Development and evaluation of an entirely solution-based combinative sample preparation method for membrane proteomics

Analytical Biochemistry

Volumn 432, Issue 1, 2013, Pages 41-48

  Lin, Yong ^a,b   Liu, Hui ^a   Liu, Zhonghua ^b   Liu, Yi ^a   He, Quanze ^a   Chen, Ping ^a   Wang, Xianchun ^a   Liang, Songping ^a  

^a HUNAN NORMAL UNIVERSITY   (China)

^b HUNAN AGRICULTURAL UNIVERSITY   (China)

Author keywords

Combinative method; LC MS MS; Membrane proteome; Sample preparation; Shotgun analysis

Indexed keywords

ACETONE; ACTIVATION ANALYSIS; HYDROPHOBICITY; MASS SPECTROMETRY; PEPTIDES; PRECIPITATION (CHEMICAL); PROTEOMICS; SODIUM DODECYL SULFATE; SULFUR COMPOUNDS;

COMBINATIVE METHOD; LC-MS/MS; MEMBRANE PROTEOME; SAMPLE PREPARATION; SHOTGUN ANALYSIS;

MEMBRANES;

ACETONE; DEOXYCHOLATE SODIUM; DODECYL SULFATE SODIUM; MEMBRANE PROTEIN;

ANIMAL TISSUE; ARTICLE; COMBINATIVE SAMPLE PREPARATION METHOD; EVALUATION; HYDROPHOBICITY; LIQUID CHROMATOGRAPHY; LIVER MEMBRANE; LYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEOMICS; RAT; SAMPLE; SOLUBILIZATION; TANDEM MASS SPECTROMETRY;

RATTUS;

EID: 84868219097     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2012.09.023     Document Type: Article

References (32)

1. J.R. Yates III, A. Gilchrist, K.E. Howell, and J.J. Bergeron Proteomics of organelles and large cellular structures Nat. Rev. Mol. Cell Biol. 6 2005 702 714 (Pubitemid 41742794)
2. J.S. Andersen, and M. Mann Organellar proteomics: turning inventories into insights EMBO Rep. 7 2006 874 879 (Pubitemid 44523965)
3. M.P. Washburn, D. Wolters, and J.R. Yates III Large-scale analysis of the yeast proteome by multidimensional protein identification technology Nat. Biotechnol. 19 2001 242 247 (Pubitemid 32220565)
4. C.C. Wu, M.J. MacCoss, K.E. Howell, and J.R. Yates III A method for the comprehensive proteomic analysis of membrane proteins Nat. Biotechnol. 21 2003 532 538 (Pubitemid 36532018)
5. E.I. Chen, D. McClatchy, S.K. Park, and J.R. Yates III Comparisons of mass spectrometry compatible surfactants for global analysis of the mammalian brain proteome Anal. Chem. 80 2008 8694 8701
6. N. Wang, L. MacKenzie, A.G. De Souza, H. Zhong, G. Goss, and L. Li Proteome profile of cytosolic component of zebrafish liver generated by LC-ESI MS/MS combined with trypsin digestion and microwave-assisted acid hydrolysis J. Proteome Res. 6 2007 263 272 (Pubitemid 46173678)
7. V. Santoni, M. Molloy, and T. Rabilloud Membrane proteins and proteomics: un amour impossible? Electrophoresis 21 2000 1054 1070 (Pubitemid 30230772)
8. Y.Q. Yu, M. Gilar, P.J. Lee, E.S.P. Bouvier, and J.C. Gebler Enzyme-friendly, mass spectrometry-compatible surfactant for in-solution enzymatic digestion of proteins Anal. Chem. 75 2003 6023 6028 (Pubitemid 37356487)
9. A. Bosserhoff, J. Wallach, and R.W. Frank Micropreparative separation of peptides derived from sodium dodecyl sulphate-solubilized proteins J. Chromatogr. A 473 1989 71 77 (Pubitemid 19170263)
10. Y. Lin, J. Zhou, D. Bi, P. Chen, X.C. Wang, and S.P. Liang Sodium-deoxycholate-assisted tryptic digestion and identification of proteolytically resistant proteins Anal. Biochem. 377 2008 259 266
11. X.N. Lu, and H.N. Zhu Tube-gel digestion: a novel proteomic approach for high throughput analysis of membrane proteins Mol. Cell. Proteomics 4 2005 1948 1958
12. H. Zischka, C.J. Gloeckner, C. Klein, S. Willmann, M. Swiatek-de Lange, and M. Ueffing Improved mass spectrometric identification of gel separated hydrophobic membrane proteins after sodium dodecyl sulfate removal by ion-pair extraction Proteomics 4 2004 3776 3782 (Pubitemid 39657455)
13. Y. Lin, Y. Liu, J.J. Li, Y. Zhao, Q.Z. He, W.J. Han, P. Chen, X.C. Wang, and S.P. Liang Evaluation and optimization of removal of an acid-insoluble surfactant for shotgun analysis of membrane proteome Electrophoresis 31 2010 2705 2713
14. T. Masuda, M. Tomita, and Y. Ishihama Phase transfer surfactant-aided trypsin digestion for membrane proteome analysis J. Proteome Res. 7 2008 731 740 (Pubitemid 351294035)
15. C.S. Kadiyala, S.E. Tomechko, and M. Miyagi Perfluorooctanoic acid for shotgun proteomics PLoS One 5 2010 e15332
16. L.Y. Zhu, and J.H. Lin Pollution trend and environmental behavior of perfluorooctanoic acid: a review Chin. J. Appl. Ecol. 19 2008 1149 1157
17. A.B. Lindstrom, M.J. Strynar, and E.L. Libelo Polyfluorinated compounds: past, present, and future Environ. Sci. Technol. 45 2011 7954 7961
18. D. Botelho, M.J. Wall, D.B. Vieira, S. Fitzsimmons, F. Liu, and A. Doucette Top-down and bottom-up proteomics of SDS-containing solutions following mass-based separation J. Proteome Res. 9 2010 2863 2870
19. R. Cao, Q.Y. He, J. Zhou, Q.Z. He, Z. Liu, X.C. Wang, P. Chen, J.Y. Xie, and S.P. Liang High-throughput analysis of rat liver plasma membrane proteome by a nonelectrophoretic in-gel tryptic digestion coupled with mass spectrometry identification J. Proteome Res. 7 2008 535 545 (Pubitemid 351294016)
20. Y. Lin, Y. Li, Y. Liu, W.J. Han, Q.Z. He, J.L. Li, P. Chen, X.C. Wang, and S.P. Liang Improvement of gel-separated protein identification by DMF-assisted digestion and peptide recovery after electroblotting Electrophoresis 30 2009 3626 3635
21. J.L. Luque-Garcia, G. Zhou, T.T. Sun, and T.A. Neubert Use of nitrocellulose membranes for protein characterization by matrix-assisted laser desorption/ionization mass spectrometry Anal. Chem. 78 2006 5102 5108 (Pubitemid 44100647)
22. Y. Liu, Y. Lin, Y.Z. Yan, J.J. Li, Q.Z. He, P. Chen, X.C. Wang, and S.P. Liang Electrophoretically driven SDS removal and protein fractionation in the shotgun analysis of membrane proteomes Electrophoresis 33 2012 316 324
23. T.K. Ray A modified method for the isolation of the plasma membrane from rat liver Biochim. Biophys. Acta 196 1970 1 9
24. F. Rusconi, E. Valton, R. Nguyen, and E. Dufourc Quantification of sodium dodecyl sulfate in microliter-volume biochemical samples by visible light spectroscopy Anal. Biochem. 295 2001 31 37 (Pubitemid 32721737)
25. U.K. Laemmli Cleavage of structural proteins during the assembly of the head of bacteriophage T4 Nature 227 1970 680 685
26. J. Zhou, T.Y. Zhou, R. Cao, Z. Liu, J.Y. Shen, P. Chen, X.C. Wang, and S.P. Liang Evaluation of the application of sodium deoxycholate to proteomic analysis of rat hippocampal plasma membrane J. Proteome Res. 5 2006 2547 2553 (Pubitemid 44595157)
27. J.E. Elias, and S.P. Gygi Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry Nat. Methods 4 2007 207 214 (Pubitemid 46358868)
28. M. Ashburner, C.A. Ball, J.A. Blake, D. Botstein, H. Butler, J.M. Cherry, A.P. Davis, K. Dolinski, S.S. Dwight, J.T. Eppig, M.A. Harris, D.P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J.C. Matese, J.E. Richardson, M. Ringwald, G.M. Rubin, and G. Sherlock Gene ontology: tool for the unification of biology - the Gene Ontology Consortium Nat. Genet. 25 2000 25 29 (Pubitemid 30257031)
29. A. Krogh, B. Larsson, G. von Heijne, and E.L. Sonnhammer Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes J. Mol. Biol. 305 2001 567 580 (Pubitemid 33032862)
30. J. Kyte, and R.F. Doolittle A simple method for displaying the hydropathic character of a protein J. Mol. Biol. 157 1982 105 132
31. S.J. Johns, TOPO2, transmembrane protein display software. < http://www.sacs.ucsf.edu/TOPO2 >, 2005.
32. L.A. Eichacker, B. Granvogl, O. Mirus, B.C. Muller, C. Miess, and E. Schleiff Hiding behind hydrophobicity: transmembrane segments in mass spectrometry J. Biol. Chem. 279 2004 50915 50922 (Pubitemid 40017830)