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LIU FJ, YE ML, PAN YB, ZOU HF. High Concentration Trypsin Assisted Fast In-Gel Digestion for Phosphoproteome Analysis. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2015. [DOI: 10.1016/s1872-2040(15)60864-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Lin Y, Wang K, Liu Z, Lin H, Yu L. Enhanced SDC-assisted digestion coupled with lipid chromatography-tandem mass spectrometry for shotgun analysis of membrane proteome. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1002:144-51. [PMID: 26319803 DOI: 10.1016/j.jchromb.2015.08.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 07/07/2015] [Accepted: 08/14/2015] [Indexed: 01/09/2023]
Abstract
Despite the biological importance of membrane proteins, their analysis has lagged behind that of soluble proteins and still presents a great challenge mainly because of their highly hydrophobic nature and low abundance. Sodium deoxycholate (SDC)-assisted digestion strategy has been introduced in our previous papers, which cleverly circumvents many of the challenges in shotgun membrane proteomics. However, it is associated with significant sample loss due to the slightly weaker extraction/solubilization ability of 1% SDC. In this study, an enhanced SDC-assisted digestion method (ESDC method) was developed that incorporates the almost strongest ability of SDC with a high concentration (5%) to lyse membrane and extract/solubilize hydrophobic membrane proteins, and then dilution to 1% for more efficient digestion. The comparative study using rat liver membrane-enriched sample showed that, compared with previous SDC-assisted method and the "universal" filter-aided sample preparation (FASP) method, the ESDC method not only increased the identified number of total proteins, membrane proteins, hydrophobic proteins, integral membrane proteins (IMPs) and IMPs with more than 5 transmembrane domains (TMDs) by an average of 10.8%, 13.2%, 17.8%, 17.9% and 52.9%, respectively, but also enhanced the identified number of total peptides and hydrophobic peptides by averagely 12.5% and 14.2%. These results demonstrated that the ESDC method provides a substantial improvement in the recovery and identification of membrane proteins, especially those with high hydrophobicity and multiple TMDs, and thereby displaying more potential for shotgun membrane proteomics.
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Affiliation(s)
- Yong Lin
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China; Hunan Collaborative Innovation Center for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha 410128, PR China.
| | - Kunbo Wang
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China; Key Laboratory of Tea Science of Ministry of Education, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China
| | - Zhonghua Liu
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China; Key Laboratory of Tea Science of Ministry of Education, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China; Hunan Collaborative Innovation Center for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha 410128, PR China.
| | - Haiyan Lin
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China
| | - Lijun Yu
- Key Laboratory of Tea Science of Ministry of Education, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China
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Liu Z, Lin Y, Zhang S, Wang D, Liang Q, Luo G. Comparative proteomic analysis using 2DE-LC-MS/MS reveals the mechanism of Fuzhuan brick tea extract against hepatic fat accumulation in rats with nonalcoholic fatty liver disease. Electrophoresis 2015; 36:2002-16. [DOI: 10.1002/elps.201500076] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Revised: 04/14/2015] [Accepted: 05/11/2015] [Indexed: 01/10/2023]
Affiliation(s)
- Zhonghua Liu
- Department of Chemistry of Tsinghua University and Key Laboratory of Biological Organic Phosphorus and Chemical Biology of Ministry of Education; Beijing P. R. China
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
- Key Laboratory of Tea Science of Ministry of Education, College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
| | - Yong Lin
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
| | - Sheng Zhang
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
| | - Die Wang
- Key Laboratory of Tea Science of Ministry of Education, College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
| | - Qionglin Liang
- Department of Chemistry of Tsinghua University and Key Laboratory of Biological Organic Phosphorus and Chemical Biology of Ministry of Education; Beijing P. R. China
| | - Guoan Luo
- Department of Chemistry of Tsinghua University and Key Laboratory of Biological Organic Phosphorus and Chemical Biology of Ministry of Education; Beijing P. R. China
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Lin Y, Lin H, Liu Z, Wang K, Yan Y. Improvement of a sample preparation method assisted by sodium deoxycholate for mass-spectrometry-based shotgun membrane proteomics†. J Sep Sci 2014; 37:3321-9. [DOI: 10.1002/jssc.201400569] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 08/18/2014] [Accepted: 08/24/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Yong Lin
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P.R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P.R. China
| | - Haiyan Lin
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P.R. China
| | - Zhonghua Liu
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P.R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P.R. China
| | - Kunbo Wang
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P.R. China
| | - Yujun Yan
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P.R. China
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Lin Y, Wang K, Yan Y, Lin H, Peng B, Liu Z. Evaluation of the combinative application of SDS and sodium deoxycholate to the LC-MS-based shotgun analysis of membrane proteomes. J Sep Sci 2013; 36:3026-34. [DOI: 10.1002/jssc.201300413] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 06/06/2013] [Accepted: 06/21/2013] [Indexed: 12/17/2022]
Affiliation(s)
- Yong Lin
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
| | - Kunbo Wang
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
| | - Yujun Yan
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
| | - Haiyan Lin
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
| | - Bin Peng
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
| | - Zhonghua Liu
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
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Liu F, Ye M, Wang C, Hu Z, Zhang Y, Qin H, Cheng K, Zou H. Polyacrylamide Gel with Switchable Trypsin Activity for Analysis of Proteins. Anal Chem 2013; 85:7024-8. [DOI: 10.1021/ac4017693] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Fangjie Liu
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingliang Ye
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chunli Wang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengyan Hu
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongqiang Qin
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Cheng
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanfa Zou
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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Lin Y, Liu H, Liu Z, Liu Y, He Q, Chen P, Wang X, Liang S. Development and evaluation of an entirely solution-based combinative sample preparation method for membrane proteomics. Anal Biochem 2013; 432:41-8. [DOI: 10.1016/j.ab.2012.09.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 08/31/2012] [Accepted: 09/17/2012] [Indexed: 10/27/2022]
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Lin Y, Jiang H, Yan Y, Peng B, Chen J, Lin H, Liu Z. Shotgun analysis of membrane proteomes by an improved SDS-assisted sample preparation method coupled with liquid chromatography–tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 911:6-14. [DOI: 10.1016/j.jchromb.2012.10.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 10/14/2012] [Accepted: 10/15/2012] [Indexed: 10/27/2022]
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Wang X, Liang S. Sample preparation for the analysis of membrane proteomes by mass spectrometry. Protein Cell 2012; 3:661-8. [PMID: 22926766 DOI: 10.1007/s13238-012-2062-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 07/18/2012] [Indexed: 11/27/2022] Open
Abstract
The low abundance and highly hydrophobic nature of most membrane proteins make their analysis more difficult than that for common soluble proteins. Successful membrane protein identification is largely dependent on the sample preparation including the enrichment and dissolution of the membrane proteins. A series of conventional and newly developed methods has been applied to the enrichment of low-abundance membrane proteins at membrane and/or protein levels and to the dissolution of hydrophobic membrane proteins. However, all the existing methods have inherent advantages and limitations. Up to now, there has been no unique method that can universally be employed to solve all the problems and more efforts are needed in improving sample preparation for the analysis of membrane proteomes.
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Affiliation(s)
- Xianchun Wang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
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Lin Y, Liu H, Liu Z, Wang X, Liang S. Shotgun analysis of membrane proteomes using a novel combinative strategy of solution-based sample preparation coupled with liquid chromatography-tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 901:18-24. [PMID: 22721709 DOI: 10.1016/j.jchromb.2012.05.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 05/28/2012] [Accepted: 05/29/2012] [Indexed: 11/30/2022]
Abstract
Although much effort has been made in the field of membrane proteomics, the analysis of membrane proteins particularly integral membrane proteins with poor water solubility still presents a great challenge. In this paper, 2% SDS was used to extract membrane proteins and experimental conditions for the application of acetone precipitation method to the cleanup of SDS-solubilized membrane protein sample were optimized. For improving the re-dissolution and trypsinolysis of acetone-precipitated proteins, several commonly used additives, urea, methanol and sodium deoxycholate (SDC), were employed and compared. The results showed that, when the pre-cooled acetone-to-sample ratio was 6:1 (v/v) with one additional washing step, residual SDS in the protein sample could be lowered to below 0.01% and more than 90% of the proteins were precipitated and therefore recovered. 1% SDC-containing buffer could improve the re-dissolution and digestion of the acetone precipitated proteins more efficiently than the others. Using the combinative sample preparation strategy developed, 398 proteins were identified from the rat liver membrane-enriched fraction, including 188 membrane proteins. Compared with other three representative solution-based sample preparation methods commonly used in membrane proteomics, the newly developed combinative strategy increased the number of identified total proteins and membrane proteins on average by 29.2% and 28.5%, respectively. This combinative strategy was demonstrated to be easily operated at low cost and suitable for the analysis of membrane proteins varying in type and sample volume, etc.
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Affiliation(s)
- Yong Lin
- Key Laboratory of Protein Chemistry and Developmental Biology of National Education Committee, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, PR China
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11
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Liu Y, Lin Y, Yan Y, Li J, He Q, Chen P, Wang X, Liang S. Electrophoretically driven SDS removal and protein fractionation in the shotgun analysis of membrane proteomes. Electrophoresis 2012; 33:316-24. [PMID: 22222976 DOI: 10.1002/elps.201100364] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yi Liu
- Key Laboratory of Protein Chemistry and Developmental Biology of National Education Committee, College of Life Sciences, Hunan Normal University, Changsha, P. R. China
| | - Yong Lin
- Key Laboratory of Protein Chemistry and Developmental Biology of National Education Committee, College of Life Sciences, Hunan Normal University, Changsha, P. R. China
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients, College of Horticulture and Landscape, Hunan Agricultural University, Changsha, P. R. China
| | - Yizhong Yan
- Key Laboratory of Protein Chemistry and Developmental Biology of National Education Committee, College of Life Sciences, Hunan Normal University, Changsha, P. R. China
| | - Jianjun Li
- Key Laboratory of Protein Chemistry and Developmental Biology of National Education Committee, College of Life Sciences, Hunan Normal University, Changsha, P. R. China
| | - Quanze He
- Key Laboratory of Protein Chemistry and Developmental Biology of National Education Committee, College of Life Sciences, Hunan Normal University, Changsha, P. R. China
| | - Ping Chen
- Key Laboratory of Protein Chemistry and Developmental Biology of National Education Committee, College of Life Sciences, Hunan Normal University, Changsha, P. R. China
| | - Xianchun Wang
- Key Laboratory of Protein Chemistry and Developmental Biology of National Education Committee, College of Life Sciences, Hunan Normal University, Changsha, P. R. China
| | - Songping Liang
- Key Laboratory of Protein Chemistry and Developmental Biology of National Education Committee, College of Life Sciences, Hunan Normal University, Changsha, P. R. China
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Zhou J, Li J, Li J, Chen P, Wang X, Liang S. Dried polyacrylamide gel absorption: a method for efficient elimination of the interferences from SDS-solubilized protein samples in mass spectrometry-based proteome analysis. Electrophoresis 2011; 31:3816-22. [PMID: 21064138 DOI: 10.1002/elps.201000255] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Sample preparation holds an important place in MS-based proteome analysis. For effective proteolysis and MS analysis, it is essential to eliminate the interferences while extracting the analytes of interest from complex mixtures. To address this, herein we describe a new dried polyacrylamide gel absorption method. In this method, the protein sample prepared using high concentration of SDS was directly and completely absorbed by vacuum-dried polyacrylamide gel, and then the interfering substances including SDS and some other salts were efficiently removed by in-gel washing steps while retaining the denatured proteins in the gel, thus offering a clean environment amenable to downstream buffer exchange, proteolytic digestion and digest recovery, etc. In combination with in-gel digestion and LC-MS/MS, the newly developed method was applied to the proteome analyses of membrane-enriched fraction and whole tissue homogenate. It was demonstrated that the method is suitable for the analysis of a complex biological sample and can be widely used for sample cleanup in shotgun proteome analyses.
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Affiliation(s)
- Jian Zhou
- The Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, PR China
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Welinder C, Ekblad L. Coomassie Staining as Loading Control in Western Blot Analysis. J Proteome Res 2011; 10:1416-9. [DOI: 10.1021/pr1011476] [Citation(s) in RCA: 352] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Lars Ekblad
- Department of Oncology, Clinical Sciences, Lund University, Sweden
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Lin Y, Liu Y, Li J, Zhao Y, He Q, Han W, Chen P, Wang X, Liang S. Evaluation and optimization of removal of an acid-insoluble surfactant for shotgun analysis of membrane proteome. Electrophoresis 2010; 31:2705-2713. [PMID: 20665523 DOI: 10.1002/elps.201000161] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Due to its compatibility with protease activity at high concentration, sodium deoxycholate (SDC) can be used to effectively improve the solubilization and enzymolysis of membrane proteins and has received increasing attention in the field of membrane proteome analysis in recent years. SDC can be removed from digests by means of acidification followed by centrifugation (i.e. acid precipitation, AP) or extraction with ethyl acetate (i.e. phase transfer, PT) so as not to interfere with the downstream analyses like LC-MS/MS. In this study, the two strategies were systematically evaluated, compared and optimized. The results of the study demonstrated that both of the AP and PT strategies led to a certain amount of tryptic peptides being lost, and in PT strategy even more peptides were lost during SDC removal process. However, the lost peptides could be mostly recovered by washing the pellet and solid content produced during AP and PT, respectively. By recovering the lost peptides, the identification efficiency of proteins, especially transmembrane and low abundance ones, was significantly improved. Comparatively, after optimization by recovering the lost peptides, AP strategy was superior to PT strategy because the former not only could achieve the comparable identification efficiency with the latter but also was more economical, safer and easier to operate than the latter.
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Affiliation(s)
- Yong Lin
- Key Laboratory of Protein Chemistry and Developmental Biology of National Education Committee, College of Life Sciences, Hunan Normal University, Changsha, P. R. China
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