly influenced the physiological characteristics of protein isolates. C. korshinskii Kom. protein isolate by traditional alkaline extraction (Al-CPI) exhibited good performance on emulsifying activity index, oil and water absorption capacity, and foaming property compared to A-CPI ( C. korshinskii Kom. protein isolate by the acetone precipitation method) and TCA-CPI ( C. korshinskii Kom. protein isolate by trichloroacetic acid-acetone precipitation). The water and oil adsorption capacities of Al-CPI were observed at 4.99 and 3.45 g/g, respectively, even much higher than those of soy protein isolate (SPI) (3.94 and 2.95 g/g, respectively). The highest foaming capacity was observed by Al-CPI at 185.0%, followed by A-CPI (177.5%), TCA-CPI (142.5%), and SPI (141.9%), respectively. It has to be noted that A-CPI showed good solubility at acidic pH and excellent in vitro digestibility. After sequential pepsin-trypsin digestion, the percentage of N release of A-CPI reached up to 83.7%, which was 1.63 times that of Al-CPI (51.2%), 1.19 times that of TCA-CPI (70.1%), and slightly higher than that of the commercial SPI (82.5%). These results indicate that C. korshinskii Kom. holds great potential for application in the animal feed and food additive industry.

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Evaluation of sample extraction methods for proteomic analysis of coniferous seeds

Cited by 13 publications

References 20 publications

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

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

Evaluation of six different protocols for protein extraction from rice young panicles by two-dimensional electrophoresis

Functional Properties of Protein Isolates from Caragana korshinskii Kom. Extracted by Three Different Methods

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