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Volumn 72, Issue 10, 2011, Pages 1192-1218

Next generation functional proteomics in non-model plants: A survey on techniques and applications for the analysis of protein complexes and post-translational modifications

Author keywords

Computational methods; Cross species; Post translational modifications; Protein protein interactions

Indexed keywords

VEGETABLE PROTEIN;

EID: 79958139420     PISSN: 00319422     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.phytochem.2011.01.003     Document Type: Review
Times cited : (27)

References (338)
  • 1
    • 67650354415 scopus 로고    scopus 로고
    • Protein tyrosine nitration: Selectivity, physicochemical and biological consequences, denitration, and proteomics methods for the identification of tyrosine-nitrated proteins
    • N. Abello, H.A.M. Kerstjens, D.S. Postma, and R. Bischoff Protein tyrosine nitration: selectivity, physicochemical and biological consequences, denitration, and proteomics methods for the identification of tyrosine-nitrated proteins J. Proteome Res. 8 2009 3222 3238
    • (2009) J. Proteome Res. , vol.8 , pp. 3222-3238
    • Abello, N.1    Kerstjens, H.A.M.2    Postma, D.S.3    Bischoff, R.4
  • 2
    • 33751401609 scopus 로고    scopus 로고
    • Large scale identification and quantitative profiling of phosphoproteins expressed during seed filling in oilseed rape
    • DOI 10.1074/mcp.M600084-MCP200
    • G.K. Agrawal, and J.J. Thelen Large scale identification and quantitative profiling of phosphoproteins expressed during seed filling in oilseed rape Mol. Cell. Proteomics 5 2006 2044 2059 (Pubitemid 44817017)
    • (2006) Molecular and Cellular Proteomics , vol.5 , Issue.11 , pp. 2044-2059
    • Agrawal, G.K.1    Thelen, J.J.2
  • 3
    • 77149158441 scopus 로고    scopus 로고
    • Unrestricted identification of modified proteins using MS/MS
    • E. Ahrne, M. Muller, and F. Lisacek Unrestricted identification of modified proteins using MS/MS Proteomics 10 2010 671 686
    • (2010) Proteomics , vol.10 , pp. 671-686
    • Ahrne, E.1    Muller, M.2    Lisacek, F.3
  • 4
    • 78650549848 scopus 로고    scopus 로고
    • Regulation of callose synthase activity in situ in alamethicin- permeabilized Arabidopsis and tobacco suspension cells
    • M. Aidemark, C.J. Andersson, A.G. Rasmusson, and S. Widell Regulation of callose synthase activity in situ in alamethicin-permeabilized Arabidopsis and tobacco suspension cells BMC Plant Biol. 9 2009 27
    • (2009) BMC Plant Biol. , vol.9 , pp. 27
    • Aidemark, M.1    Andersson, C.J.2    Rasmusson, A.G.3    Widell, S.4
  • 6
    • 0030896924 scopus 로고    scopus 로고
    • Identification of protein transport complexes in the chloroplastic envelope membranes via chemical cross-linking
    • DOI 10.1083/jcb.136.5.983
    • M. Akita, E. Nielsen, and K. Keegstra Identification of protein transport complexes in the chloroplastic envelope membranes via chemical cross-linking J. Cell Biol. 136 1997 983 994 (Pubitemid 27131731)
    • (1997) Journal of Cell Biology , vol.136 , Issue.5 , pp. 983-994
    • Akita, M.1    Nielsen, E.2    Keegstra, K.3
  • 7
    • 70349593722 scopus 로고    scopus 로고
    • Plant cell wall proteomics: Mass spectrometry data, a trove for research on protein structure/function relationships
    • C. Albenne, H. Canut, G. Boudart, Y. Zhang, H. San Clemente, R. Pont-Lezica, and E. Jamet Plant cell wall proteomics: mass spectrometry data, a trove for research on protein structure/function relationships Mol. Plant 2 2009 977 989
    • (2009) Mol. Plant , vol.2 , pp. 977-989
    • Albenne, C.1    Canut, H.2    Boudart, G.3    Zhang, Y.4    San Clemente, H.5    Pont-Lezica, R.6    Jamet, E.7
  • 8
    • 0032489015 scopus 로고    scopus 로고
    • The cell as a collection of protein machines: Preparing the next generation of molecular biologists
    • DOI 10.1016/S0092-8674(00)80922-8
    • B. Alberts The cell as a collection of protein machines: preparing the next generation of molecular biologists Cell 92 1998 291 294 (Pubitemid 28093007)
    • (1998) Cell , vol.92 , Issue.3 , pp. 291-294
    • Alberts, B.1
  • 9
    • 41149110237 scopus 로고    scopus 로고
    • Electrostatic repulsion hydrophilic interaction chromatography for isocratic separation of charged solutes and selective isolation of phosphopeptides
    • DOI 10.1021/ac070997p
    • A.J. Alpert Electrostatic repulsion hydrophilic interaction chromatography for isocratic separation of charged solutes and selective isolation of phosphopeptides Anal. Chem. 80 2008 62 76 (Pubitemid 351448406)
    • (2008) Analytical Chemistry , vol.80 , Issue.1 , pp. 62-76
    • Alpert, A.J.1
  • 12
    • 70349113034 scopus 로고    scopus 로고
    • Determination of glycosylation sites and site-specific heterogeneity in glycoproteins
    • H.J. An, J.W. Froehlich, and C.B. Lebrilla Determination of glycosylation sites and site-specific heterogeneity in glycoproteins Curr. Opin. Chem. Biol. 13 2009 421 426
    • (2009) Curr. Opin. Chem. Biol. , vol.13 , pp. 421-426
    • An, H.J.1    Froehlich, J.W.2    Lebrilla, C.B.3
  • 13
    • 0346874342 scopus 로고    scopus 로고
    • Proteomic characterization of the human centrosome by protein correlation profiling
    • DOI 10.1038/nature02166
    • J.S. Andersen, C.J. Wilkinson, T. Mayor, P. Mortensen, E.A. Nigg, and M. Mann Proteomic characterization of the human centrosome by protein correlation profiling Nature 426 2003 570 574 (Pubitemid 37522644)
    • (2003) Nature , vol.426 , Issue.6966 , pp. 570-574
    • Andersen, J.S.1    Wilkinson, C.J.2    Mayor, T.3    Mortensen, P.4    Nigg, E.A.5    Mann, M.6
  • 14
    • 0022541790 scopus 로고
    • 3+) affinity chromatography
    • L. Andersson, and J. Porath Isolation of phosphoproteins by immobilized metal (Fe-3+) affinity-chromatography Anal. Biochem. 154 1986 250 254 (Pubitemid 16063367)
    • (1986) Analytical Biochemistry , vol.154 , Issue.1 , pp. 250-254
    • Andersson, L.1    Porath, J.2
  • 15
    • 0033202958 scopus 로고    scopus 로고
    • The lectin ERGIC-53 is a cargo transport receptor for glycoproteins
    • C. Appenzeller, H. Andersson, F. Kappeler, and H.P. Hauri The lectin ERGIC-53 is a cargo transport receptor for glycoproteins Nat. Cell Biol. 1 1999 330 334 (Pubitemid 129493573)
    • (1999) Nature Cell Biology , vol.1 , Issue.6 , pp. 330-334
    • Appenzeller, C.1    Andersson, H.2    Kappeler, F.3    Hauri, H.-P.4
  • 20
    • 77950656228 scopus 로고    scopus 로고
    • 'Interactome' analysis: A step forward in proteomics research
    • S. Babu 'Interactome' analysis: a step forward in proteomics research Biotechnol. J. 5 2010 357 358
    • (2010) Biotechnol. J. , vol.5 , pp. 357-358
    • Babu, S.1
  • 25
    • 44949113306 scopus 로고    scopus 로고
    • New insights into nitric oxide signaling in plants
    • DOI 10.1146/annurev.arplant.59.032607.092830
    • A. Besson-Bard, A. Pugin, and D. Wendehenne New insights into nitric oxide signaling in plants Annu. Rev. Plant Biol. 59 2008 21 39 (Pubitemid 351813022)
    • (2008) Annual Review of Plant Biology , vol.59 , pp. 21-39
    • Besson-Bard, A.1    Pugin, A.2    Wendehenne, D.3
  • 26
    • 77956307609 scopus 로고    scopus 로고
    • Differential proteomics based on O-18 labeling to determine the cyclin dependent kinase 9 lnteractome
    • K. Bezstarosti, A. Ghamari, F.G. Grosveld, and J.A.A. Demmers Differential proteomics based on O-18 labeling to determine the cyclin dependent kinase 9 lnteractome J. Proteome Res. 9 2010 4464 4475
    • (2010) J. Proteome Res. , vol.9 , pp. 4464-4475
    • Bezstarosti, K.1    Ghamari, A.2    Grosveld, F.G.3    Demmers, J.A.A.4
  • 27
    • 33748456465 scopus 로고    scopus 로고
    • The visible touch: In planta visualization of protein-protein interactions by fluorophore-based methods
    • R. Bhat, T. Lahaye, and R. Panstruga The visible touch: in planta visualization of protein-protein interactions by fluorophore-based methods Plant Methods 2 2006 12
    • (2006) Plant Methods , vol.2 , pp. 12
    • Bhat, R.1    Lahaye, T.2    Panstruga, R.3
  • 29
    • 0033579464 scopus 로고    scopus 로고
    • Sequence and structure-based prediction of eukaryotic protein phosphorylation sites
    • DOI 10.1006/jmbi.1999.3310
    • N. Blom, S. Gammeltoft, and S. Brunak Sequence and structure-based prediction of eukaryotic protein phosphorylation sites J. Mol. Biol. 294 1999 1351 1362 (Pubitemid 30008805)
    • (1999) Journal of Molecular Biology , vol.294 , Issue.5 , pp. 1351-1362
    • Blom, N.1    Gammeltoft, S.2    Brunak, S.3
  • 30
    • 2942564430 scopus 로고    scopus 로고
    • Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence
    • DOI 10.1002/pmic.200300771
    • N. Blom, T. Sicheritz-Ponten, R. Gupta, S. Gammeltoft, and S.Ã. Brunak Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence Proteomics 4 2004 1633 1649 (Pubitemid 38738322)
    • (2004) Proteomics , vol.4 , Issue.6 , pp. 1633-1649
    • Blom, N.1    Sicheritz-Ponten, T.2    Gupta, R.3    Gammeltoft, S.4    Brunak, So.5
  • 31
    • 67649213067 scopus 로고    scopus 로고
    • Phosphopeptide fragmentation and analysis by mass spectrometry
    • P.J. Boersema, S. Mohammed, and A.J.R. Heck Phosphopeptide fragmentation and analysis by mass spectrometry J. Mass Spectrom. 44 2009 861 878
    • (2009) J. Mass Spectrom. , vol.44 , pp. 861-878
    • Boersema, P.J.1    Mohammed, S.2    Heck, A.J.R.3
  • 32
    • 77955485244 scopus 로고    scopus 로고
    • Affinity purification of the Arabidopsis 26 S proteasome reveals a diverse array of plant proteolytic complexes
    • A.J. Book, N.P. Gladman, S.S. Lee, M. Scalf, L.M. Smith, and R.D. Vierstra Affinity purification of the Arabidopsis 26 S proteasome reveals a diverse array of plant proteolytic complexes J. Biol. Chem. 285 2010 25554 25569
    • (2010) J. Biol. Chem. , vol.285 , pp. 25554-25569
    • Book, A.J.1    Gladman, N.P.2    Lee, S.S.3    Scalf, M.4    Smith, L.M.5    Vierstra, R.D.6
  • 33
    • 0037783246 scopus 로고    scopus 로고
    • Identification of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A proteomic and genomic analysis
    • DOI 10.1104/pp.103.021170
    • G.H.H. Borner, K.S. Lilley, T.J. Stevens, and P. Dupree Identification of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A proteomic and genomic analysis Plant Physiol. 132 2003 568 577 (Pubitemid 36715058)
    • (2003) Plant Physiology , vol.132 , Issue.2 , pp. 568-577
    • Borner, G.H.H.1    Lilley, K.S.2    Stevens, T.J.3    Dupree, P.4
  • 40
    • 70349696256 scopus 로고    scopus 로고
    • On the analysis of sedimentation velocity in the study of protein complexes
    • P.H. Brown, A. Balbo, and P. Schuck On the analysis of sedimentation velocity in the study of protein complexes Eur. Biophys. J. 38 2009 1079 1099
    • (2009) Eur. Biophys. J. , vol.38 , pp. 1079-1099
    • Brown, P.H.1    Balbo, A.2    Schuck, P.3
  • 42
    • 67649511917 scopus 로고    scopus 로고
    • Isotope dilution strategies for absolute quantitative proteomics
    • V. Brun, C. Masselon, J. Garin, and A. Dupuis Isotope dilution strategies for absolute quantitative proteomics J. Proteomics 72 2009 740 749
    • (2009) J. Proteomics , vol.72 , pp. 740-749
    • Brun, V.1    Masselon, C.2    Garin, J.3    Dupuis, A.4
  • 43
    • 63549126844 scopus 로고    scopus 로고
    • Substrates related to chromatin and to RNA-dependent processes are modified by Arabidopsis SUMO isoforms that differ in a conserved residue with influence on desumoylation
    • R. Budhiraja, R. Hermkes, S. Muller, R. Schmidt, T. Colby, K. Panigrahi, G. Coupland, and A. Bachmair Substrates related to chromatin and to RNA-dependent processes are modified by Arabidopsis SUMO isoforms that differ in a conserved residue with influence on desumoylation Plant Physiol. 149 2009 1529 1540
    • (2009) Plant Physiol. , vol.149 , pp. 1529-1540
    • Budhiraja, R.1    Hermkes, R.2    Muller, S.3    Schmidt, R.4    Colby, T.5    Panigrahi, K.6    Coupland, G.7    Bachmair, A.8
  • 44
    • 33751211249 scopus 로고    scopus 로고
    • An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells
    • DOI 10.1038/nmeth968, PII NMETH968
    • T. Burckstummer, K.L. Bennett, A. Preradovic, G. Schutze, O. Hantschel, G. Superti-Furga, and A. Bauch An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells Nat. Methods 3 2006 1013 1019 (Pubitemid 44782701)
    • (2006) Nature Methods , vol.3 , Issue.12 , pp. 1013-1019
    • Burckstummer, T.1    Bennett, K.L.2    Preradovic, A.3    Schutze, G.4    Hantschel, O.5    Superti-Furga, G.6    Bauch, A.7
  • 45
    • 0037431026 scopus 로고    scopus 로고
    • Identification of 14 new phosphoproteins involved in important plant mitochondrial processes
    • DOI 10.1016/S0014-5793(03)00250-3
    • N.V. Bykova, H. Egsgaard, and I.M. Moller Identification of 14 new phosphoproteins involved in important plant mitochondrial processes FEBS Lett. 540 2003 141 146 (Pubitemid 36398046)
    • (2003) FEBS Letters , vol.540 , Issue.1-3 , pp. 141-146
    • Bykova, N.V.1    Egsgaard, H.2    Moller, I.M.3
  • 47
    • 58349111875 scopus 로고    scopus 로고
    • AmiGO: Online access to ontology and annotation data
    • AmiGO Hub, Web Presence Working Group S.
    • S. Carbon, A. Ireland, C.J. Mungall, S. Shu, B. Marshall, S. Lewis AmiGO Hub, Web Presence Working Group AmiGO: online access to ontology and annotation data Bioinformatics 25 2009 288 289
    • (2009) Bioinformatics , vol.25 , pp. 288-289
    • Carbon, S.1    Ireland, A.2    Mungall, C.J.3    Shu, S.4    Marshall, B.5    Lewis, S.6
  • 48
    • 33847734406 scopus 로고    scopus 로고
    • Banana (Musa spp.) as a model to study the meristem proteome: Acclimation to osmotic stress
    • S.C. Carpentier, E. Witters, K. Laukens, H. Van Onckelen, R. Swennen, and B. Panis Banana (Musa spp.) as a model to study the meristem proteome: acclimation to osmotic stress Proteomics 7 2007 92 105
    • (2007) Proteomics , vol.7 , pp. 92-105
    • Carpentier, S.C.1    Witters, E.2    Laukens, K.3    Van Onckelen, H.4    Swennen, R.5    Panis, B.6
  • 51
    • 70349130317 scopus 로고    scopus 로고
    • Chemical tools for understanding protein lipidation in eukaryotes
    • G. Charron, J. Wilson, and H.C. Hang Chemical tools for understanding protein lipidation in eukaryotes Curr. Opin. Chem. Biol. 13 2009 382 391
    • (2009) Curr. Opin. Chem. Biol. , vol.13 , pp. 382-391
    • Charron, G.1    Wilson, J.2    Hang, H.C.3
  • 52
    • 4444282070 scopus 로고    scopus 로고
    • Studying the interactome with the yeast two-hybrid system and mass spectrometry
    • B. Causier Studying the interactome with the yeast two-hybrid system and mass spectrometry Mass Spectrom. Rev. 23 2004 350 367
    • (2004) Mass Spectrom. Rev. , vol.23 , pp. 350-367
    • Causier, B.1
  • 53
    • 33644787447 scopus 로고    scopus 로고
    • OrthoMCL-DB: Querying a comprehensive multi-species collection of ortholog groups
    • F. Chen, A.J. Mackey, C.J. Stoeckert, and D.S. Roos OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups Nucleic Acids Res. 34 2006 D363 D368
    • (2006) Nucleic Acids Res. , vol.34
    • Chen, F.1    MacKey, A.J.2    Stoeckert, C.J.3    Roos, D.S.4
  • 55
    • 0035170507 scopus 로고    scopus 로고
    • GlycoSuiteDB: A new curated relational database of glycoprotein glycan structures and their biological sources
    • C.A. Cooper, M.J. Harrison, M.R. Wilkins, and N.H. Packer GlycoSuiteDB: a new curated relational database of glycoprotein glycan structures and their biological sources Nucleic Acids Res. 29 2001 332 335 (Pubitemid 32054485)
    • (2001) Nucleic Acids Research , vol.29 , Issue.1 , pp. 332-335
    • Cooper, C.A.1    Harrison, M.J.2    Wilkins, M.R.3    Packer, N.H.4
  • 56
    • 1542787841 scopus 로고    scopus 로고
    • Label-free screening of bio-molecular interactions
    • DOI 10.1007/s00216-003-2111-y
    • M.A. Cooper Label-free screening of bio-molecular interactions Anal. Bioanal. Chem. 377 2003 834 842 (Pubitemid 40882959)
    • (2003) Analytical and Bioanalytical Chemistry , vol.377 , Issue.5 , pp. 834-842
    • Cooper, M.A.1
  • 57
    • 38549123986 scopus 로고    scopus 로고
    • AtPID: Arabidopsis thaliana protein interactome database-an integrative platform for plant systems biology
    • J. Cui, P. Li, G. Li, F. Xu, C. Zhao, Y. Li, Z. Yang, G. Wang, Q. Yu, Y. Li, and T. Shi AtPID: Arabidopsis thaliana protein interactome database-an integrative platform for plant systems biology Nucleic Acids Res. 36 2008 D999 D1008
    • (2008) Nucleic Acids Res. , vol.36
    • Cui, J.1    Li, P.2    Li, G.3    Xu, F.4    Zhao, C.5    Li, Y.6    Yang, Z.7    Wang, G.8    Yu, Q.9    Li, Y.10    Shi, T.11
  • 58
    • 44449145111 scopus 로고    scopus 로고
    • Coupling of native liquid phase isoelectrofocusing and blue native polyacrylamide gel electrophoresis: A potent tool for native membrane multiprotein complex separation
    • G.M. D'Amici, A.M. Timperio, and L. Zolla Coupling of native liquid phase isoelectrofocusing and blue native polyacrylamide gel electrophoresis: a potent tool for native membrane multiprotein complex separation J. Proteome Res. 7 2008 1326 1340
    • (2008) J. Proteome Res. , vol.7 , pp. 1326-1340
    • D'Amici, G.M.1    Timperio, A.M.2    Zolla, L.3
  • 59
    • 62449151233 scopus 로고    scopus 로고
    • Separation of thylakoid membrane proteins by sucrose gradient ultracentrifugation or Blue Native-SDS-PAGE two-dimensional electrophoresis
    • G.M. D'Amici, C.G. Huber, and L. Zolla Separation of thylakoid membrane proteins by sucrose gradient ultracentrifugation or Blue Native-SDS-PAGE two-dimensional electrophoresis Methods Mol. Biol. 528 2009 61 70
    • (2009) Methods Mol. Biol. , vol.528 , pp. 61-70
    • D'Amici, G.M.1    Huber, C.G.2    Zolla, L.3
  • 60
    • 57249105125 scopus 로고    scopus 로고
    • Prediction of kinase-specific phosphorylation sites using conditional random fields
    • T.H. Dang, K. Van Leemput, A. Verschoren, and K. Laukens Prediction of kinase-specific phosphorylation sites using conditional random fields Bioinformatics 24 2008 2857 2864
    • (2008) Bioinformatics , vol.24 , pp. 2857-2864
    • Dang, T.H.1    Van Leemput, K.2    Verschoren, A.3    Laukens, K.4
  • 61
    • 48949119270 scopus 로고    scopus 로고
    • Native-DIGE: A new look at the mitochondrial membrane proteome
    • D. Dani, and N.A. Dencher Native-DIGE: a new look at the mitochondrial membrane proteome Biotechnol. J. 3 2008 817 822
    • (2008) Biotechnol. J. , vol.3 , pp. 817-822
    • Dani, D.1    Dencher, N.A.2
  • 63
    • 68849117733 scopus 로고    scopus 로고
    • Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression
    • S. De Bodt, S. Proost, K. Vandepoele, P. Rouzé, and Y. Van de Peer Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression BMC Genomics 10 2009 288
    • (2009) BMC Genomics , vol.10 , pp. 288
    • De Bodt, S.1    Proost, S.2    Vandepoele, K.3    Rouzé, P.4    Van De Peer, Y.5
  • 68
    • 46549085153 scopus 로고    scopus 로고
    • A "tagless" strategy for identification of stable protein complexes genome-wide by multidimensional orthogonal chromatographic separation and iTRAQ reagent tracking
    • M. Dong, L.L. Yang, K. Williams, S.J. Fisher, S.C. Hall, M.D. Biggin, J. Jin, and H.E. Witkowska A "Tagless" strategy for identification of stable protein complexes genome-wide by multidimensional orthogonal chromatographic separation and iTRAQ reagent tracking J. Proteome Res. 7 2008 1836 1849
    • (2008) J. Proteome Res. , vol.7 , pp. 1836-1849
    • Dong, M.1    Yang, L.L.2    Williams, K.3    Fisher, S.J.4    Hall, S.C.5    Biggin, M.D.6    Jin, J.7    Witkowska, H.E.8
  • 69
  • 70
    • 77954299992 scopus 로고    scopus 로고
    • AgriGO: A GO analysis toolkit for the agricultural community
    • Z. Du, X. Zhou, Y. Ling, Z. Zhang, and Z. Su AgriGO: a GO analysis toolkit for the agricultural community Nucleic Acids Res. 38 2010 W64 W70
    • (2010) Nucleic Acids Res. , vol.38
    • Du, Z.1    Zhou, X.2    Ling, Y.3    Zhang, Z.4    Su, Z.5
  • 71
    • 73849110528 scopus 로고    scopus 로고
    • Techniques for phosphopeptide enrichment prior to analysis by mass spectrometry
    • J.D. Dunn, G.E. Reid, and M.L. Bruening Techniques for phosphopeptide enrichment prior to analysis by mass spectrometry Mass Spectrom. Rev. 29 2010 29 54
    • (2010) Mass Spectrom. Rev. , vol.29 , pp. 29-54
    • Dunn, J.D.1    Reid, G.E.2    Bruening, M.L.3
  • 72
    • 33646874523 scopus 로고    scopus 로고
    • Two-hybrid protein-protein interaction analysis in Arabidopsis protoplasts: Establishment of a heterodimerization map of group C and group S bZIP transcription factors
    • DOI 10.1111/j.1365-313X.2006.02731.x
    • A. Ehlert, F. Weltmeier, X. Wang, C.S. Mayer, S. Smeekens, J. Vicente-Carbajosa, and W. Droge-Laser Two-hybrid protein-protein interaction analysis in Arabidopsis protoplasts: establishment of a heterodimerization map of group C and group S bZIP transcription factors Plant J. 46 2006 890 900 (Pubitemid 43780633)
    • (2006) Plant Journal , vol.46 , Issue.5 , pp. 890-900
    • Ehlert, A.1    Weltmeier, F.2    Wang, X.3    Mayer, C.S.4    Smeekens, S.5    Vicente-Carbajosa, J.6    Droge-Laser, W.7
  • 74
    • 33645795446 scopus 로고    scopus 로고
    • Modification-specific proteomics of plasma membrane proteins: Identification and characterization of glycosylphosphatidylinositol-anchored proteins released upon phospholipase D treatment
    • F. Elortza, S. Mohammed, J. Bunkenborg, L.J. Foster, T.S. Nuhse, U. Brodbeck, S.C. Peck, and O.N. Jensen Modification-specific proteomics of plasma membrane proteins: identification and characterization of glycosylphosphatidylinositol-anchored proteins released upon phospholipase D treatment J. Proteome Res. 5 2006 935 943
    • (2006) J. Proteome Res. , vol.5 , pp. 935-943
    • Elortza, F.1    Mohammed, S.2    Bunkenborg, J.3    Foster, L.J.4    Nuhse, T.S.5    Brodbeck, U.6    Peck, S.C.7    Jensen, O.N.8
  • 76
    • 60349118495 scopus 로고    scopus 로고
    • In vivo phosphorylation sites of barley tonoplast proteins identified by a phosphoproteomic approach
    • A. Endler, S. Reiland, B. Gerrits, U.G. Schmidt, S. Baginsky, and E. Martinoia In vivo phosphorylation sites of barley tonoplast proteins identified by a phosphoproteomic approach Proteomics 9 2009 310 321
    • (2009) Proteomics , vol.9 , pp. 310-321
    • Endler, A.1    Reiland, S.2    Gerrits, B.3    Schmidt, U.G.4    Baginsky, S.5    Martinoia, E.6
  • 77
    • 33744901613 scopus 로고    scopus 로고
    • Blue-native PAGE in plants: A tool in analysis of protein-protein interactions
    • H. Eubel, H. Braun, and A.H. Millar Blue-native PAGE in plants: a tool in analysis of protein-protein interactions Plant Methods 1 2005 11
    • (2005) Plant Methods , vol.1 , pp. 11
    • Eubel, H.1    Braun, H.2    Millar, A.H.3
  • 78
    • 0036233772 scopus 로고    scopus 로고
    • Development of a high-throughput yeast two-hybrid screening system to study protein-protein interactions in plants
    • DOI 10.1007/s00438-002-0656-7
    • Y. Fang, D.J. Macool, Z. Xue, E.P. Heppard, C.F. Hainey, S.V. Tingey, and G.H. Miao Development of a high-throughput yeast two-hybrid screening system to study protein-protein interactions in plants Mol. Genet. Genomics 267 2002 142 153 (Pubitemid 34437989)
    • (2002) Molecular Genetics and Genomics , vol.267 , Issue.2 , pp. 142-153
    • Fang, Y.1    Macool, D.2    Xue, Z.3    Heppard, E.4    Hainey, C.5    Tingey, S.6    Miao, G.-H.7
  • 80
    • 0024406857 scopus 로고
    • A novel genetic system to detect protein-protein interactions
    • DOI 10.1038/340245a0
    • S. Fields, and O.K. Song A novel genetic system to detect protein-protein interactions Nature 340 1989 245 246 (Pubitemid 19171591)
    • (1989) Nature , vol.340 , Issue.6230 , pp. 245-246
    • Fields, S.1    Song, O.-K.2
  • 81
    • 0014800108 scopus 로고
    • Distinguishing homologous from analogous proteins
    • W.M. Fitch Distinguishing homologous from analogous proteins Syst. Zool. 19 1970 99
    • (1970) Syst. Zool. , vol.19 , pp. 99
    • Fitch, W.M.1
  • 82
    • 77955161346 scopus 로고    scopus 로고
    • Native capillary isoelectric focusing for the separation of protein complex isoforms and subcomplexes
    • B.R. Fonslow, S.A. Kang, D.R. Gestaut, B. Graczyk, T.N. Davis, D.M. Sabatini, and J.R. Yates Native capillary isoelectric focusing for the separation of protein complex isoforms and subcomplexes Anal. Chem. 82 2010 6643 6651
    • (2010) Anal. Chem. , vol.82 , pp. 6643-6651
    • Fonslow, B.R.1    Kang, S.A.2    Gestaut, D.R.3    Graczyk, B.4    Davis, T.N.5    Sabatini, D.M.6    Yates, J.R.7
  • 83
    • 77949565231 scopus 로고    scopus 로고
    • Reconstruction of metabolic pathways, protein expression, and homeostasis machineries across maize bundle sheath and mesophyll chloroplasts: Large-scale quantitative proteomics using the first maize genome assembly
    • G. Friso, W. Majeran, M.S. Huang, Q. Sun, and K.J. van Wijk Reconstruction of metabolic pathways, protein expression, and homeostasis machineries across maize bundle sheath and mesophyll chloroplasts: large-scale quantitative proteomics using the first maize genome assembly Plant Physiol. 152 2010 1219 1250
    • (2010) Plant Physiol. , vol.152 , pp. 1219-1250
    • Friso, G.1    Majeran, W.2    Huang, M.S.3    Sun, Q.4    Van Wijk, K.J.5
  • 84
    • 34748874756 scopus 로고    scopus 로고
    • Split luciferase complementation assay to study protein-protein interactions in Arabidopsis protoplasts
    • DOI 10.1111/j.1365-313X.2007.03214.x
    • Y. Fujikawa, and N. Kato Split luciferase complementation assay to study protein-protein interactions in Arabidopsis protoplasts Plant J. 52 2007 185 195 (Pubitemid 47476162)
    • (2007) Plant Journal , vol.52 , Issue.1 , pp. 185-195
    • Fujikawa, Y.1    Kato, N.2
  • 86
    • 85127045455 scopus 로고    scopus 로고
    • Evolution of proteins and proteomes: A phylogenetics approach
    • T. Gabaldon Evolution of proteins and proteomes: a phylogenetics approach Evol. Bioinform. Online 1 2005 51 61
    • (2005) Evol. Bioinform. Online , vol.1 , pp. 51-61
    • Gabaldon, T.1
  • 88
    • 33847274309 scopus 로고    scopus 로고
    • GOlorize: A Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring
    • DOI 10.1093/bioinformatics/btl605
    • O. Garcia, C. Saveanu, M. Cline, M. Fromont-Racine, A. Jacquier, B. Schwikowski, and T. Aittokallio GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring Bioinformatics 23 2007 394 396 (Pubitemid 46323170)
    • (2007) Bioinformatics , vol.23 , Issue.3 , pp. 394-396
    • Garcia, O.1    Saveanu, C.2    Cline, M.3    Fromont-Racine, M.4    Jacquier, A.5    Schwikowski, B.6    Aittokallio, T.7
  • 91
    • 75849158230 scopus 로고    scopus 로고
    • The Gene Ontology in 2010: Extensions and refinements. The Gene Ontology Consortium
    • Gene Ontology Consortium The Gene Ontology in 2010: extensions and refinements. The Gene Ontology Consortium Nucleic Acids Res. 38 2010 D331 D335
    • (2010) Nucleic Acids Res. , vol.38
  • 92
    • 54049151543 scopus 로고    scopus 로고
    • Proteomic profiling of cellular targets of lipopolysaccharide-induced signalling in Nicotiana tabacum BY-2 cells
    • I.B. Gerber, K. Laukens, T. De Vijlder, E. Witters, and I.A. Dubery Proteomic profiling of cellular targets of lipopolysaccharide-induced signalling in Nicotiana tabacum BY-2 cells BBA-Proteins Proteomics 1784 2008 1750 1762
    • (2008) BBA-Proteins Proteomics , vol.1784 , pp. 1750-1762
    • Gerber, I.B.1    Laukens, K.2    De Vijlder, T.3    Witters, E.4    Dubery, I.A.5
  • 93
    • 33747794597 scopus 로고    scopus 로고
    • Lipopolysaccharide-responsive phosphoproteins in Nicotiana tabacum cells
    • DOI 10.1016/j.plaphy.2006.06.015, PII S0981942806000994
    • I.B. Gerber, K. Laukens, E. Witters, and I.A. Dubery Lipopolysaccharide- responsive phosphoproteins in Nicotiana tabacum cells Plant Physiol. Biochem. 44 2006 369 379 (Pubitemid 44278610)
    • (2006) Plant Physiology and Biochemistry , vol.44 , Issue.5-6 , pp. 369-379
    • Gerber, I.B.1    Laukens, K.2    Witters, E.3    Dubery, I.A.4
  • 94
    • 0038333588 scopus 로고    scopus 로고
    • Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides
    • DOI 10.1038/nbt810
    • K. Gevaert, M. Goethals, L. Martens, J. Van Damme, A. Staes, G.R. Thomas, and J. Vandekerckhove Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides Nat. Biotechnol. 21 2003 566 569 (Pubitemid 36532024)
    • (2003) Nature Biotechnology , vol.21 , Issue.5 , pp. 566-569
    • Gevaert, K.1    Goethals, M.2    Martens, L.3    Van Damme, J.4    Staes, A.5    Thomas, G.R.6    Vandekerckhove, J.7
  • 95
    • 21044456097 scopus 로고    scopus 로고
    • Biomolecular interaction network database
    • DOI 10.1093/bib/6.2.194
    • D. Gilbert Biomolecular interaction network database Brief Bioinform. 6 2005 194 198 (Pubitemid 40872285)
    • (2005) Briefings in Bioinformatics , vol.6 , Issue.2 , pp. 194-198
    • Gilbert, D.1
  • 96
    • 14844314804 scopus 로고    scopus 로고
    • Advances in protein complex analysis using mass spectrometry
    • DOI 10.1113/jphysiol.2004.080440
    • A.C. Gingras, R. Aebersold, and B. Raught Advances in protein complex analysis using mass spectrometry J. Physiol. (Lond.) 563 2005 11 21 (Pubitemid 40340364)
    • (2005) Journal of Physiology , vol.563 , Issue.1 , pp. 11-21
    • Gingras, A.-C.1    Aebersold, R.2    Raught, B.3
  • 99
    • 44149105911 scopus 로고    scopus 로고
    • PHOSIDA (phosphorylation site database): Management, structural and evolutionary investigation, and prediction of phosphosites
    • F. Gnad, S.B. Ren, J. Cox, J.V. Olsen, B. Macek, M. Oroshi, and M. Mann PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites Genome Biol. 8 2007
    • (2007) Genome Biol. , vol.8
    • Gnad, F.1    Ren, S.B.2    Cox, J.3    Olsen, J.V.4    MacEk, B.5    Oroshi, M.6    Mann, M.7
  • 101
    • 33745683588 scopus 로고    scopus 로고
    • Mapping the proteome of thylakoid membranes by de novo sequencing of intermembrane peptide domains
    • DOI 10.1002/pmic.200500924
    • B. Granvogl, V. Reisinger, and L.A. Eichacker Mapping the proteome of thylakoid membranes by de novo sequencing of intermembrane peptide domains Proteomics 6 2006 3681 3695 (Pubitemid 44000195)
    • (2006) Proteomics , vol.6 , Issue.12 , pp. 3681-3695
    • Granvogl, B.1    Reisinger, V.2    Eichacker, L.A.3
  • 102
    • 38949101254 scopus 로고    scopus 로고
    • Split-ubiquitin system for identifying protein-protein interactions in membrane and full-length proteins
    • C. Grefen, S. Lalonde, and P. Obrdlik Split-ubiquitin system for identifying protein-protein interactions in membrane and full-length proteins Curr. Protoc. Neurosci. 41 2007 5.27.1 5.27.4
    • (2007) Curr. Protoc. Neurosci. , vol.41 , pp. 5271-5274
    • Grefen, C.1    Lalonde, S.2    Obrdlik, P.3
  • 103
    • 73249138597 scopus 로고    scopus 로고
    • Large-scale phosphoprotein analysis in Medicago truncatula roots provides insight into in vivo kinase activity in legumes
    • P.A. Grimsrud, D. den Os, C.D. Wenger, D.L. Swaney, D. Schwartz, M.R. Sussman, J.M. Ane, and J.J. Coon Large-scale phosphoprotein analysis in Medicago truncatula roots provides insight into in vivo kinase activity in legumes Plant Physiol. 152 2010 19 28
    • (2010) Plant Physiol. , vol.152 , pp. 19-28
    • Grimsrud, P.A.1    Den Os, D.2    Wenger, C.D.3    Swaney, D.L.4    Schwartz, D.5    Sussman, M.R.6    Ane, J.M.7    Coon, J.J.8
  • 104
    • 37049006551 scopus 로고    scopus 로고
    • A workflow to increase the detection rate of proteins from unsequenced organisms in high-throughput proteomics experiments
    • DOI 10.1002/pmic.200700474
    • J. Grossmann, B. Fischer, K. Baerenfaller, J. Owiti, J.M. Buhmann, W. Gruissem, and S. Baginsky A workflow to increase the detection rate of proteins from unsequenced organisms in high-throughput proteomics experiments Proteomics 7 2007 4245 4254 (Pubitemid 350250470)
    • (2007) Proteomics , vol.7 , Issue.23 , pp. 4245-4254
    • Grossmann, J.1    Fischer, B.2    Baerenfaller, K.3    Owiti, J.4    Buhmann, J.M.5    Gruissem, W.6    Baginsky, S.7
  • 105
    • 28644448658 scopus 로고    scopus 로고
    • Stable isotope labeling of Arabidopsis thaliana cells and quantitative proteomics by mass spectrometry
    • DOI 10.1074/mcp.M500190-MCP200
    • A. Gruhler, W.X. Schulze, R. Matthiesen, M. Mann, and O.N. Jensen Stable isotope labeling of Arabidopsis thaliana cells and quantitative proteomics by mass spectrometry Mol. Cell. Proteomics 4 2005 1697 1709 (Pubitemid 41749263)
    • (2005) Molecular and Cellular Proteomics , vol.4 , Issue.11 , pp. 1697-1709
    • Gruhler, A.1    Schulze, W.X.2    Matthiesen, R.3    Mann, M.4    Jensen, O.N.5
  • 106
    • 4444301196 scopus 로고    scopus 로고
    • Phylogenetic profiling of the Arabidopsis thaliana proteome: What proteins distinguish plants from other organisms?
    • R.A. Gutierrez, P.J. Green, K. Keegstra, and J.B. Ohlrogge Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms? Genome Biol. 5 2004
    • (2004) Genome Biol. , vol.5
    • Gutierrez, R.A.1    Green, P.J.2    Keegstra, K.3    Ohlrogge, J.B.4
  • 107
    • 0032875697 scopus 로고    scopus 로고
    • Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
    • DOI 10.1038/13690
    • S.P. Gygi, B. Rist, S.A. Gerber, F. Turecek, M.H. Gelb, and R. Aebersold Quantitative analysis of complex protein mixtures using isotope-coded affinity tags Nat. Biotechnol. 17 1999 994 999 (Pubitemid 29474856)
    • (1999) Nature Biotechnology , vol.17 , Issue.10 , pp. 994-999
    • Gygi, S.P.1    Rist, B.2    Gerber, S.A.3    Turecek, F.4    Gelb, M.H.5    Aebersold, R.6
  • 108
    • 61349103096 scopus 로고    scopus 로고
    • Identification of thioredoxin disulfide targets using a quantitative proteomics approach based on isotope-coded affinity tags
    • P. Hagglund, J. Bunkenborg, K. Maeda, and B. Svensson Identification of thioredoxin disulfide targets using a quantitative proteomics approach based on isotope-coded affinity tags J. Proteome Res. 7 2008 5270 5276
    • (2008) J. Proteome Res. , vol.7 , pp. 5270-5276
    • Hagglund, P.1    Bunkenborg, J.2    Maeda, K.3    Svensson, B.4
  • 109
    • 33847680078 scopus 로고    scopus 로고
    • Proteomic complex detection using sedimentation
    • DOI 10.1021/ac061959t
    • N.T. Hartman, F. Sicilia, K.S. Lilley, and P. Dupree Proteomic complex detection using sedimentation Anal. Chem. 79 2007 2078 2083 (Pubitemid 46355241)
    • (2007) Analytical Chemistry , vol.79 , Issue.5 , pp. 2078-2083
    • Hartman, N.T.1    Sicilia, F.2    Lilley, K.S.3    Dupree, P.4
  • 110
    • 34548461256 scopus 로고    scopus 로고
    • Subcellular shotgun proteomics in plants: Looking beyond the usual suspects
    • DOI 10.1002/pmic.200700216
    • P.A. Haynes, and T.H. Roberts Subcellular shotgun proteomics in plants: looking beyond the usual suspects Proteomics 7 2007 2963 2975 (Pubitemid 47359933)
    • (2007) Proteomics , vol.7 , Issue.16 , pp. 2963-2975
    • Haynes, P.A.1    Roberts, T.H.2
  • 111
    • 38549127781 scopus 로고    scopus 로고
    • PhosPhAt: A database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor
    • J.L. Heazlewood, P. Durek, J. Hummel, J. Selbig, W. Weckwerth, D. Walther, and W.X. Schulze PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor Nucleic Acids Res. 36 2008 D1015 D1021
    • (2008) Nucleic Acids Res. , vol.36
    • Heazlewood, J.L.1    Durek, P.2    Hummel, J.3    Selbig, J.4    Weckwerth, W.5    Walther, D.6    Schulze, W.X.7
  • 113
    • 63349099933 scopus 로고    scopus 로고
    • Blue native DIGE as a tool for comparative analyses of protein complexes
    • J. Heinemeyer, B. Scheibe, U.K. Schmitz, and H.P. Braun Blue native DIGE as a tool for comparative analyses of protein complexes J. Proteomics 72 2009 539 544
    • (2009) J. Proteomics , vol.72 , pp. 539-544
    • Heinemeyer, J.1    Scheibe, B.2    Schmitz, U.K.3    Braun, H.P.4
  • 114
    • 37549042703 scopus 로고    scopus 로고
    • Blue-native gel electrophoresis for the characterization of protein complexes in plants
    • J. Heinemeyer, D. Lewejohann, and H.P. Braun Blue-native gel electrophoresis for the characterization of protein complexes in plants Methods Mol. Biol. 355 2007 343 352
    • (2007) Methods Mol. Biol. , vol.355 , pp. 343-352
    • Heinemeyer, J.1    Lewejohann, D.2    Braun, H.P.3
  • 115
    • 2342518184 scopus 로고    scopus 로고
    • An efficient protocol for the identification of protein phosphorylation in a seedless plant, sensitive enough to detect members of signalling cascades
    • D. Heintz, V. Wurtz, A.A. High, A. Van Dorsselaer, R. Reski, and E. Sarnighausen An efficient protocol for the identification of protein phosphorylation in a seedless plant, sensitive enough to detect members of signalling cascades Electrophoresis 25 2004 1149 1159 (Pubitemid 38578957)
    • (2004) Electrophoresis , vol.25 , Issue.7-8 , pp. 1149-1159
    • Heintz, D.1    Wurtz, V.2    High, A.A.3    Van Dorsselaer, A.4    Reski, R.5    Sarnighausen, E.6
  • 117
    • 33646832552 scopus 로고    scopus 로고
    • The Arabidopsis FLC protein interacts directly in vivo with SOC1 and FT chromatin and is part of a high-molecular-weight protein complex
    • DOI 10.1111/j.1365-313X.2006.02686.x
    • C.A. Helliwell, C.C. Wood, M. Robertson, W.J. Peacock, and E.S. Dennis The Arabidopsis FLC protein interacts directly in vivo with SOC1 and FT chromatin and is part of a high-molecular-weight protein complex Plant J. 46 2006 183 192 (Pubitemid 43773560)
    • (2006) Plant Journal , vol.46 , Issue.2 , pp. 183-192
    • Helliwell, C.A.1    Wood, C.C.2    Robertson, M.3    James Peacock, W.4    Dennis, E.S.5
  • 118
    • 36549032156 scopus 로고    scopus 로고
    • SPINE: A method for the rapid detection and analysis of protein-protein interactions in vivo
    • DOI 10.1002/pmic.200700491
    • C. Herzberg, L.A.F. Weidinger, B. Dorrbecker, S. Hubner, J. Stulke, and F.M. Commichau SPINE: a method for the rapid detection and analysis of protein-protein interactions in vivo Proteomics 7 2007 4032 4035 (Pubitemid 350190274)
    • (2007) Proteomics , vol.7 , Issue.22 , pp. 4032-4035
    • Herzberg, C.1    Weidinger, L.A.F.2    Dorrbecker, B.3    Hubner, S.4    Stulke, J.5    Commichau, F.M.6
  • 121
    • 17444375706 scopus 로고    scopus 로고
    • Complementary structural information from a tryptic N-linked glycopeptide via electron transfer ion/ion reactions and collision-induced dissociation
    • DOI 10.1021/pr049770q
    • J.M. Hogan, S.J. Pitteri, P.A. Chrisman, and S.A. McLuckey Complementary structural information from a tryptic N-linked glycopeptide via electron transfer ion/ion reactions and collision-induced dissociation J. Proteome Res. 4 2005 628 632 (Pubitemid 40548173)
    • (2005) Journal of Proteome Research , vol.4 , Issue.2 , pp. 628-632
    • Hogan, J.M.1    Pitteri, S.J.2    Chrisman, P.A.3    McLuckey, S.A.4
  • 122
    • 80355135321 scopus 로고    scopus 로고
    • Bimolecular fluorescence complementation (BiFC) assay for protein-protein interaction in onion cells using the helios gene gun
    • Hollender Court pii:1963
    • Hollender Court, Liu, Z., 2010. Bimolecular fluorescence complementation (BiFC) assay for protein-protein interaction in onion cells using the helios gene gun. J. Vis. Exp. 40. pii:1963.
    • (2010) J. Vis. Exp. , vol.40
    • Liu, Z.1
  • 123
    • 2942598149 scopus 로고    scopus 로고
    • PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation
    • DOI 10.1002/pmic.200300772
    • P.V. Hornbeck, I. Chabra, J.M. Kornhauser, E. Skrzypek, and B. Zhang Phosphosite: a bioinformatics resource dedicated to physiological protein phosphorylation Proteomics 4 2004 1551 1561 (Pubitemid 38738314)
    • (2004) Proteomics , vol.4 , Issue.6 , pp. 1551-1561
    • Hornbeck, P.V.1    Chabra, I.2    Kornhauser, J.M.3    Skrzypek, E.4    Zhang, B.5
  • 124
    • 0037995710 scopus 로고    scopus 로고
    • Simultaneous visualization of multiple protein interactions in living cells using multicolor fluorescence complementation analysis
    • DOI 10.1038/nbt816
    • C.D. Hu, and T.K. Kerppola Simultaneous visualization of multiple protein interactions in living cells using multicolor fluorescence complementation analysis Nat. Biotechnol. 21 2003 539 545 (Pubitemid 36532019)
    • (2003) Nature Biotechnology , vol.21 , Issue.5 , pp. 539-545
    • Hu, C.-D.1    Kerppola, T.K.2
  • 125
    • 67849122322 scopus 로고    scopus 로고
    • VisANT 3.5: Multi-scale network visualization, analysis and inference based on the gene ontology
    • Z. Hu, J.H. Hung, Y. Wang, Y.C. Chang, C.L. Huang, M. Huyck, and C. DeLisi VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology Nucleic Acids Res. 37 2009 W115 W121
    • (2009) Nucleic Acids Res. , vol.37
    • Hu, Z.1    Hung, J.H.2    Wang, Y.3    Chang, Y.C.4    Huang, C.L.5    Huyck, M.6    Delisi, C.7
  • 126
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • D.W. Huang, B.T. Sherman, and R.A. Lempicki Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources Nat. Protoc. 4 2009 44 57
    • (2009) Nat. Protoc. , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 127
    • 0034614490 scopus 로고    scopus 로고
    • Signaling - 2000 and beyond
    • T. Hunter Signaling - 2000 and beyond Cell 100 2000 113 127 (Pubitemid 30046300)
    • (2000) Cell , vol.100 , Issue.1 , pp. 113-127
    • Hunter, T.1
  • 131
    • 75849155011 scopus 로고    scopus 로고
    • The 'ABC' of MADS domain protein behaviour and interactions
    • R.G. Immink, K. Kaufmann, and G.C. Angenent The 'ABC' of MADS domain protein behaviour and interactions Semin. Cell Dev. Biol. 21 2010 87 93
    • (2010) Semin. Cell Dev. Biol. , vol.21 , pp. 87-93
    • Immink, R.G.1    Kaufmann, K.2    Angenent, G.C.3
  • 133
    • 26844559000 scopus 로고    scopus 로고
    • Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein
    • DOI 10.1074/mcp.M500061-MCP200
    • Y. Ishihama, Y. Oda, T. Tabata, T. Sato, T. Nagasu, J. Rappsilber, and M. Mann Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein Mol. Cell. Proteomics 4 2005 1265 1272 (Pubitemid 41448714)
    • (2005) Molecular and Cellular Proteomics , vol.4 , Issue.9 , pp. 1265-1272
    • Ishihama, Y.1    Oda, Y.2    Tabata, T.3    Sato, T.4    Nagasu, T.5    Rappsilber, J.6    Mann, M.7
  • 137
    • 0035042776 scopus 로고    scopus 로고
    • A literature network of human genes for high-throughput analysis of gene expression
    • DOI 10.1038/88213
    • T.K. Jenssen, A. Laegreid, J. Komorowski, and E. Hovig A literature network of human genes for high-throughput analysis of gene expression Nat. Genet. 28 2001 21 28 (Pubitemid 32405811)
    • (2001) Nature Genetics , vol.28 , Issue.1 , pp. 21-28
    • Jenssen, T.-K.1    Laegreid, A.2    Komorowski, J.3    Hovig, E.4
  • 140
    • 77955345941 scopus 로고    scopus 로고
    • Profiling of protein interaction networks of protein complexes using affinity purification and quantitative mass spectrometry
    • R.M. Kaake, X.R. Wang, and L. Huang Profiling of protein interaction networks of protein complexes using affinity purification and quantitative mass spectrometry Mol. Cell. Proteomics 9 2010 1650 1665
    • (2010) Mol. Cell. Proteomics , vol.9 , pp. 1650-1665
    • Kaake, R.M.1    Wang, X.R.2    Huang, L.3
  • 141
    • 44049093832 scopus 로고    scopus 로고
    • Isolation of proteins and protein complexes by immunoprecipitation
    • B. Kaboord, and M. Perr Isolation of proteins and protein complexes by immunoprecipitation A. Posch, 2D PAGE: Sample Preparation and Fractionation 424th ed. 2008 Humana Press 349 364
    • (2008) 2D PAGE: Sample Preparation and Fractionation , pp. 349-364
    • Kaboord, B.1    Perr, M.2
  • 143
    • 54449083188 scopus 로고    scopus 로고
    • Browsing multidimensional molecular networks with the generic network browser (N-Browse)
    • (Chapter 9: Unit 9.11)
    • Kao, H.L., Gunsalus, K.C., 2008. Browsing multidimensional molecular networks with the generic network browser (N-Browse). Curr. Protoc. Bioinformatics (Chapter 9: Unit 9.11).
    • (2008) Curr. Protoc. Bioinformatics
    • Kao, H.L.1    Gunsalus, K.C.2
  • 144
    • 78651092959 scopus 로고    scopus 로고
    • Development of a novel cross-linking strategy for fast and accurate identification of cross-linked peptides of protein complexes
    • doi:10.1074/mcp.M110.002212
    • Kao, A., Chiu, C.l., Vellucci, D., Yang, Y., Patel, V.R., Guan, S., Randall, A., Baldi, P., Rychnovsky, S.D., Huang, L., 2011. Development of a novel cross-linking strategy for fast and accurate identification of cross-linked peptides of protein complexes. Mol. Cell. Proteomics. doi:10.1074/mcp.M110.002212.
    • (2011) Mol. Cell. Proteomics.
    • Kao, A.1    Chiu, C.L.2    Vellucci, D.3    Yang, Y.4    Patel, V.R.5    Guan, S.6    Randall, A.7    Baldi, P.8    Rychnovsky, S.D.9    Huang, L.10
  • 145
    • 0035984025 scopus 로고    scopus 로고
    • Spectral profiling for the simultaneous observation of four distinct fluorescent proteins and detection of protein-protein interaction via
    • DOI 10.1104/pp.005496
    • N. Kato, D. Pontier, and E. Lam Spectral profiling for the simultaneous observation of four distinct fluorescent proteins and detection of protein-protein interaction via fluorescence resonance energy transfer in tobacco leaf nuclei Plant Physiol. 129 2002 931 942 (Pubitemid 34801067)
    • (2002) Plant Physiology , vol.129 , Issue.3 , pp. 931-942
    • Kato, N.1    Pontier, D.2    Lam, E.3
  • 146
    • 33750579665 scopus 로고    scopus 로고
    • Plant phosphoproteomics: A long road ahead
    • DOI 10.1002/pmic.200600232
    • B. Kersten, G.K. Agrawal, H. Iwahashi, and R. Rakwal Plant phosphoproteomics: a long road ahead Proteomics 6 2006 5517 5528 (Pubitemid 44683219)
    • (2006) Proteomics , vol.6 , Issue.20 , pp. 5517-5528
    • Kersten, B.1    Agrawal, G.K.2    Iwahashi, H.3    Rakwal, R.4
  • 149
    • 8844219516 scopus 로고    scopus 로고
    • Prediction of phosphorylation sites using SVMs
    • DOI 10.1093/bioinformatics/bth382
    • J.H. Kim, J. Lee, B. Oh, K. Kimm, and I. Koh Prediction of phosphorylation sites using SVMs Bioinformatics 20 2004 3179 3184 (Pubitemid 39619207)
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 3179-3184
    • Kim, J.H.1    Lee, J.2    Oh, B.3    Kimm, K.4    Koh, I.5
  • 150
    • 4344627295 scopus 로고    scopus 로고
    • Protein complexes of the plant plasma membrane resolved by Blue Native PAGE
    • DOI 10.1111/j.1399-3054.2004.00354.x
    • J. Kjell, A.G. Rasmusson, H. Larsson, and S. Widell Protein complexes of the plant plasma membrane resolved by Blue Native PAGE Physiol. Plant. 121 2004 546 555 (Pubitemid 39123188)
    • (2004) Physiologia Plantarum , vol.121 , Issue.4 , pp. 546-555
    • Kjell, J.1    Rasmusson, A.G.2    Larsson, H.3    Widell, S.4
  • 151
    • 1842432608 scopus 로고    scopus 로고
    • The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions
    • DOI 10.1016/j.cub.2004.02.039, PII S0960982204000909
    • T. Kleffmann, D. Russenberger, A. von Zychlinski, W. Christopher, K. Sjolander, W. Gruissem, and S. Baginsky The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions Curr. Biol. 14 2004 354 362 (Pubitemid 38431168)
    • (2004) Current Biology , vol.14 , Issue.5 , pp. 354-362
    • Kleffmann, T.1    Russenberger, D.2    Von Zychlinski, A.3    Christopher, W.4    Sjolander, K.5    Gruissem, W.6    Baginsky, S.7
  • 152
    • 77955394572 scopus 로고    scopus 로고
    • Optimization of formaldehyde cross-linking for protein interaction analysis of non-tagged integrin beta 1
    • doi:10.1155/2010/927585
    • Klockenbusch, C., Kast, J., 2010. Optimization of formaldehyde cross-linking for protein interaction analysis of non-tagged integrin beta 1. J. Biomed. Biotechnol. doi:10.1155/2010/927585.
    • (2010) J. Biomed. Biotechnol.
    • Klockenbusch, C.1    Kast, J.2
  • 153
    • 10844254729 scopus 로고    scopus 로고
    • Shared components of protein complexes - Versatile building blocks or biochemical artefacts?
    • DOI 10.1002/bies.20141
    • R. Krause, C. von Mering, P. Bork, and T. Dandekar Shared components of protein complexes-versatile building blocks or biochemical artefacts? Bioessays 26 2004 1333 1343 (Pubitemid 39664627)
    • (2004) BioEssays , vol.26 , Issue.12 , pp. 1333-1343
    • Krause, R.1    Von Mering, C.2    Bork, P.3    Dandekar, T.4
  • 154
    • 65649133057 scopus 로고    scopus 로고
    • Assembly of the cysteine synthase complex and the regulatory role of protein-protein interactions
    • S. Kumaran, H. Yi, H.B. Krishnan, and J.M. Jez Assembly of the cysteine synthase complex and the regulatory role of protein-protein interactions J. Biol. Chem. 284 2009 10268 10275
    • (2009) J. Biol. Chem. , vol.284 , pp. 10268-10275
    • Kumaran, S.1    Yi, H.2    Krishnan, H.B.3    Jez, J.M.4
  • 155
    • 77949520163 scopus 로고    scopus 로고
    • Combined bimolecular fluorescence complementation and forster resonance energy transfer reveals ternary SNARE complex formation in living plant cells
    • M. Kwaaitaal, N.F. Keinath, S. Pajonk, C. Biskup, and R. Panstruga Combined bimolecular fluorescence complementation and forster resonance energy transfer reveals ternary SNARE complex formation in living plant cells Plant Physiol. 152 2010 1135 1147
    • (2010) Plant Physiol. , vol.152 , pp. 1135-1147
    • Kwaaitaal, M.1    Keinath, N.F.2    Pajonk, S.3    Biskup, C.4    Panstruga, R.5
  • 156
    • 38949195338 scopus 로고    scopus 로고
    • Molecular and cellular approaches for the detection of protein-protein interactions: Latest techniques and current limitations
    • DOI 10.1111/j.1365-313X.2007.03332.x
    • S. Lalonde, D.W. Ehrhardt, D. Loque, J. Chen, S.Y. Rhee, and W.B. Frommer Molecular and cellular approaches for the detection of protein-protein interactions: latest techniques and current limitations Plant J. 53 2008 610 635 (Pubitemid 351227327)
    • (2008) Plant Journal , vol.53 , Issue.4 , pp. 610-635
    • Lalonde, S.1    Ehrhardt, D.W.2    Loque, D.3    Chen, J.4    Rhee, S.Y.5    Frommer, W.B.6
  • 158
    • 35649011957 scopus 로고    scopus 로고
    • Exploring the sialiome using titanium dioxide chromatography and mass spectrometry
    • DOI 10.1074/mcp.M700086-MCP200
    • M.R. Larsen, S.S. Jensen, L.A. Jakobsen, and N.H.H. Heegaard Exploring the sialiome using titanium dioxide chromatography and mass spectrometry Mol. Cell. Proteomics 6 2007 1778 1787 (Pubitemid 350031679)
    • (2007) Molecular and Cellular Proteomics , vol.6 , Issue.10 , pp. 1778-1787
    • Larsen, M.R.1    Jensen, S.S.2    Jakobsen, L.A.3    Heegaard, N.H.H.4
  • 159
  • 160
    • 65549102777 scopus 로고    scopus 로고
    • Protein-protein interaction databases: Keeping up with growing interactomes
    • B. Lehne, and T. Schlitt Protein-protein interaction databases: keeping up with growing interactomes Hum. Genomics 3 2009 291 297
    • (2009) Hum. Genomics , vol.3 , pp. 291-297
    • Lehne, B.1    Schlitt, T.2
  • 161
    • 77957298297 scopus 로고    scopus 로고
    • Complex assembly and metabolic profiling of Arabidopsis thaliana Plants overexpressing vitamin B6 biosynthesis proteins
    • doi:10.1093/mp/ssq041
    • Leuendorf, J.E., Osorio, S., Szewczyk, A., Fernie, A.R., Hellmann, H., 2010. Complex assembly and metabolic profiling of Arabidopsis thaliana Plants overexpressing vitamin B6 biosynthesis proteins. Mol. Plant doi:10.1093/mp/ ssq041.
    • (2010) Mol. Plant
    • Leuendorf, J.E.1    Osorio, S.2    Szewczyk, A.3    Fernie, A.R.4    Hellmann, H.5
  • 163
    • 70349977142 scopus 로고    scopus 로고
    • S-nitrosylation in plants: Pattern and function
    • C. Lindermayr, and J. Durner S-nitrosylation in plants: pattern and function J. Proteomics 73 2009 1 9
    • (2009) J. Proteomics , vol.73 , pp. 1-9
    • Lindermayr, C.1    Durner, J.2
  • 165
    • 34247185926 scopus 로고    scopus 로고
    • The chloroplast HSP70B-CDJ2-CGE1 chaperones catalyse assembly and disassembly of VIPP1 oligomers in Chlamydomonas
    • DOI 10.1111/j.1365-313X.2007.03047.x
    • C.M. Liu, F. Willmund, J.R. Golecki, S. Cacace, B. Hess, C. Markert, and M. Schroda The chloroplast HSP70B-CDJ2-CGE1 chaperones catalyse assembly and disassembly of VIPP1 oligomers in Chlamydomonas Plant J. 50 2007 265 277 (Pubitemid 46624135)
    • (2007) Plant Journal , vol.50 , Issue.2 , pp. 265-277
    • Liu, C.1    Willmund, F.2    Golecki, J.R.3    Cacace, S.4    Hess, B.5    Markert, C.6    Schroda, M.7
  • 166
    • 3242731195 scopus 로고    scopus 로고
    • A model for random sampling and estimation of relative protein abundance in shotgun proteomics
    • DOI 10.1021/ac0498563
    • H.B. Liu, R.G. Sadygov, and J.R. Yates A model for random sampling and estimation of relative protein abundance in shotgun proteomics Anal. Chem. 76 2004 4193 4201 (Pubitemid 38943698)
    • (2004) Analytical Chemistry , vol.76 , Issue.14 , pp. 4193-4201
    • Liu, H.1    Sadygov, R.G.2    Yates III, J.R.3
  • 167
    • 77954259264 scopus 로고    scopus 로고
    • PCFamily: A web server for searching homologous protein complexes
    • Y.S. Lo, C.Y. Lin, and J.M. Yang PCFamily: a web server for searching homologous protein complexes Nucleic Acids Res. 38 2010 W516 W522
    • (2010) Nucleic Acids Res. , vol.38
    • Lo, Y.S.1    Lin, C.Y.2    Yang, J.M.3
  • 168
    • 24044440971 scopus 로고    scopus 로고
    • BiNGO: A Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks
    • DOI 10.1093/bioinformatics/bti551
    • S. Maere, K. Heymans, and M. Kuiper BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks Bioinformatics 21 2005 3448 3449 (Pubitemid 41222459)
    • (2005) Bioinformatics , vol.21 , Issue.16 , pp. 3448-3449
    • Maere, S.1    Heymans, K.2    Kuiper, M.3
  • 169
    • 52649096494 scopus 로고    scopus 로고
    • Consequences of C-4 differentiation for chloroplast membrane proteomes in maize mesophyll and bundle sheath cells
    • W. Majeran, B. Zybailov, A.J. Ytterberg, J. Dunsmore, Q. Sun, and K.J. van Wijk Consequences of C-4 differentiation for chloroplast membrane proteomes in maize mesophyll and bundle sheath cells Mol. Cell. Proteomics 7 2008 1609 1638
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 1609-1638
    • Majeran, W.1    Zybailov, B.2    Ytterberg, A.J.3    Dunsmore, J.4    Sun, Q.5    Van Wijk, K.J.6
  • 170
    • 77949732319 scopus 로고    scopus 로고
    • From proteome lists to biological impact-tools and strategies for the analysis of large MS data sets
    • R. Malik, K. Dulla, E.A. Nigg, and R. Körner From proteome lists to biological impact-tools and strategies for the analysis of large MS data sets Proteomics 10 2010 1270 1283
    • (2010) Proteomics , vol.10 , pp. 1270-1283
    • Malik, R.1    Dulla, K.2    Nigg, E.A.3    Körner, R.4
  • 171
    • 0037032835 scopus 로고    scopus 로고
    • The protein kinase complement of the human genome
    • DOI 10.1126/science.1075762
    • G. Manning, D.B. Whyte, R. Martinez, T. Hunter, and S. Sudarsanam The protein kinase complement of the human genome Science 298 2002 1912 1934 (Pubitemid 35425239)
    • (2002) Science , vol.298 , Issue.5600 , pp. 1912-1934
    • Manning, G.1    Whyte, D.B.2    Martinez, R.3    Hunter, T.4    Sudarsanam, S.5
  • 173
    • 34247342702 scopus 로고    scopus 로고
    • Multidimensional protein identification technology (Mud(PIT) analysis of ubiquitinated proteins in plants
    • DOI 10.1074/mcp.M600408-MCP200
    • R. Maor, A. Jones, T.S. Nuhse, D.J. Studholme, S.C. Peck, and K. Shirasu Multidimensional protein identification technology (MudPIT) analysis of ubiquitinated proteins in plants Mol. Cell. Proteomics 6 2007 601 610 (Pubitemid 46630093)
    • (2007) Molecular and Cellular Proteomics , vol.6 , Issue.4 , pp. 601-610
    • Maor, R.1    Jones, A.2    Nuhse, T.S.3    Studholme, D.J.4    Peck, S.C.5    Shirasu, K.6
  • 174
    • 36749034740 scopus 로고    scopus 로고
    • A high content in lipid-modified peripheral proteins and integral receptor kinases features in the Arabidopsis plasma membrane proteome
    • DOI 10.1074/mcp.M700099-MCP200
    • A. Marmagne, M. Ferro, T. Meinnel, C. Bruley, L. Kuhn, J. Garin, H. Barbier-Brygoo, and G. Ephritikhine A high content in lipid-modified peripheral proteins and integral receptor kinases features in the Arabidopsis plasma membrane proteome Mol. Cell. Proteomics 6 2007 1980 1996 (Pubitemid 350201872)
    • (2007) Molecular and Cellular Proteomics , vol.6 , Issue.11 , pp. 1980-1996
    • Marmagne, A.1    Ferro, M.2    Meinnel, T.3    Bruley, C.4    Kuhn, L.5    Garin, J.6    Barbier-Brygoo, H.7    Ephritikhine, G.8
  • 176
    • 0035211290 scopus 로고    scopus 로고
    • Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs"
    • DOI 10.1101/gr.205301
    • L.R. Matthews, P. Vaglio, J. Reboul, H. Ge, B.P. Davis, J. Garrels, S. Vincent, and M. Vidal Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs" Genome Res. 11 2001 2120 2126 (Pubitemid 33138810)
    • (2001) Genome Research , vol.11 , Issue.12 , pp. 2120-2126
    • Matthews, L.R.1    Vaglio, P.2    Reboul, J.3    Ge, H.4    Davis, B.P.5    Garrels, J.6    Vincent, S.7    Vidal, M.8
  • 178
    • 0035478125 scopus 로고    scopus 로고
    • Surface plasmon resonance: Towards an understanding of the mechanisms of biological molecular recognition
    • DOI 10.1016/S1367-5931(00)00251-9
    • J.M. McDonnell Surface plasmon resonance: towards an understanding of the mechanisms of biological molecular recognition Curr. Opin. Chem. Biol. 5 2001 572 577 (Pubitemid 32907610)
    • (2001) Current Opinion in Chemical Biology , vol.5 , Issue.5 , pp. 572-577
    • McDonnell, J.M.1
  • 179
    • 43849091451 scopus 로고    scopus 로고
    • Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection
    • DOI 10.1074/mcp.M700543-MCP200
    • D.E. McNulty, and R.S. Annan Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection Mol. Cell. Proteomics 7 2008 971 980 (Pubitemid 351737096)
    • (2008) Molecular and Cellular Proteomics , vol.7 , Issue.5 , pp. 971-980
    • McNulty, D.E.1    Annan, R.S.2
  • 180
    • 40549132858 scopus 로고    scopus 로고
    • Tools for analyzing and predicting N-terminal protein modifications
    • DOI 10.1002/pmic.200700592
    • T. Meinnel, and C. Giglione Tools for analyzing and predicting N-terminal protein modifications Proteomics 8 2008 626 649 (Pubitemid 351362927)
    • (2008) Proteomics , vol.8 , Issue.4 , pp. 626-649
    • Meinnel, T.1    Giglione, C.2
  • 182
    • 34548442008 scopus 로고    scopus 로고
    • A sub-proteome of Arabidopsis thaliana mature stems trapped on Concanavalin a is enriched in cell wall glycoside hydrolases
    • DOI 10.1093/jxb/erm082
    • Z. Minic, E. Jamet, L. Negroni, P.A. der Garabedian, M. Zivy, and L. Jouanin A sub-proteome of Arabidopsis thaliana mature stems trapped on Concanavalin A is enriched in cell wall glycoside hydrolases J. Exp. Bot. 58 2007 2503 2512 (Pubitemid 47357550)
    • (2007) Journal of Experimental Botany , vol.58 , Issue.10 , pp. 2503-2512
    • Minic, Z.1    Jamet, E.2    Negroni, L.3    Arsene Der Garabedian, P.4    Zivy, M.5    Jouanin, L.6
  • 183
    • 77950865637 scopus 로고    scopus 로고
    • Sumoylation and other ubiquitin-like post-translational modifications in plants
    • K. Miura, and P.M. Hasegawa Sumoylation and other ubiquitin-like post-translational modifications in plants Trends Cell Biol. 20 2010 223 232
    • (2010) Trends Cell Biol. , vol.20 , pp. 223-232
    • Miura, K.1    Hasegawa, P.M.2
  • 184
    • 33746263848 scopus 로고    scopus 로고
    • Automated ultra-high-pressure multidimensional protein identification technology (UHP-MudPIT) for improved peptide identification of proteomic samples
    • DOI 10.1021/ac060354u
    • A. Motoyama, J.D. Venable, C.I. Ruse, and J.R. Yates Automated ultra-high-pressure multidimensional protein identification technology (UHP-MudPIT) for improved peptide identification of proteomic samples Anal. Chem. 78 2006 5109 5118 (Pubitemid 44100648)
    • (2006) Analytical Chemistry , vol.78 , Issue.14 , pp. 5109-5118
    • Motoyama, A.1    Venable, J.D.2    Ruse, C.I.3    Yates III, J.R.4
  • 185
    • 77956275838 scopus 로고    scopus 로고
    • Functional characterization of the tomato cyclin-dependent kinase inhibitor SlKRP1 domains involved in protein-protein interactions
    • M. Nafati, N. Frangne, M. Hernould, C. Chevalier, and F. Gévaudant Functional characterization of the tomato cyclin-dependent kinase inhibitor SlKRP1 domains involved in protein-protein interactions New Phytol. 188 2010 136 149
    • (2010) New Phytol. , vol.188 , pp. 136-149
    • Nafati, M.1    Frangne, N.2    Hernould, M.3    Chevalier, C.4    Gévaudant, F.5
  • 186
    • 77952384755 scopus 로고    scopus 로고
    • Topological analysis of the extrinsic PsbO, PsbP and PsbQ proteins in a green algal PSII complex by cross-linking with a water-soluble carbodiimide
    • R. Nagao, T. Suzuki, A. Okumura, A. Niikura, M. Iwai, N. Dohmae, T. Tomo, J.R. Shen, M. Ikeuchi, and I. Enami Topological analysis of the extrinsic PsbO, PsbP and PsbQ proteins in a green algal PSII complex by cross-linking with a water-soluble carbodiimide Plant Cell Physiol. 51 2010 718 727
    • (2010) Plant Cell Physiol. , vol.51 , pp. 718-727
    • Nagao, R.1    Suzuki, T.2    Okumura, A.3    Niikura, A.4    Iwai, M.5    Dohmae, N.6    Tomo, T.7    Shen, J.R.8    Ikeuchi, M.9    Enami, I.10
  • 189
    • 34248161925 scopus 로고    scopus 로고
    • 15N-metabolic labeling for automated peptide identification in Arabidopsis thaliana
    • DOI 10.1002/pmic.200600832
    • C.J. Nelson, E.L. Huttlin, A.D. Hegeman, A.C. Harms, and M.R. Sussman Implications of N-15-metabolic labeling for automated peptide identification in Arabidopsis thaliana Proteomics 7 2007 1279 1292 (Pubitemid 46722452)
    • (2007) Proteomics , vol.7 , Issue.8 , pp. 1279-1292
    • Nelson, C.J.1    Huttlin, E.L.2    Hegeman, A.D.3    Harms, A.C.4    Sussman, M.R.5
  • 190
    • 33745936562 scopus 로고    scopus 로고
    • Structure and function of photosystems I and II
    • DOI 10.1146/annurev.arplant.57.032905.105350
    • N. Nelson, and C.F. Yocum Structure and function of photosystems I and II Annu. Rev. Plant Biol. 57 2006 521 565 (Pubitemid 44061036)
    • (2006) Annual Review of Plant Biology , vol.57 , pp. 521-565
    • Nelson, N.1    Yocum, C.F.2
  • 191
    • 3242755176 scopus 로고    scopus 로고
    • Plant proteome analysis by mass spectrometry: Principles, problems, pitfalls and recent developments
    • DOI 10.1016/j.phytochem.2004.04.015, PII S0031942204001645
    • R.P. Newton, A.G. Brenton, C.J. Smith, and E. Dudley Plant proteome analysis by mass spectrometry: principles, problems, pitfalls and recent developments Phytochemistry 65 2004 1449 1485 (Pubitemid 38969930)
    • (2004) Phytochemistry , vol.65 , Issue.11 , pp. 1449-1485
    • Newton, R.P.1    Brenton, A.G.2    Smith, C.J.3    Dudley, E.4
  • 192
    • 33846010726 scopus 로고    scopus 로고
    • Extent of modifications in human proteome samples and their effect on dynamic range of analysis in shotgun proteomics
    • DOI 10.1074/mcp.M600248-MCP200
    • M.L. Nielsen, M.M. Savitski, and R.A. Zubarev Extent of modifications in human proteome samples and their effect on dynamic range of analysis in shotgun proteomics Mol. Cell. Proteomics 5 2006 2384 2391 (Pubitemid 46040642)
    • (2006) Molecular and Cellular Proteomics , vol.5 , Issue.12 , pp. 2384-2391
    • Nielsen, M.L.1    Savitski, M.M.2    Zubarev, R.A.3
  • 193
    • 35648996970 scopus 로고    scopus 로고
    • Temporal analysis of sucrose-induced phosphorylation changes in plasma membrane proteins of Arabidopsis
    • DOI 10.1074/mcp.M700164-MCP200
    • T. Niittylae, A.T. Fuglsang, M.G. Palmgren, W.B. Frommer, and W.X. Schulze Temporal analysis of sucrose-induced phosphorylation changes in plasma membrane proteins of Arabidopsis Mol. Cell. Proteomics 6 2007 1711 1726 (Pubitemid 350031673)
    • (2007) Molecular and Cellular Proteomics , vol.6 , Issue.10 , pp. 1711-1726
    • Niittyla, T.1    Fuglsang, A.T.2    Palmgren, M.G.3    Frommer, W.B.4    Schulze, W.X.5
  • 194
    • 11444263845 scopus 로고    scopus 로고
    • Large-scale analysis of in vivo phosphorylated membrane proteins by immobilized metal ion affinity chromatography and mass spectrometry
    • T.S. Nuhse, A. Stensballe, O.N. Jensen, and S.C. Peck Large-scale analysis of in vivo phosphorylated membrane proteins by immobilized metal ion affinity chromatography and mass spectrometry Mol. Cell. Proteomics 2 2003 1234 1243
    • (2003) Mol. Cell. Proteomics , vol.2 , pp. 1234-1243
    • Nuhse, T.S.1    Stensballe, A.2    Jensen, O.N.3    Peck, S.C.4
  • 195
    • 0042622251 scopus 로고    scopus 로고
    • Scansite 2.0: Proteome-wide prediction of cell signalling interactions using short sequence motifs
    • DOI 10.1093/nar/gkg584
    • J.C. Obenauer, L.C. Cantley, and M.B. Yaffe Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs Nucleic Acids Res. 31 2003 3635 3641 (Pubitemid 37442212)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3635-3641
    • Obenauer, J.C.1    Cantley, L.C.2    Yaffe, M.B.3
  • 196
    • 0035067251 scopus 로고    scopus 로고
    • Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome
    • DOI 10.1038/86783
    • Y. Oda, T. Nagasu, and B.T. Chait Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome Nat. Biotechnol. 19 2001 379 382 (Pubitemid 32275350)
    • (2001) Nature Biotechnology , vol.19 , Issue.4 , pp. 379-382
    • Oda, Y.1    Nagasu, T.2    Chait, B.T.3
  • 198
    • 37249039990 scopus 로고    scopus 로고
    • The analysis of protein-protein interactions in plants by bimolecular fluorescence complementation
    • DOI 10.1104/pp.107.107284
    • N. Ohad, K. Shichrur, and S. Yalovsky The analysis of protein-protein interactions in plants by bimolecular fluorescence complementation Plant Physiol. 145 2007 1090 1099 (Pubitemid 350276728)
    • (2007) Plant Physiology , vol.145 , Issue.4 , pp. 1090-1099
    • Ohad, N.1    Shichrur, K.2    Yalovsky, S.3
  • 199
    • 67649369328 scopus 로고    scopus 로고
    • Reconstitution of Arabidopsis thaliana SUMO pathways in E. coli: Functional evaluation of SUMO machinery proteins and mapping of SUMOylation sites by mass spectrometry
    • S. Okada, M. Nagabuchi, Y. Takamura, T. Nakagawa, K. Shinmyozu, J. Nakayama, and K. Tanaka Reconstitution of Arabidopsis thaliana SUMO pathways in E. coli: functional evaluation of SUMO machinery proteins and mapping of SUMOylation sites by mass spectrometry Plant Cell Physiol. 50 2009 1049 1061
    • (2009) Plant Cell Physiol. , vol.50 , pp. 1049-1061
    • Okada, S.1    Nagabuchi, M.2    Takamura, Y.3    Nakagawa, T.4    Shinmyozu, K.5    Nakayama, J.6    Tanaka, K.7
  • 200
    • 77954711237 scopus 로고    scopus 로고
    • Megadalton complexes in the chloroplast stroma of Arabidopsis thaliana characterized by size exclusion chromatography, mass spectrometry, and hierarchical clustering
    • P.D.B. Olinares, L. Ponnala, and K.J. van Wijk Megadalton complexes in the chloroplast stroma of Arabidopsis thaliana characterized by size exclusion chromatography, mass spectrometry, and hierarchical clustering Mol. Cell. Proteomics 9 2010 1594 1615
    • (2010) Mol. Cell. Proteomics , vol.9 , pp. 1594-1615
    • Olinares, P.D.B.1    Ponnala, L.2    Van Wijk, K.J.3
  • 201
    • 77956956487 scopus 로고    scopus 로고
    • The publication and database deposition of molecular interaction data
    • (Chapter 25, Unit 25.3)
    • Orchard, S., Aranda, B., Hermjakob, H., 2010. The publication and database deposition of molecular interaction data. Curr. Protoc. Protein Sci. (Chapter 25, Unit 25.3).
    • (2010) Curr. Protoc. Protein Sci.
    • Orchard, S.1    Aranda, B.2    Hermjakob, H.3
  • 204
    • 73949135134 scopus 로고    scopus 로고
    • Photosystem II organisation in chloroplasts of Arum italicum leaf depends on tissue location
    • L. Pantaleoni, L. Ferroni, C. Baldisserotto, E.M. Aro, and S. Pancaldi Photosystem II organisation in chloroplasts of Arum italicum leaf depends on tissue location Planta 230 2009 1019 1031
    • (2009) Planta , vol.230 , pp. 1019-1031
    • Pantaleoni, L.1    Ferroni, L.2    Baldisserotto, C.3    Aro, E.M.4    Pancaldi, S.5
  • 205
    • 65249165427 scopus 로고    scopus 로고
    • Comparative interactomics: Analysis of Arabidopsis 14-3-3 complexes reveals highly conserved 14-3-3 interactions between humans and plants
    • A.L. Paul, L. Liu, S. McClung, B. Laughner, S. Chen, and R.J. Ferl Comparative interactomics: analysis of Arabidopsis 14-3-3 complexes reveals highly conserved 14-3-3 interactions between humans and plants J. Proteome Res. 8 2009 1913 1924
    • (2009) J. Proteome Res. , vol.8 , pp. 1913-1924
    • Paul, A.L.1    Liu, L.2    McClung, S.3    Laughner, B.4    Chen, S.5    Ferl, R.J.6
  • 208
    • 34547098143 scopus 로고    scopus 로고
    • Three hydroxyproline-rich glycopeptides derived from a single petunia polyprotein precursor activate defensin I, a pathogen defense response gene
    • DOI 10.1074/jbc.M701543200
    • G. Pearce, W.F. Siems, R. Bhattacharya, Y.C. Chen, and C.A. Ryan Three hydroxyproline-rich glycopeptides derived from a single petunia polyprotein precursor activate defensin I, a pathogen defense response gene J. Biol. Chem. 282 2007 17777 17784 (Pubitemid 47100327)
    • (2007) Journal of Biological Chemistry , vol.282 , Issue.24 , pp. 17777-17784
    • Pearce, G.1    Siems, W.F.2    Bhattacharya, R.3    Chen, Y.-C.4    Ryan, C.A.5
  • 209
    • 42049091467 scopus 로고    scopus 로고
    • Evaluation of proteomic strategies for analyzing ubiquitinated proteins
    • J.M. Peng Evaluation of proteomic strategies for analyzing ubiquitinated proteins BMC Reports 41 2008 177 183
    • (2008) BMC Reports , vol.41 , pp. 177-183
    • Peng, J.M.1
  • 210
    • 0037277179 scopus 로고    scopus 로고
    • Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: The yeast proteome
    • DOI 10.1021/pr025556v
    • J.M. Peng, J.E. Elias, C.C. Thoreen, L.J. Licklider, and S.P. Gygi Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome J. Proteome Res. 2 2003 43 50 (Pubitemid 36207189)
    • (2003) Journal of Proteome Research , vol.2 , Issue.1 , pp. 43-50
    • Peng, J.1    Elias, J.E.2    Thoreen, C.C.3    Licklider, L.J.4    Gygi, S.P.5
  • 211
    • 77954436604 scopus 로고    scopus 로고
    • Chloroplast stromal proteins, CRR6 and CRR7, are required for assembly of the NAD(P)H dehydrogenase subcomplex A in Arabidopsis
    • L.W. Peng, W.H. Cai, and T. Shikanai Chloroplast stromal proteins, CRR6 and CRR7, are required for assembly of the NAD(P)H dehydrogenase subcomplex A in Arabidopsis Plant J. 63 2010 203 211
    • (2010) Plant J. , vol.63 , pp. 203-211
    • Peng, L.W.1    Cai, W.H.2    Shikanai, T.3
  • 212
    • 20444398508 scopus 로고    scopus 로고
    • 2 levels and alters mitochondrial physiology in Arabidopsis
    • DOI 10.1016/j.jmb.2005.04.062, PII S0022283605004948
    • M. Perales, H. Eubel, J. Heinemeyer, A. Colaneri, E. Zabaleta, and H.P. Braun Disruption of a nuclear gene encoding a mitochondrial gamma carbonic anhydrase reduces complex I and supercomplex I+III2 levels and alters mitochondrial physiology in Arabidopsis J. Mol. Biol. 350 2005 263 277 (Pubitemid 40805461)
    • (2005) Journal of Molecular Biology , vol.350 , Issue.2 , pp. 263-277
    • Perales, M.1    Eubel, H.2    Heinemeyer, J.3    Colaneri, A.4    Zabaleta, E.5    Braun, H.-P.6
  • 213
    • 84934444630 scopus 로고    scopus 로고
    • Analysis of protein-protein interactions using bioluminescence resonance energy transfer
    • K.D.G. Pfleger Analysis of protein-protein interactions using bioluminescence resonance energy transfer Methods Mol. Biol. 574 2009 173 183
    • (2009) Methods Mol. Biol. , vol.574 , pp. 173-183
    • Pfleger, K.D.G.1
  • 215
    • 1542344435 scopus 로고    scopus 로고
    • Proteasomes and their kin: Proteases in the machine age
    • DOI 10.1038/nrm1336
    • C.M. Pickart, and R.E. Cohen Proteasomes and their kin: proteases in the machine age Nat. Rev. Mol. Cell Biol. 5 2004 177 187 (Pubitemid 38325799)
    • (2004) Nature Reviews Molecular Cell Biology , vol.5 , Issue.3 , pp. 177-187
    • Pickart, C.M.1    Cohen, R.E.2
  • 216
    • 60549116192 scopus 로고    scopus 로고
    • Mass spectrometric characterization of membrane integral low molecular weight proteins from photosystem II in barley etioplasts
    • M. Ploscher, B. Granvogl, M. Zoryan, V. Reisinger, and L.A. Eichacker Mass spectrometric characterization of membrane integral low molecular weight proteins from photosystem II in barley etioplasts Proteomics 9 2009 625 635
    • (2009) Proteomics , vol.9 , pp. 625-635
    • Ploscher, M.1    Granvogl, B.2    Zoryan, M.3    Reisinger, V.4    Eichacker, L.A.5
  • 217
    • 33747853260 scopus 로고    scopus 로고
    • APID: Agile protein interaction dataanalyzer
    • C. Prieto, and J. De Las Rivas APID: agile protein interaction dataanalyzer Nucleic Acids Res. 34 2006 W298 W302
    • (2006) Nucleic Acids Res. , vol.34
    • Prieto, C.1    De Las Rivas, J.2
  • 219
    • 77957326091 scopus 로고    scopus 로고
    • Quantitative analysis of protein complex constituents and their phosphorylation states on a LTQ-orbitrap instrument
    • doi:10.1021/pr1003888
    • Przybylski, C., Junger, M.A., Aubertin, J., Radvanyi, F., Aebersold, R., Pflieger, D., 2010. Quantitative analysis of protein complex constituents and their phosphorylation states on a LTQ-orbitrap instrument. J. Proteome Res. doi:10.1021/pr1003888.
    • (2010) J. Proteome Res.
    • Przybylski, C.1    Junger, M.A.2    Aubertin, J.3    Radvanyi, F.4    Aebersold, R.5    Pflieger, D.6
  • 220
    • 0034841844 scopus 로고    scopus 로고
    • The tandem affinity purification (TAP) method: A general procedure of protein complex purification
    • DOI 10.1006/meth.2001.1183
    • O. Puig, F. Caspary, G. Rigaut, B. Rutz, E. Bouveret, E. Bragado-Nilsson, M. Wilm, and B. Seraphin The tandem affinity purification (TAP) method: a general procedure of protein complex purification Methods 24 2001 218 229 (Pubitemid 32846428)
    • (2001) Methods , vol.24 , Issue.3 , pp. 218-229
    • Puig, O.1    Caspary, F.2    Rigaut, G.3    Rutz, B.4    Bouveret, E.5    Bragado-Nilsson, E.6    Wilm, M.7    Seraphin, B.8
  • 221
    • 61349113308 scopus 로고    scopus 로고
    • Purification of low-abundance Arabidopsis plasma-membrane protein complexes and identification of candidate components
    • Y.P. Qi, and F. Katagiri Purification of low-abundance Arabidopsis plasma-membrane protein complexes and identification of candidate components Plant J. 57 2009 932 944
    • (2009) Plant J. , vol.57 , pp. 932-944
    • Qi, Y.P.1    Katagiri, F.2
  • 223
    • 77953128629 scopus 로고    scopus 로고
    • Iron stabilizes thylakoid protein-pigment complexes in Indian mustard during Cd-phytoremediation as revealed by BN-SDS-PAGE and ESI-MS/MS
    • M.H. Qureshi, G.M. D'Amici, M. Fagioni, S. Rinalducci, and L. Zolla Iron stabilizes thylakoid protein-pigment complexes in Indian mustard during Cd-phytoremediation as revealed by BN-SDS-PAGE and ESI-MS/MS J. Plant Physiol. 167 2010 761 770
    • (2010) J. Plant Physiol. , vol.167 , pp. 761-770
    • Qureshi, M.H.1    D'Amici, G.M.2    Fagioni, M.3    Rinalducci, S.4    Zolla, L.5
  • 224
    • 64649106078 scopus 로고    scopus 로고
    • Yeast two-hybrid detection of integrase-host factor interactions
    • J.C. Rain, A. Cribier, A. Gerard, S. Emiliani, and R. Benarous Yeast two-hybrid detection of integrase-host factor interactions Methods 47 2009 291 297
    • (2009) Methods , vol.47 , pp. 291-297
    • Rain, J.C.1    Cribier, A.2    Gerard, A.3    Emiliani, S.4    Benarous, R.5
  • 226
    • 67749152091 scopus 로고    scopus 로고
    • Analysis of protein-protein interactions using array-based yeast two-hybrid screens
    • S.V. Rajagopala, and P. Uetz Analysis of protein-protein interactions using array-based yeast two-hybrid screens Methods Mol. Biol. 548 2009 223 245
    • (2009) Methods Mol. Biol. , vol.548 , pp. 223-245
    • Rajagopala, S.V.1    Uetz, P.2
  • 227
    • 77952545683 scopus 로고    scopus 로고
    • The SUMO conjugation pathway in Populus: Genomic analysis, tissue-specific and inducible SUMOylation and in vitro de-SUMOylation
    • J.M. Reed, C. Dervinis, A.M. Morse, and J.M. Davis The SUMO conjugation pathway in Populus: genomic analysis, tissue-specific and inducible SUMOylation and in vitro de-SUMOylation Planta 232 2010 51 59
    • (2010) Planta , vol.232 , pp. 51-59
    • Reed, J.M.1    Dervinis, C.2    Morse, A.M.3    Davis, J.M.4
  • 228
  • 229
    • 48849107198 scopus 로고    scopus 로고
    • Solubilization of membrane protein complexes for blue native PAGE
    • V. Reisinger, and L.A. Eichacker Solubilization of membrane protein complexes for blue native PAGE J. Proteomics 71 2008 277 283
    • (2008) J. Proteomics , vol.71 , pp. 277-283
    • Reisinger, V.1    Eichacker, L.A.2
  • 230
    • 42249088081 scopus 로고    scopus 로고
    • How to analyze protein complexes by 2D blue native SDS-PAGE
    • DOI 10.1002/pmic.200700205
    • V. Reisinger, and L.A. Eichacker How to analyze protein complexes by 2D blue native SDS-PAGE Proteomics 7 Suppl. 1 2007 6 16 (Pubitemid 351547765)
    • (2007) Proteomics - Practical Proteomics , vol.2 , Issue.1 , pp. 6-16
    • Reisinger, V.1    Eichacker, L.A.2
  • 232
    • 38449114080 scopus 로고    scopus 로고
    • Using the β-lactamase protein-fragment complementation assay to probe dynamic protein-protein interactions
    • DOI 10.1038/nprot.2007.356, PII NPROT.2007.356
    • I. Remy, G. Ghaddar, and S.W. Michnick Using the beta-lactamase protein-fragment complementation assay to probe dynamic protein-protein interactions Nat. Protoc. 2 2007 2302 2306 (Pubitemid 351565868)
    • (2007) Nature Protocols , vol.2 , Issue.9 , pp. 2302-2306
    • Remy, I.1    Ghaddar, G.2    Michnick, S.W.3
  • 233
    • 3242657478 scopus 로고    scopus 로고
    • Mapping biochemical networks with protein-fragment complementation assays
    • I. Remy, and S.W. Michnick Mapping biochemical networks with protein-fragment complementation assays Methods Mol. Biol. 261 2004 411 426
    • (2004) Methods Mol. Biol. , vol.261 , pp. 411-426
    • Remy, I.1    Michnick, S.W.2
  • 234
    • 0032828715 scopus 로고    scopus 로고
    • A generic protein purification method for protein complex characterization and proteome exploration
    • DOI 10.1038/13732
    • G. Rigaut, A. Shevchenko, B. Rutz, M. Wilm, M. Mann, and B. Seraphin A generic protein purification method for protein complex characterization and proteome exploration Nat. Biotechnol. 17 1999 1030 1032 (Pubitemid 29474865)
    • (1999) Nature Biotechnology , vol.17 , Issue.10 , pp. 1030-1032
    • Rigaut, G.1    Shevchenko, A.2    Rutz, B.3    Wilm, M.4    Mann, M.5    Seraphin, B.6
  • 235
    • 33645779695 scopus 로고    scopus 로고
    • Novel protein phosphorylation site identification in spinach stroma membranes by titanium dioxide microcolumns and tandem mass spectrometry
    • S. Rinalducci, M.R. Larsen, S. Mohammed, and L. Zolla Novel protein phosphorylation site identification in spinach stroma membranes by titanium dioxide microcolumns and tandem mass spectrometry J. Proteome Res. 5 2006 973 982
    • (2006) J. Proteome Res. , vol.5 , pp. 973-982
    • Rinalducci, S.1    Larsen, M.R.2    Mohammed, S.3    Zolla, L.4
  • 236
    • 33947182552 scopus 로고    scopus 로고
    • An integrated mass spectrometric and computational framework for the analysis of protein interaction networks
    • DOI 10.1038/nbt1289, PII NBT1289
    • O. Rinner, L.N. Mueller, M. Hubalek, M. Muller, M. Gstaiger, and R. Aebersold An integrated mass spectrometric and computational framework for the analysis of protein interaction networks Nat. Biotechnol. 25 2007 345 352 (Pubitemid 46398770)
    • (2007) Nature Biotechnology , vol.25 , Issue.3 , pp. 345-352
    • Rinner, O.1    Mueller, L.N.2    Hubalek, M.3    Muller, M.4    Gstaiger, M.5    Aebersold, R.6
  • 237
    • 1842430185 scopus 로고    scopus 로고
    • Improved tandem affinity purification tag and methods for isolation of protein heterocomplexes from plants
    • DOI 10.1111/j.1365-313X.2004.02031.x
    • J.S. Rohila, M. Chen, R. Cerny, and M.E. Fromm Improved tandem affinity purification tag and methods for isolation of protein heterocomplexes from plants Plant J. 38 2004 172 181 (Pubitemid 38448454)
    • (2004) Plant Journal , vol.38 , Issue.1 , pp. 172-181
    • Rohila, J.S.1    Chen, M.2    Cerny, R.3    Fromm, M.E.4
  • 240
    • 52649094926 scopus 로고    scopus 로고
    • Analysis of desiccation-induced candidate phosphoproteins from Craterostigma plantagineum isolated with a modified metal oxide affinity chromatography procedure
    • H. Rohrig, T. Colby, J. Schmidt, A. Harzen, F. Facchinelli, and D. Bartels Analysis of desiccation-induced candidate phosphoproteins from Craterostigma plantagineum isolated with a modified metal oxide affinity chromatography procedure Proteomics 8 2008 3548 3560
    • (2008) Proteomics , vol.8 , pp. 3548-3560
    • Rohrig, H.1    Colby, T.2    Schmidt, J.3    Harzen, A.4    Facchinelli, F.5    Bartels, D.6
  • 242
    • 0035866205 scopus 로고    scopus 로고
    • The draft sequences. Comparing species
    • G.M. Rubin The draft sequences. Comparing species Nature 409 2001 820 821
    • (2001) Nature , vol.409 , pp. 820-821
    • Rubin, G.M.1
  • 243
    • 14844310253 scopus 로고    scopus 로고
    • An alternative tandem affinity purification strategy applied to Arabidopsis protein complex isolation
    • DOI 10.1111/j.1365-313X.2004.02328.x
    • V. Rubio, Y.P. Shen, Y. Saijo, Y.L. Liu, G. Gusmaroli, S.P. Dinesh-Kumar, and X.W. Deng An alternative tandem affinity purification strategy applied to Arabidopsis protein complex isolation Plant J. 41 2005 767 778 (Pubitemid 40336007)
    • (2005) Plant Journal , vol.41 , Issue.5 , pp. 767-778
    • Rubio, V.1    Shen, Y.2    Saijo, Y.3    Liu, Y.4    Gusmaroli, G.5    Dinesh-Kumar, S.P.6    Xing, W.D.7
  • 244
    • 77955484871 scopus 로고    scopus 로고
    • Large scale interaction analysis predicts that the Gerbera hybrida floral e function is provided both by general and specialized proteins
    • S. Ruokolainen, Y.P. Ng, V.A. Albert, P. Elomaa, and T.H. Teeri Large scale interaction analysis predicts that the Gerbera hybrida floral E function is provided both by general and specialized proteins BMC Plant Biol. 10 2010
    • (2010) BMC Plant Biol. , vol.10
    • Ruokolainen, S.1    Ng, Y.P.2    Albert, V.A.3    Elomaa, P.4    Teeri, T.H.5
  • 245
    • 19944408829 scopus 로고    scopus 로고
    • Heterodimerization and endocytosis of Arabidopsis brassinosteroid receptors BRI1 and AtSERK3 (BAK1)
    • DOI 10.1105/tpc.104.025387
    • E. Russinova, J.W. Borst, M. Kwaaitaal, A. Cano-Delgado, Y.H. Yin, J. Chory, and S.C. de Vries Heterodimerization and endocytosis of Arabidopsis brassinosteroid receptors BRI1 and AtSERK3 (BAK1) Plant Cell 16 2004 3216 3229 (Pubitemid 41096002)
    • (2004) Plant Cell , vol.16 , Issue.12 , pp. 3216-3229
    • Russinova, E.1    Borst, J.-W.2    Kwaaitaal, M.3    Cano-Delgado, A.4    Yin, Y.5    Chory, J.6    De Vries, S.C.7
  • 246
    • 67649696034 scopus 로고    scopus 로고
    • Tandem affinity purification and mass spectrometric analysis of ubiquitylated proteins in Arabidopsis
    • S.A. Saracco, M. Hansson, M. Scalf, J.M. Walker, L.M. Smith, and R.D. Vierstra Tandem affinity purification and mass spectrometric analysis of ubiquitylated proteins in Arabidopsis Plant J. 59 2009 344 358
    • (2009) Plant J. , vol.59 , pp. 344-358
    • Saracco, S.A.1    Hansson, M.2    Scalf, M.3    Walker, J.M.4    Smith, L.M.5    Vierstra, R.D.6
  • 247
    • 44849086809 scopus 로고    scopus 로고
    • Predikin and PredikinDB: A computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites
    • N.F.W. Saunders, R.I. Brinkworth, T. Huber, B.E. Kemp, and B. Kobe Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites BMC Bioinformatics 9 2008 245
    • (2008) BMC Bioinformatics , vol.9 , pp. 245
    • Saunders, N.F.W.1    Brinkworth, R.I.2    Huber, T.3    Kemp, B.E.4    Kobe, B.5
  • 248
    • 33646903914 scopus 로고    scopus 로고
    • ModifiComb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures
    • DOI 10.1074/mcp.T500034-MCP200
    • M.M. Savitski, M.L. Nielsen, and R.A. Zubarev ModifiComb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures Mol. Cell. Proteomics 5 2006 935 948 (Pubitemid 43792802)
    • (2006) Molecular and Cellular Proteomics , vol.5 , Issue.5 , pp. 935-948
    • Savitski, M.M.1    Nielsen, M.L.2    Zubarev, R.A.3
  • 249
    • 57649093858 scopus 로고    scopus 로고
    • SILIP: A novel stable isotope labeling method for in planta quantitative proteomic analysis
    • J.E. Schaff, F. Mbeunkui, K. Blackburn, D.M. Bird, and M.B. Goshe SILIP: a novel stable isotope labeling method for in planta quantitative proteomic analysis Plant J. 56 2008 840 854
    • (2008) Plant J. , vol.56 , pp. 840-854
    • Schaff, J.E.1    Mbeunkui, F.2    Blackburn, K.3    Bird, D.M.4    Goshe, M.B.5
  • 250
    • 0028214450 scopus 로고
    • Analysis of molecular masses and oligomeric states of protein complexes by blue native electrophoresis and isolation of membrane protein complexes by two-dimensional native electrophoresis
    • DOI 10.1006/abio.1994.1112
    • H. Schagger, W.A. Cramer, and G. Vonjagow Analysis of molecular masses and oligomeric states of protein complexes by blue native electrophoresis and isolation of membrane-protein complexes by 2-dimensional native electrophoresis Anal. Biochem. 217 1994 220 230 (Pubitemid 24080754)
    • (1994) Analytical Biochemistry , vol.217 , Issue.2 , pp. 220-230
    • Schagger, H.1    Cramer, W.A.2    Von Jagow, G.3
  • 251
    • 0026409298 scopus 로고
    • Blue native electrophoresis for isolation of membrane-protein complexes in enzymatically active form
    • H. Schagger, and G. Vonjagow Blue native electrophoresis for isolation of membrane-protein complexes in enzymatically active form Anal. Biochem. 199 1991 223 231
    • (1991) Anal. Biochem. , vol.199 , pp. 223-231
    • Schagger, H.1    Vonjagow, G.2
  • 253
    • 24144486554 scopus 로고    scopus 로고
    • Local modeling of global interactome networks
    • DOI 10.1093/bioinformatics/bti567
    • D. Scholtens, M. Vidal, and R. Gentleman Local modeling of global interactome networks Bioinformatics 21 2005 3548 3557 (Pubitemid 41236000)
    • (2005) Bioinformatics , vol.21 , Issue.17 , pp. 3548-3557
    • Scholtens, D.1    Vidal, M.2    Gentleman, R.3
  • 254
    • 3042824849 scopus 로고    scopus 로고
    • A neutral loss activation method for improved phosphopeptide sequence analysis by quadrupole ion trap mass spectrometry
    • DOI 10.1021/ac0497104
    • M.J. Schroeder, J. Shabanowitz, J.C. Schwartz, D.F. Hunt, and J.J. Coon A neutral loss activation method for improved phosphopeptide sequence analysis by quadrupole ion trap mass spectrometry Anal. Chem. 76 2004 3590 3598 (Pubitemid 38868819)
    • (2004) Analytical Chemistry , vol.76 , Issue.13 , pp. 3590-3598
    • Schroeder, M.J.1    Shabanowitz, J.2    Schwartz, J.C.3    Hunt, D.F.4    Coon, J.J.5
  • 255
    • 77952999879 scopus 로고    scopus 로고
    • Analysis of oligomeric protein complexes in the chloroplast sub-proteome of nucleic acid-binding proteins from mustard reveals potential redox regulators of plastid gene expression
    • Y. Schroter, S. Steiner, K. Matthai, and T. Pfannschmidt Analysis of oligomeric protein complexes in the chloroplast sub-proteome of nucleic acid-binding proteins from mustard reveals potential redox regulators of plastid gene expression Proteomics 10 2010 2191 2204
    • (2010) Proteomics , vol.10 , pp. 2191-2204
    • Schroter, Y.1    Steiner, S.2    Matthai, K.3    Pfannschmidt, T.4
  • 256
    • 77952538049 scopus 로고    scopus 로고
    • Quantitation in mass-spectrometry-based proteomics
    • W.X. Schulze, and B. Usadel Quantitation in mass-spectrometry-based proteomics Annu. Rev. Plant Biol. 61 2010 491 516
    • (2010) Annu. Rev. Plant Biol. , vol.61 , pp. 491-516
    • Schulze, W.X.1    Usadel, B.2
  • 257
    • 33947411954 scopus 로고    scopus 로고
    • 1 ATP synthase in Chlamydomonas reinhardtii
    • DOI 10.1016/j.febslet.2007.02.057, PII S0014579307002232
    • H.J. Schwassmann, S. Rexroth, H. Seelert, and N.A. Dencher Metabolism controls dimerization of the chloroplast F0F1 ATP synthase in Chlamydomonas reinhardtii FEBS Lett. 581 2007 1391 1396 (Pubitemid 46452612)
    • (2007) FEBS Letters , vol.581 , Issue.7 , pp. 1391-1396
    • Schwassmann, H.J.1    Rexroth, S.2    Seelert, H.3    Dencher, N.A.4
  • 258
    • 38649114671 scopus 로고    scopus 로고
    • Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies
    • DOI 10.1021/pr070540w
    • B.C. Searle, M. Turner, and A.I. Nesvizhskii Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies J. Proteome Res. 7 2008 245 253 (Pubitemid 351171137)
    • (2008) Journal of Proteome Research , vol.7 , Issue.1 , pp. 245-253
    • Searle, B.C.1    Turner, M.2    Nesvizhskii, A.I.3
  • 259
    • 33751230224 scopus 로고    scopus 로고
    • Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK)
    • DOI 10.1038/nmeth972, PII NMETH972
    • M. Selbach, and M. Mann Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK) Nat. Methods 3 2006 981 983 (Pubitemid 44782696)
    • (2006) Nature Methods , vol.3 , Issue.12 , pp. 981-983
    • Selbach, M.1    Mann, M.2
  • 260
    • 0035326344 scopus 로고    scopus 로고
    • Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching
    • DOI 10.1021/ac0013709
    • A. Shevchenko, S. Sunyaev, A. Loboda, A. Shevehenko, P. Bork, W. Ens, and K.G. Standing Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time of flight mass spectrometry and BLAST homology searching Anal. Chem. 73 2001 1917 1926 (Pubitemid 32862395)
    • (2001) Analytical Chemistry , vol.73 , Issue.9 , pp. 1917-1926
    • Shevchenko, A.1    Sunyaev, S.2    Loboda, A.3    Shevchenko, A.4    Bork, P.5    Ens, W.6    Standing, K.G.7
  • 262
    • 0036124032 scopus 로고    scopus 로고
    • Identification of the 19S regulatory particle subunits from the rice 26S proteasome
    • DOI 10.1046/j.1432-1033.2002.02792.x
    • T. Shibahara, H. Kawasaki, and H. Hirano Identification of the 19S regulatory particle subunits from the rice 26S proteasome Eur. J. Biochem. 269 2002 1474 1483 (Pubitemid 34227088)
    • (2002) European Journal of Biochemistry , vol.269 , Issue.5 , pp. 1474-1483
    • Shibahara, T.1    Kawasaki, H.2    Hirano, H.3
  • 263
    • 34247586171 scopus 로고    scopus 로고
    • Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners
    • B.A. Shoemaker, and A.R. Panchenko Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners PLoS Comput. Biol. 3 2007 e43
    • (2007) PLoS Comput. Biol. , vol.3 , pp. 43
    • Shoemaker, B.A.1    Panchenko, A.R.2
  • 267
    • 0037059770 scopus 로고    scopus 로고
    • Tyrosine phosphorylation mapping of the epidermal growth factor receptor signaling pathway
    • DOI 10.1074/jbc.M109992200
    • H. Steen, B. Kuster, M. Fernandez, A. Pandey, and M. Mann Tyrosine phosphorylation mapping of the epidermal growth factor receptor signaling pathway J. Biol. Chem. 277 2002 1031 1039 (Pubitemid 34968848)
    • (2002) Journal of Biological Chemistry , vol.277 , Issue.2 , pp. 1031-1039
    • Steen, H.1    Kuster, B.2    Fernandez, M.3    Pandey, A.4    Mann, M.5
  • 269
    • 0035408680 scopus 로고    scopus 로고
    • Rapid and simple single nanogram detection of glycoproteins in polyacrylamide gels and on electroblots
    • T.H. Steinberg, K.P.O. Top, K.N. Berggren, C. Kemper, L. Jones, Z.J. Diwu, R.P. Haugland, and W.F. Patton Rapid and simple single nanogram detection of glycoproteins in polyacrylamide gels and on electroblots Proteomics 1 2001 841 855 (Pubitemid 33587410)
    • (2001) Proteomics , vol.1 , Issue.7 , pp. 841-855
    • Steinberg, T.H.1    Pretty, K.2    Berggren, K.N.3    Kemper, C.4    Jones, L.5    Diwu, Z.6    Haugland, R.P.7    Patton, W.F.8
  • 271
    • 33847325742 scopus 로고    scopus 로고
    • How many genes are there in plants (... and why are they there)?
    • DOI 10.1016/j.pbi.2007.01.004, PII S1369526607000088, Genome Studies and Molecular Genetics
    • L. Sterck, S. Rombauts, K. Vandepoele, P. Rouze, and Y. Van de Peer How many genes are there in plants (...and why are they there)? Curr. Opin. Plant Biol. 10 2007 199 203 (Pubitemid 46330107)
    • (2007) Current Opinion in Plant Biology , vol.10 , Issue.2 , pp. 199-203
    • Sterck, L.1    Rombauts, S.2    Vandepoele, K.3    Rouze, P.4    Van De Peer, Y.5
  • 272
    • 77956496090 scopus 로고    scopus 로고
    • Large pore gels to separate mega protein complexes larger than 10 MDa by blue native electrophoresis: Isolation of putative respiratory strings or patches
    • doi:10.1002/pmic.201000343
    • Strecker, V., Wumaier, Z., Wittig, I., Schagger, H., 2010. Large pore gels to separate mega protein complexes larger than 10 MDa by blue native electrophoresis: isolation of putative respiratory strings or patches. Proteomics doi:10.1002/pmic.201000343.
    • (2010) Proteomics
    • Strecker, V.1    Wumaier, Z.2    Wittig, I.3    Schagger, H.4
  • 273
    • 65249173459 scopus 로고    scopus 로고
    • Quantitative phosphoproteomics of tomato mounting a hypersensitive response reveals a swift suppression of photosynthetic activity and a differential role for Hsp90 isoforms
    • I.J.E. Stulemeijer, M.H.A.J. Joosten, and O.N. Jensen Quantitative phosphoproteomics of tomato mounting a hypersensitive response reveals a swift suppression of photosynthetic activity and a differential role for Hsp90 isoforms J. Proteome Res. 8 2009 1168 1182
    • (2009) J. Proteome Res. , vol.8 , pp. 1168-1182
    • Stulemeijer, I.J.E.1    Joosten, M.H.A.J.2    Jensen, O.N.3
  • 274
    • 70649104060 scopus 로고    scopus 로고
    • Highly sensitive detection of ATPase activity in native gels
    • T. Suhai, N.G. Heidrich, N.A. Dencher, and H. Seelert Highly sensitive detection of ATPase activity in native gels Electrophoresis 30 2009 3622 3625
    • (2009) Electrophoresis , vol.30 , pp. 3622-3625
    • Suhai, T.1    Heidrich, N.G.2    Dencher, N.A.3    Seelert, H.4
  • 277
    • 40949142795 scopus 로고    scopus 로고
    • Two-dimensional blue native/blue native polyacrylamide gel electrophoresis for the characterization of mitochondrial protein complexes and supercomplexes
    • S. Sunderhaus, H. Eubel, and H.P. Braun Two-dimensional blue native/blue native polyacrylamide gel electrophoresis for the characterization of mitochondrial protein complexes and supercomplexes Methods Mol. Biol. 372 2007 315 324
    • (2007) Methods Mol. Biol. , vol.372 , pp. 315-324
    • Sunderhaus, S.1    Eubel, H.2    Braun, H.P.3
  • 279
    • 46849099222 scopus 로고    scopus 로고
    • Utility of formaldehyde cross-linking and mass spectrometry in the study of protein-protein interactions
    • DOI 10.1002/jms.1415
    • B.W. Sutherland, J. Toews, and J. Kast Utility of formaldehyde cross-linking and mass spectrometry in the study of protein-protein interactions J. Mass Spectrom. 43 2008 699 715 (Pubitemid 351954805)
    • (2008) Journal of Mass Spectrometry , vol.43 , Issue.6 , pp. 699-715
    • Sutherland, B.W.1    Toews, J.2    Kast, J.3
  • 280
    • 0028822007 scopus 로고
    • Surface-plasmon resonance and its use in biomolecular interaction analysis (Bia)
    • A. Szabo, L. Stolz, and R. Granzow Surface-plasmon resonance and its use in biomolecular interaction analysis (Bia) Curr. Opin. Struct. Biol. 5 1995 699 705
    • (1995) Curr. Opin. Struct. Biol. , vol.5 , pp. 699-705
    • Szabo, A.1    Stolz, L.2    Granzow, R.3
  • 281
    • 71949124535 scopus 로고    scopus 로고
    • Proteomics reveals the overlapping roles of hydrogen peroxide and nitric oxide in the acclimation of citrus plants to salinity
    • G. Tanou, C. Job, L. Rajjou, E. Arc, M. Belghazi, G. Diamantidis, A. Molassiotis, and D. Job Proteomics reveals the overlapping roles of hydrogen peroxide and nitric oxide in the acclimation of citrus plants to salinity Plant J. 60 2009 795 804
    • (2009) Plant J. , vol.60 , pp. 795-804
    • Tanou, G.1    Job, C.2    Rajjou, L.3    Arc, E.4    Belghazi, M.5    Diamantidis, G.6    Molassiotis, A.7    Job, D.8
  • 283
    • 42249086071 scopus 로고    scopus 로고
    • Integrated analytical strategies for the study of phosphorylation and glycosylation in proteins
    • DOI 10.1002/mas.20164
    • C. Temporini, E. Callerli, G. Massolini, and G. Caccialanza Integrated analytical strategies for the study of phosphorylation and glycosylation in proteins Mass Spectrom. Rev. 27 2008 207 236 (Pubitemid 351547982)
    • (2008) Mass Spectrometry Reviews , vol.27 , Issue.3 , pp. 207-236
    • Temporini, C.1    Calleri, E.2    Massolini, G.3    Caccialanza, G.4
  • 284
    • 39749178251 scopus 로고    scopus 로고
    • Cytokinin signaling: Two-components and more
    • J.P.C. To, and J.J. Kieber Cytokinin signaling: two-components and more Trends Plant Sci. 13 2008 85 92
    • (2008) Trends Plant Sci. , vol.13 , pp. 85-92
    • To, J.P.C.1    Kieber, J.J.2
  • 286
    • 22644437896 scopus 로고    scopus 로고
    • Identification and mapping of protein-protein interactions by a combination of cross-linking, cleavage, and proteomics
    • DOI 10.1021/bc050043a
    • M.A. Trakselis, S.C. Alley, and F.T. Ishmael Identification and mapping of protein-protein interactions by a combination of cross-linking, cleavage, and proteomics Bioconj. Chem. 16 2005 741 750 (Pubitemid 41026159)
    • (2005) Bioconjugate Chemistry , vol.16 , Issue.4 , pp. 741-750
    • Trakselis, M.A.1    Alley, S.C.2    Ishmael, F.T.3
  • 292
    • 53149142072 scopus 로고    scopus 로고
    • Boosting tandem affinity purification of plant protein complexes
    • J. Van Leene, E. Witters, D. Inze, and G. De Jaeger Boosting tandem affinity purification of plant protein complexes Trends Plant Sci. 13 2008 517 520
    • (2008) Trends Plant Sci. , vol.13 , pp. 517-520
    • Van Leene, J.1    Witters, E.2    Inze, D.3    De Jaeger, G.4
  • 293
    • 10644254712 scopus 로고    scopus 로고
    • Identification of protein-protein interactions using in vivo cross-linking and mass spectrometry
    • DOI 10.1002/pmic.200400856
    • J. Vasilescu, X.C. Guo, and J. Kast Identification of protein-protein interactions using in vivo cross-linking and mass spectrometry Proteomics 4 2004 3845 3854 (Pubitemid 39657461)
    • (2004) Proteomics , vol.4 , Issue.12 , pp. 3845-3854
    • Vasilescu, J.1    Guo, X.2    Kast, J.3
  • 295
    • 67349254570 scopus 로고    scopus 로고
    • The ubiquitin-26S proteasome system at the nexus of plant biology
    • R.D. Vierstra The ubiquitin-26S proteasome system at the nexus of plant biology Nat. Rev. Mol. Cell Biol. 10 2009 385 397
    • (2009) Nat. Rev. Mol. Cell Biol. , vol.10 , pp. 385-397
    • Vierstra, R.D.1
  • 296
    • 45749101309 scopus 로고    scopus 로고
    • Surface plasmon resonance mass spectrometry in proteomics
    • DOI 10.1586/14789450.5.3.425
    • N.F.C. Visser, and A.J.R. Heck Surface plasmon resonance mass spectrometry in proteomics Expert Rev. Proteomics 5 2008 425 433 (Pubitemid 351871118)
    • (2008) Expert Review of Proteomics , vol.5 , Issue.3 , pp. 425-433
    • Visser, N.F.C.1    Heck, A.J.R.2
  • 298
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • C. von Mering, R. Krause, B. Snel, M. Cornell, S.G. Oliver, S. Fields, and P. Bork Comparative assessment of large-scale data sets of protein-protein interactions Nature 417 2002 399 403 (Pubitemid 34563526)
    • (2002) Nature , vol.417 , Issue.6887 , pp. 399-403
    • Von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 300
    • 33846632394 scopus 로고    scopus 로고
    • A comparative proteome and phosphoproteome analysis of differentially regulated proteins during fertilization in the self-incompatible species Solanum chacoense Bitt
    • DOI 10.1002/pmic.200600399
    • K. Vyetrogon, F. Tebbji, D.J.H. Olson, A.R.S. Ross, and D.P. Matton A comparative proteome and phosphoproteome analysis of differentially regulated proteins during fertilization in the self-incompatible species Solanum chacoense Bitt Proteomics 7 2007 232 247 (Pubitemid 46184087)
    • (2007) Proteomics , vol.7 , Issue.2 , pp. 232-247
    • Vyetrogon, K.1    Tebbji, F.2    Olson, D.J.H.3    Ross, A.R.S.4    Matton, D.P.5
  • 302
    • 13844297577 scopus 로고    scopus 로고
    • Imaging protein molecules using FRET and FLIM microscopy
    • DOI 10.1016/j.copbio.2004.12.002, PII S0958166904001673
    • H. Wallrabe, and A. Periasamy Imaging protein molecules using FRET and FLIM microscopy Curr. Opin. Biotechnol. 16 2005 19 27 (Pubitemid 40249755)
    • (2005) Current Opinion in Biotechnology , vol.16 , Issue.1 SPEC. ISSUE , pp. 19-27
    • Wallrabe, H.1    Periasamy, A.2
  • 304
    • 76149146038 scopus 로고    scopus 로고
    • Comparison of extensive protein fractionation and repetitive LC-MS/MS analyses on depth of analysis for complex proteomes
    • H. Wang, T. Chang-Wong, H.Y. Tang, and D.W. Speicher Comparison of extensive protein fractionation and repetitive LC-MS/MS analyses on depth of analysis for complex proteomes J. Proteome Res. 9 2010 1032 1040
    • (2010) J. Proteome Res. , vol.9 , pp. 1032-1040
    • Wang, H.1    Chang-Wong, T.2    Tang, H.Y.3    Speicher, D.W.4
  • 305
    • 67649124461 scopus 로고    scopus 로고
    • A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila
    • L. Wang, Z.D. Tu, and F.Z. Sun A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila BMC Genomics 10 2009
    • (2009) BMC Genomics , vol.10
    • Wang, L.1    Tu, Z.D.2    Sun, F.Z.3
  • 306
    • 70449133428 scopus 로고    scopus 로고
    • The transcriptional regulation of protein complexes; A cross-species perspective
    • E.C. Webb, and D.R. Westhead The transcriptional regulation of protein complexes; a cross-species perspective Genomics 94 2009 369 376
    • (2009) Genomics , vol.94 , pp. 369-376
    • Webb, E.C.1    Westhead, D.R.2
  • 309
    • 52649180552 scopus 로고    scopus 로고
    • Identification of novel proteins and phosphorylation sites in a tonoplast enriched membrane fraction of Arabidopsis thaliana
    • S.A. Whiteman, L. Serazetdinova, A.M.E. Jones, D. Sanders, J. Rathjen, S.C. Peck, and F.J.M. Meathuis Identification of novel proteins and phosphorylation sites in a tonoplast enriched membrane fraction of Arabidopsis thaliana Proteomics 8 2008 3536 3547
    • (2008) Proteomics , vol.8 , pp. 3536-3547
    • Whiteman, S.A.1    Serazetdinova, L.2    Jones, A.M.E.3    Sanders, D.4    Rathjen, J.5    Peck, S.C.6    Meathuis, F.J.M.7
  • 310
    • 77957228856 scopus 로고    scopus 로고
    • Arabidopsis thaliana as a model organism for plant proteome research
    • S. Wienkoop, S. Baginsky, and W. Weckwerth Arabidopsis thaliana as a model organism for plant proteome research J. Proteomics 73 2010 2239 2248
    • (2010) J. Proteomics , vol.73 , pp. 2239-2248
    • Wienkoop, S.1    Baginsky, S.2    Weckwerth, W.3
  • 311
    • 33646251130 scopus 로고    scopus 로고
    • Relative and absolute quantitative shotgun proteomics: Targeting low-abundance proteins in Arabidopsis thaliana
    • S. Wienkoop, and W. Weckwerth Relative and absolute quantitative shotgun proteomics: targeting low-abundance proteins in Arabidopsis thaliana J. Exp. Bot. 57 2006 1529 1535
    • (2006) J. Exp. Bot. , vol.57 , pp. 1529-1535
    • Wienkoop, S.1    Weckwerth, W.2
  • 313
    • 33644674733 scopus 로고    scopus 로고
    • Automated identification and quantification of protein phosphorylation sites by LC/MS on a hybrid triple quadrupole linear ion trap mass spectrometer
    • DOI 10.1074/mcp.M500210-MCP200
    • B.L. Williamson, J. Marchese, and N.A. Morrice Automated identification and quantification of protein phosphorylation sites by LC/MS on a hybrid triple quadrupole linear ion trap mass spectrometer Mol. Cell. Proteomics 5 2006 337 346 (Pubitemid 43329311)
    • (2006) Molecular and Cellular Proteomics , vol.5 , Issue.2 , pp. 337-346
    • Williamson, B.L.1    Marchese, J.2    Morrice, N.A.3
  • 314
    • 57749111847 scopus 로고    scopus 로고
    • The chloroplast DnaJ homolog CDJ1 of Chlamydomonas reinhardtii is part of a multichaperone complex containing HSP70B, CGE1, and HSP90C
    • DOI 10.1104/pp.108.127944
    • F. Willmund, K.V. Dorn, M. Schulz-Raffelt, and M. Schroda The chloroplast DnaJ homolog CDJ1 of Chlamydomonas reinhardtii is part of a multichaperone complex containing HSP70B, CGE1, and HSP90C Plant Physiol. 148 2008 2070 2082 (Pubitemid 352847460)
    • (2008) Plant Physiology , vol.148 , Issue.4 , pp. 2070-2082
    • Willmund, F.1    Dorn, K.V.2    Schulz-Raffelt, M.3    Schroda, M.4
  • 315
    • 0141569190 scopus 로고    scopus 로고
    • Fast liquid chromatography coupled to electrospray tandem mass spectrometry peptide sequencing for cross-species protein identification
    • E. Witters, K. Laukens, P. Deckers, W. Van Dongen, E. Esmans, and H. Van Onckelen Fast liquid chromatography coupled to electrospray tandem mass spectrometry peptide sequencing for cross-species protein identification Rapid Commun. Mass Spectrom. 17 2003 2188 2194 (Pubitemid 37203707)
    • (2003) Rapid Communications in Mass Spectrometry , vol.17 , Issue.19 , pp. 2188-2194
    • Witters, E.1    Laukens, K.2    Deckers, P.3    Van Dongen, W.4    Esmans, E.5    Van Onckelen, H.6
  • 316
    • 36348941768 scopus 로고    scopus 로고
    • Functional assays in high-resolution clear native gels to quantify mitochondrial complexes in human biopsies and cell lines
    • DOI 10.1002/elps.200700367
    • I. Wittig, R. Carrozzo, F.M. Santorelli, and H. Schagger Functional assays in high-resolution clear native gels to quantify mitochondrial complexes in human biopsies and cell lines Electrophoresis 28 2007 3811 3820 (Pubitemid 350143117)
    • (2007) Electrophoresis , vol.28 , Issue.21 , pp. 3811-3820
    • Wittig, I.1    Carrozzo, R.2    Santorelli, F.M.3    Schagger, H.4
  • 317
    • 34547138661 scopus 로고    scopus 로고
    • High resolution clear native electrophoresis for in-gel functional assays and fluorescence studies of membrane protein complexes
    • DOI 10.1074/mcp.M700076-MCP200
    • I. Wittig, M. Karas, and H. Schagger High resolution clear native electrophoresis for In-gel functional assays and fluorescence studies of membrane protein complexes Mol. Cell. Proteomics 6 2007 1215 1225 (Pubitemid 47099231)
    • (2007) Molecular and Cellular Proteomics , vol.6 , Issue.7 , pp. 1215-1225
    • Wittig, I.1    Karas, M.2    Schagger, H.3
  • 318
    • 28444497467 scopus 로고    scopus 로고
    • Advantages and limitations of clear-native PAGE
    • DOI 10.1002/pmic.200500081
    • I. Wittig, and H. Schagger Advantages and limitations of clear-native PAGE Proteomics 5 2005 4338 4346 (Pubitemid 41739912)
    • (2005) Proteomics , vol.5 , Issue.17 , pp. 4338-4346
    • Wittig, I.1    Schagger, H.2
  • 319
    • 28444487185 scopus 로고    scopus 로고
    • Enrichment of phosphorylated proteins and peptides from complex mixtures using metal oxide/hydroxide affinity chromatography (MOAC)
    • DOI 10.1002/pmic.200402049
    • F. Wolschin, S. Wienkoop, and W. Weckwerth Enrichment of phosphorylated proteins and peptides from complex mixtures using metal oxide/hydroxide affinity chromatography (MOAC) Proteomics 5 2005 4389 4397 (Pubitemid 41739917)
    • (2005) Proteomics , vol.5 , Issue.17 , pp. 4389-4397
    • Wolschin, F.1    Wienkoop, S.2    Weckwerth, W.3
  • 321
    • 63449114764 scopus 로고    scopus 로고
    • Two-dimensional native electrophoresis for fluorescent and functional assays of mitochondrial complexes
    • Z. Wumaier, E. Nubel, I. Wittig, and H. Schagger Two-dimensional native electrophoresis for fluorescent and functional assays of mitochondrial complexes Methods Enzymol. 456 2009 153 168
    • (2009) Methods Enzymol. , vol.456 , pp. 153-168
    • Wumaier, Z.1    Nubel, E.2    Wittig, I.3    Schagger, H.4
  • 322
    • 77957222651 scopus 로고    scopus 로고
    • Modification-specific proteomics in plant biology
    • doi:10.1016/j.jprot.2010.06.00
    • Ytterberg, A.J., Jensen, O.N., 2010. Modification-specific proteomics in plant biology. J. Proteomics doi:10.1016/j.jprot.2010.06.00.
    • (2010) J. Proteomics
    • Ytterberg, A.J.1    Jensen, O.N.2
  • 323
    • 57149100750 scopus 로고    scopus 로고
    • Root proteomic responses to heat stress in two Agrostis grass species contrasting in heat tolerance
    • C.P. Xu, and B.R. Huang Root proteomic responses to heat stress in two Agrostis grass species contrasting in heat tolerance J. Exp. Bot. 59 2008 4183 4194
    • (2008) J. Exp. Bot. , vol.59 , pp. 4183-4194
    • Xu, C.P.1    Huang, B.R.2
  • 325
    • 77955415819 scopus 로고    scopus 로고
    • The tandem affinity purification method: An efficient system for protein complex purification and protein interaction identification
    • X.L. Xu, Y. Song, Y.H. Li, J.F. Chang, H. Zhang, and L.Z. An The tandem affinity purification method: an efficient system for protein complex purification and protein interaction identification Protein Expr. Purif. 72 2010 149 156
    • (2010) Protein Expr. Purif. , vol.72 , pp. 149-156
    • Xu, X.L.1    Song, Y.2    Li, Y.H.3    Chang, J.F.4    Zhang, H.5    An, L.Z.6
  • 326
    • 33645758540 scopus 로고    scopus 로고
    • PPSP: Prediction of PK-specific phosphorylation site with Bayesian decision theory
    • Y. Xue, A. Li, L. Wang, H. Feng, and X. Yao PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory BMC Bioinformatics 7 2006 163
    • (2006) BMC Bioinformatics , vol.7 , pp. 163
    • Xue, Y.1    Li, A.2    Wang, L.3    Feng, H.4    Yao, X.5
  • 327
    • 52649145895 scopus 로고    scopus 로고
    • GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy
    • Y. Xue, J. Ren, X. Gao, C. Jin, L. Wen, and X. Yao GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy Mol. Cell. Proteomics 7 2008 1598 1608
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 1598-1608
    • Xue, Y.1    Ren, J.2    Gao, X.3    Jin, C.4    Wen, L.5    Yao, X.6
  • 329
    • 1342346597 scopus 로고    scopus 로고
    • Purification of the Arabidopsis 26 S proteasome: Biochemical and molecular analyses revealed the presence of multiple isoforms
    • DOI 10.1074/jbc.M311977200
    • P.Z. Yang, H.Y. Fu, J. Walker, C.M. Papa, J. Smalle, Y.M. Ju, and R.D. Vierstra Purification of the Arabidopsis 26 S proteasome - biochemical and molecular analyses revealed the presence of multiple isoforms J. Biol. Chem. 279 2004 6401 6413 (Pubitemid 38248774)
    • (2004) Journal of Biological Chemistry , vol.279 , Issue.8 , pp. 6401-6413
    • Yang, P.1    Fu, H.2    Walker, J.3    Papa, C.M.4    Smalle, J.5    Ju, Y.-M.6    Vierstra, R.D.7
  • 330
    • 60549095573 scopus 로고    scopus 로고
    • Isoelectric focusing of high-molecular-weight protein complex under native conditions using agarose gel
    • R. Yokoyama, Y. Iwafune, H. Kawasaki, and H. Hirano Isoelectric focusing of high-molecular-weight protein complex under native conditions using agarose gel Anal. Biochem. 387 2009 60 63
    • (2009) Anal. Biochem. , vol.387 , pp. 60-63
    • Yokoyama, R.1    Iwafune, Y.2    Kawasaki, H.3    Hirano, H.4
  • 331
    • 77956067362 scopus 로고    scopus 로고
    • Characterization of an intact two-component high-affinity nitrate transporter from Arabidopsis roots
    • Z. Yong, Z. Kotur, and A.D.M. Glass Characterization of an intact two-component high-affinity nitrate transporter from Arabidopsis roots Plant J. 63 2010 739 748
    • (2010) Plant J. , vol.63 , pp. 739-748
    • Yong, Z.1    Kotur, Z.2    Glass, A.D.M.3
  • 333
    • 77949768663 scopus 로고    scopus 로고
    • Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines
    • W. Yu, J.A. Taylor, M.T. Davis, L.E. Bonilla, K.A. Lee, P.L. Auger, C.C. Farnsworth, A.A. Welcher, and S.D. Patterson Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines Proteomics 10 2010 1172 1189
    • (2010) Proteomics , vol.10 , pp. 1172-1189
    • Yu, W.1    Taylor, J.A.2    Davis, M.T.3    Bonilla, L.E.4    Lee, K.A.5    Auger, P.L.6    Farnsworth, C.C.7    Welcher, A.A.8    Patterson, S.D.9
  • 334
    • 0030298130 scopus 로고    scopus 로고
    • A yeast three-hybrid method to clone ternary protein complex components
    • DOI 10.1006/abio.1996.0429
    • J. Zhang, and S. Lautar A yeast three-hybrid method to clone ternary protein complex components Anal. Biochem. 242 1996 68 72 (Pubitemid 26378516)
    • (1996) Analytical Biochemistry , vol.242 , Issue.1 , pp. 68-72
    • Zhang, J.1    Lautar, S.2
  • 335
    • 36749031608 scopus 로고    scopus 로고
    • Highly efficient phosphopeptide enrichment by calcium phosphate precipitation combined with subsequent IMAC enrichment
    • DOI 10.1074/mcp.M700278-MCP200
    • X. Zhang, J.Y. Ye, O.N. Jensen, and P. Roepstorff Highly efficient phosphopeptide enrichment by calcium phosphate precipitation combined with subsequent IMAC enrichment Mol. Cell. Proteomics 6 2007 2032 2042 (Pubitemid 350201876)
    • (2007) Molecular and Cellular Proteomics , vol.6 , Issue.11 , pp. 2032-2042
    • Zhang, X.1    Ye, J.2    Jensen, O.N.3    Roepstorff, P.4
  • 336
    • 77953191410 scopus 로고    scopus 로고
    • Short hypocotyl under blue1 truncations and mutations alter its association with a signaling protein complex in Arabidopsis
    • Y. Zhou, and M. Ni Short hypocotyl under blue1 truncations and mutations alter its association with a signaling protein complex in Arabidopsis Plant Cell 22 2010 703 715
    • (2010) Plant Cell , vol.22 , pp. 703-715
    • Zhou, Y.1    Ni, M.2
  • 337
    • 66149152316 scopus 로고    scopus 로고
    • Functional differentiation of Brassica napus guard cells and mesophyll cells revealed by comparative proteomics
    • M.M. Zhu, S.J. Dai, S. McClung, X.F. Yan, and S.X. Chen Functional differentiation of Brassica napus guard cells and mesophyll cells revealed by comparative proteomics Mol. Cell. Proteomics 8 2009 752 766
    • (2009) Mol. Cell. Proteomics , vol.8 , pp. 752-766
    • Zhu, M.M.1    Dai, S.J.2    McClung, S.3    Yan, X.F.4    Chen, S.X.5


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