PL EN


Preferences help
enabled [disable] Abstract
Number of results
2013 | 1 | 28-37
Article title

A sample preparation method for micro-scale membrane
proteome analysis

Content
Title variants
Languages of publication
EN
Abstracts
EN
Detergents are widely used to improve the solubilization and extraction of
hydrophobic membrane proteins in proteomics. Since most detergents
are not compatible with subsequent steps of analysis, the removal of
detergents from samples, especially those in micro-scale amounts,
is a worthy topic of investigation. In this paper, we present a novel
polyvinylidene difluoride (PVDF) membrane-mediated sample preparation
method for micro-scale membrane proteome analysis, using a rat liver
cell membrane-enriched fraction as model material. The proteins in the
fraction were extracted in a 2 % sodium dodecyl sulfate (SDS) solution and
the protein solution was applied on a piece of PVDF membrane followed
by drying and repeated washing in order to remove SDS and other salts.
Quantitative determination indicated that about 84% of the SDS in the
sample was removed and protein loss was less than 10%. Four methods
were used and compared for digesting the proteins adsorbed on PVDF
membrane. Dimethyl formamide (DMF)-assisted digestion was the most
effective with regard to the identification of membrane proteins, particularly
the highly hydrophobic multi-transmembrane proteins. These results
demonstrate that PVDF membrane-aided sample cleanup combined with
DMF-assisted digestion has potential utility in the micro-scale membrane
proteome analysis.
Publisher

Year
Volume
1
Pages
28-37
Physical description
Dates
received
09 - 2 - 2013
online
22 - 11 - 2013
accepted
24 - 08 - 2013
Contributors
author
  • Key Laboratory of Protein Chemistry
    and Developmental Biology of National
    Education Committee, College of Life
    Sciences, Hunan Normal University,
    Changsha, 410081, P. R. China
author
  • Key Laboratory of Protein Chemistry
    and Developmental Biology of National
    Education Committee, College of Life
    Sciences, Hunan Normal University,
    Changsha, 410081, P. R. China
author
  • Key Laboratory of Protein Chemistry
    and Developmental Biology of National
    Education Committee, College of Life
    Sciences, Hunan Normal University,
    Changsha, 410081, P. R. China
author
  • Key Laboratory of Protein Chemistry
    and Developmental Biology of National
    Education Committee, College of Life
    Sciences, Hunan Normal University,
    Changsha, 410081, P. R. China, wang_xianchun@263.net
References
  • [1] Blonder J., Goshe M.B., Moore R.J, Pasa-Tolic L., Masselon C.D.,Lipton M.S, et al., Enrichment of integral membrane proteins forproteomic analysis using liquid chromatography-tandem massspectrometry, J. Proteome Res., 2002, 1, 351-360.
  • [2] McCarthy F.M., Burgess S.C., van den Berg B.H, KoterM.D., Pharr G.T., Differential detergent fractionation for nonelectrophoreticeukaryote cell proteomics, J. Proteome Res.,2005, 4, 316-324.[Crossref]
  • [3] Nagaraj N., Lu A., Mann M., Wiśniewski J.R., Detergentbasedbut gel-free method allows identification of severalhundred membrane proteins in single LC-MS runs, J.Proteome Res., 2008, 7, 5028-5032.[Crossref]
  • [4] Shevchenko G., Sjödin M.O., Malmström D., WetterhallM., Bergquist J.. Cloud-point extraction and delipidationof porcine brain proteins in combination with bottom-upmass spectrometry approaches for proteome analysis, J.Proteome Res., 2010.9(8),3903-3911.[WoS][Crossref]
  • [5] Wetterhall M., Shevchenko G., Artemenko K., SjödinMO., Bergquist J., Analysis of membrane and hydrophilicproteins simultaneously derived from the mouse brain usingcloud-point extraction, Anal. Bioanal. Chem., 2011, 400(9),2827-2836.
  • [6] Ferro M., Seigneurin-Berny D., Rolland N., Chapel A., SalviD., Garin J, et al., Organic solvent extraction as a versatileprocedure to identify hydrophobic chloroplast membraneproteins, Electrophoresis, 2000, 21 (16), 3517-3526.[PubMed][Crossref]
  • [7] Zhang N., Chen R., Young N., Wishart D., Winter P., WeinerJ.H, et al., Comparison of SDS- and methanol-assistedprotein solubilization and digestion methods for Escherichiacoli membrane proteome analysis by 2-D LC-MS/MS,Proteomics, 2007, 7, 484-493.[WoS][Crossref]
  • [8] Natarajan S.S., Krishnan H.B., Lakshman S., Garrett W.M.,An efficient extraction method to enhance analysis of lowabundant proteins from soybean seed, Anal. Biochem. 2009,394(2), 259-268.[WoS]
  • [9] Ye X., Johann D.J. Jr., Hakami R.M., Xiao Z., Meng Z., UlrichR.G., Issaq H.J., Veenstra T.D., Blonder J., Optimization ofprotein solubilization for the analysis of the CD14 humanmonocyte membrane proteome using LC-MS/MS, J.Proteomics, 2009, 73(1), 112-122.[WoS]
  • [10] Masuda T., Tomita M., Ishihama Y., Phase transfer surfactantaidedtrypsin digestion for membrane proteome analysis, J.Proteome Res., 2008, 7(2), 731-740.[Crossref][WoS]
  • [11] Vissers J.P., Chervet J.P., Salzmann J.P., Sodium dodecylsulphate removal from tryptic digest samples for onlinecapillary liquid chromatography/electrospray massspectrometry, J. Mass Spectrom., 1996, 31, 1021-1027.[Crossref]
  • [12] Zischka H., Gloeckner C.J., Klein C., Willmann S., SwiatekdeLange M., Ueffing M., Improved mass spectrometricidentification of gel-separated hydrophobic membraneproteins after sodium dodecyl sulfate removal by ion-pairextraction, Proteomics, 2004, 4, 3776-3782.[Crossref][PubMed]
  • [13] Shevchenko G., Musunuri S., Wetterhall M., Bergquist J.,Comparison of extraction methods for the comprehensiveanalysis of mouse brain proteome using shotgun-basedmass spectrometry, J. Proteome Res., 2012, 11(4), 2441-2451.[Crossref][WoS]
  • [14] Speers A.E., Wu C.C., Proteomics of integral membraneproteins--theory and application, Chem. Rev., 2007, 107,3687-3714.[WoS]
  • [15] Furth A.J., Removing unbound detergent from hydrophobicproteins, Anal. Biochem. 1980, 109, 207–215.
  • [16] Li F., Miller L.J., Naylor S., Dong M.Q., Efficient removal ofsodium dodecyl sulfate (SDS) enhances analysis of proteinsby SDS-polyacrylamide gel electrophoresis coupled withmatrix-assisted laser desorption/ionization time-of-flightmass spectrometry, Rapid Commun. Mass Spectrom., 1999,13, 464–466.[PubMed]
  • [17] Wessel, D., Flügge, U.I., A method for the quantitativerecovery of protein in dilute solution in the presence ofdetergents and lipids, Anal. Biochem., 1984, 138, 141–143.
  • [18] Puchades M., Westman A., Blennow K., Davidsson P.,Removal of sodium dodecyl sulfate from protein samplesprior to matrix-assisted laser desorption/ionization massspectrometry, Rapid Commun. Mass Spectrom. 1999, 13,344–349.[PubMed]
  • [19] Janini G.M., Conrads T.P., Veenstra T.D., Issaq H.J.,Development of a two-dimensional protein-peptide separationprotocol for comprehensive proteome measurements, J.Chromatogr. B, 2003, 787(1), 43-51.
  • [20] Gilar M., Belenky A., Wang B.H., High-throughput biopolymerdesalting by solid-phase extraction prior to mass spectrometricanalysis, J. Chromatogr. A, 2001, 921(1), 3-13.
  • [21] Kawasaki H., Suzuki K., Separation of peptides dissolved ina sodium dodecyl sulfate solution by reversed-phase liquidchromatography: removal of sodium dodecyl sulfate frompeptides using an ion-exchange precolumn, Anal. Biochem.,1990, 186(2), 264-268.
  • [22] Lu X.N., Zhu H.N., Tube-gel digestion: a novel proteomicapproach for high throughput analysis of membrane proteins,Mol. Cell Proteomics, 2005, 4, 1948-1958.[PubMed][Crossref]
  • [23] Wiśniewski J.R., Zougman A., Nagaraj N., Mann M.,Universal sample preparation method for proteome analysis,Nat. Methods, 2009, 6: (5), 359-362.[Crossref][PubMed]
  • [24] Liebler D.C., Ham A.J., Spin filter-based sample preparationfor shotgun proteomics. Nat. Methods, 2009, 6(11),785.[WoS][PubMed][Crossref]
  • [25] Bunai K., Nozaki M., Hamano M., Ogane S., InoueT., Nemoto T, et al., Proteomic analysis of acrylamide gelseparated proteins immobilized on polyvinylidene difluoridemembranes following proteolytic digestion in the presence of80% acetonitrile, Proteomics, 2003, 3, 1738-1749.[PubMed][Crossref]
  • [26] Matsudaira P., Sequence from picomole quantities of proteinselectroblotted onto polyvinylidene difluoride membranes, J.Biol. Chem., 1987, 262, 10035-10038.
  • [27] Towbin H., Staehelin T., Gordon J., Electrophoretic transferof proteins from polyacrylamide gels to nitrocellulose sheets:procedure and some applications, Proc. Natl. Acad. Sci .U SA., 1979, 76, 4350-4354.
  • [28] Lin Y., Li Y., Liu Y., Han W., He Q., Li J, et al., Improvementof gel-separated protein identification by DMF-assisteddigestion and peptide recovery after electroblotting,Electrophoresis, 2009, 30 (20), 3626-3635.[Crossref][WoS][PubMed]
  • [29] Bradford M. M., A rapid and sensitive method for thequantitation of microgram quantities of protein utilizing theprinciple of protein-dye binding, Anal. Biochem., 1976, 72,248-254.[Crossref][PubMed]
  • [30] Zhou J., Zhou T, Cao R., Liu Z., Shen J., Chen P, et al.,Evaluation of the application of sodium deoxycholate toproteomic analysis of rat hippocampal plasma membrane, J.Proteome Res., 2006, 5, 2547-2553.[Crossref]
  • [31] Rusconi F., Valton É., Nguyen R., Dufourc E., Quantificationof sodium dodecyl sulfate in microliter-volume biochemicalsamples by visible light spectroscopy, Anal. Biochem., 2001,295, 31-37.
  • [32] Laemmli U.K., Cleavage of structural proteins during theassembly of the head of bacteriophage T4, Nature, 1970,227, 680-685.
  • [33] Jonsson A.P., Aissouni Y., Palmberg C., Percipalle P., NordlingE., Daneholt B, et al., Recovery of gel-separated proteins forin-solution digestion and mass spectrometry, Anal. Chem.,2001, 73, 5370-5377.[Crossref]
  • [34] Durr E., Yu J., Krasinska K.M., Carver L.A., Yates J.R.,Testa J.E, et al., Direct proteomic mapping of the lungmicrovascular endothelial cell surface in vivo and in cellculture, Nat. Biotechnol., 2004, 22, 985-992.[Crossref]
  • [35] Elias J.E., Gygi S.P., Target-decoy search strategyfor increased confidence in large-scale protein identifications by mass spectrometry, Nat. Methods,2007, 4, 207-214.[WoS][Crossref][PubMed]
  • [36] Li X., Xie C., Cao J., He Q., Cao R., Lin Y, et al., An in vivomembrane density perturbation strategy for identificationof liver sinusoidal surface proteome accessible from thevasculature, J. Proteome Res., 2009, 8, 123-132.[WoS][Crossref]
  • [37] Luque-Garcia J.L., Zhou G., Spellman D.S., SunT.T., Neubert T.A., Analysis of electroblotted proteins by massspectrometry: protein identification after Western blotting,Mol. Cell Proteomics, 2008, 7 (308), 308-314.
  • [38] Luque-Garcia J.L., Zhou G., Sun T.T, Neubert T.A., Useof nitrocellulose membranes for protein characterizationby matrix-assisted laser desorption/ionization massspectrometry, Anal. Chem., 2006, 78, 5102-5108.[Crossref]
  • [39] Soskic V., Godovac-Zimmermann J., Improvement of an in-geltryptic digestion method for matrix-assisted laser desorption/ionization-time of flight mass spectrometry peptide mappingby use of volatile solubilizing agents, Proteomics, 2001, 1,1363-1367.
  • [40] Kyte J., Doolittle R.F., A simple method for displaying thehydropathic character of a protein, J. Mol. Biol., 1982, 157,105-132.
  • [41] Zhou J., Huang S., Bi D., Zhang H., Li J., Lin Y, et al., Analysisof integral membrane proteins by heat gel-embedmentcombined with improved in-gel digestions, Electrophoresis,2009, 30 (23), 4109-4117.[PubMed][Crossref][WoS]
  • [42] Han D.K., Eng J., Zhou H.L., Aebersold R., Quantitativeprofiling of differentiation-induced microsomal proteins usingisotope-coded affinity tags and mass spectrometry, Nat.Biotechnol., 2001, 19(10), 946–951.[PubMed][Crossref]
  • [43] Zhang N., Li N., Li L., Liquid chromatography MALDI MS/MSfor membrane proteome analysis, J. Proteome Res. 2004,3(4),719-27.[Crossref]
Document Type
Publication order reference
Identifiers
YADDA identifier
bwmeta1.element.-psjd-doi-10_2478_sampre-2013-0004
JavaScript is turned off in your web browser. Turn it on to take full advantage of this site, then refresh the page.