메뉴 건너뛰기




Volumn 79, Issue , 2013, Pages 195-199

Proteome coverage of the model plant Arabidopsis thaliana: Implications for shotgun proteomic studies

Author keywords

Arabidopsis; Coverage; Database

Indexed keywords

AMINO ACID; PEPTIDE;

EID: 84873044787     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2012.12.009     Document Type: Article
Times cited : (4)

References (33)
  • 1
    • 0031148601 scopus 로고    scopus 로고
    • New Rhizobium leguminosarum flavonoid-induced proteins revealed by proteome analysis of differentially displayed proteins
    • Guerreiro N., Redmond J.W., Rolfe B.G., Djordjevic M.A. New Rhizobium leguminosarum flavonoid-induced proteins revealed by proteome analysis of differentially displayed proteins. Mol Plant Microbe Interact 1997, 10:506-516.
    • (1997) Mol Plant Microbe Interact , vol.10 , pp. 506-516
    • Guerreiro, N.1    Redmond, J.W.2    Rolfe, B.G.3    Djordjevic, M.A.4
  • 2
    • 0034649566 scopus 로고    scopus 로고
    • Arabidopsis Genome initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
    • Arabidopsis Genome initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408:796-815.
    • (2000) Nature , vol.408 , pp. 796-815
  • 3
    • 55949129986 scopus 로고    scopus 로고
    • The Multinational Arabidopsis Steering Subcommittee for Proteomics assembles the largest proteome database resource for plant systems biology
    • Weckwerth W., Baginsky S., van Wijk K., Heazlewood J.L., Millar A.H. The Multinational Arabidopsis Steering Subcommittee for Proteomics assembles the largest proteome database resource for plant systems biology. J Proteome Res 2008, 7:4209-4210.
    • (2008) J Proteome Res , vol.7 , pp. 4209-4210
    • Weckwerth, W.1    Baginsky, S.2    van Wijk, K.3    Heazlewood, J.L.4    Millar, A.H.5
  • 6
    • 79952531916 scopus 로고    scopus 로고
    • Pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana
    • Baerenfaller K., Hirsch-Hoffmann M., Svozil J., Hull R., Russenberger D., Bischof S., et al. pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana. Integr Biol 2011, 3:225-237.
    • (2011) Integr Biol , vol.3 , pp. 225-237
    • Baerenfaller, K.1    Hirsch-Hoffmann, M.2    Svozil, J.3    Hull, R.4    Russenberger, D.5    Bischof, S.6
  • 8
    • 77953149231 scopus 로고    scopus 로고
    • AT_CHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins
    • Ferro M., Brugière S., Salvi D., Seigneurin-Berny D., Court M., Moyet L., et al. AT_CHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins. Mol Cell Proteomics 2010, 9:1063-1084.
    • (2010) Mol Cell Proteomics , vol.9 , pp. 1063-1084
    • Ferro, M.1    Brugière, S.2    Salvi, D.3    Seigneurin-Berny, D.4    Court, M.5    Moyet, L.6
  • 12
    • 77954247252 scopus 로고    scopus 로고
    • Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants
    • Nakagami H., Sugiyama N., Mochida K., Daudi A., Yoshida Y., Toyoda T., et al. Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants. Plant Physiol 2010, 153:1161-1174.
    • (2010) Plant Physiol , vol.153 , pp. 1161-1174
    • Nakagami, H.1    Sugiyama, N.2    Mochida, K.3    Daudi, A.4    Yoshida, Y.5    Toyoda, T.6
  • 14
    • 80052032987 scopus 로고    scopus 로고
    • GelMap-a novel software tool for building and presenting proteome reference maps
    • Rode C., Senkler M., Klodmann J., Winkelmann T., Braun H.P. GelMap-a novel software tool for building and presenting proteome reference maps. J Proteomics 2011, 74:2214-2219.
    • (2011) J Proteomics , vol.74 , pp. 2214-2219
    • Rode, C.1    Senkler, M.2    Klodmann, J.3    Winkelmann, T.4    Braun, H.P.5
  • 16
    • 3042662113 scopus 로고    scopus 로고
    • In silico proteome analysis to facilitate proteomics experiments using mass spectrometry
    • Cagney G., Amiri S., Premawaradena T., Lindo M., Emili A. In silico proteome analysis to facilitate proteomics experiments using mass spectrometry. Proteome Sci 2003, 1:5.
    • (2003) Proteome Sci , vol.1 , pp. 5
    • Cagney, G.1    Amiri, S.2    Premawaradena, T.3    Lindo, M.4    Emili, A.5
  • 17
    • 34248152120 scopus 로고    scopus 로고
    • Mass spectrometry data analysis in the proteomics era
    • Forner F., Foster L.J., Toppo S. Mass spectrometry data analysis in the proteomics era. Curr Bioinform 2007, 2:63-93.
    • (2007) Curr Bioinform , vol.2 , pp. 63-93
    • Forner, F.1    Foster, L.J.2    Toppo, S.3
  • 18
    • 64749093752 scopus 로고    scopus 로고
    • Charge prediction machine: tool for inferring precursor charge states of electron transfer dissociation tandem mass spectra
    • Carvalho P.C., Cociorva D., Wong C.C., Carvalho Mda G., Barbosa V.C., Yates J.R. Charge prediction machine: tool for inferring precursor charge states of electron transfer dissociation tandem mass spectra. Anal Chem 2009, 81:1996-2003.
    • (2009) Anal Chem , vol.81 , pp. 1996-2003
    • Carvalho, P.C.1    Cociorva, D.2    Wong, C.C.3    Carvalho Mda, G.4    Barbosa, V.C.5    Yates, J.R.6
  • 19
    • 79955853722 scopus 로고    scopus 로고
    • On the relevance of peptide sequence permutations in shotgun proteomics studies
    • Yu L., Tan Y., Tsai Y., Goodlett D.R., Polfer N.C. On the relevance of peptide sequence permutations in shotgun proteomics studies. J Proteome Res 2011, 10:2409-2416.
    • (2011) J Proteome Res , vol.10 , pp. 2409-2416
    • Yu, L.1    Tan, Y.2    Tsai, Y.3    Goodlett, D.R.4    Polfer, N.C.5
  • 21
    • 70349246174 scopus 로고    scopus 로고
    • Large scale comparative proteomics of a chloroplast Clp protease mutant reveals folding stress, altered protein homeostasis, and feedback regulation of metabolism
    • Zybailov B., Friso G., Kim J., Rudella A., Rodriguez V.R., Asakura Y., et al. Large scale comparative proteomics of a chloroplast Clp protease mutant reveals folding stress, altered protein homeostasis, and feedback regulation of metabolism. Mol Cell Proteomics 2009, 8:1789-1810.
    • (2009) Mol Cell Proteomics , vol.8 , pp. 1789-1810
    • Zybailov, B.1    Friso, G.2    Kim, J.3    Rudella, A.4    Rodriguez, V.R.5    Asakura, Y.6
  • 22
    • 0033565832 scopus 로고    scopus 로고
    • Role of accurate mass measurement (+/-10ppm) in protein identification strategies employing MS or MS/MS and database searching
    • Clauser K.R., Baker P., Burlingame A.L. Role of accurate mass measurement (+/-10ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal Chem 1999, 71:2871-2882.
    • (1999) Anal Chem , vol.71 , pp. 2871-2882
    • Clauser, K.R.1    Baker, P.2    Burlingame, A.L.3
  • 23
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins D.N., Pappin D.J., Creasy D.M., Cottrell J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20:3551-3567.
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.2    Creasy, D.M.3    Cottrell, J.S.4
  • 24
    • 0031865293 scopus 로고    scopus 로고
    • Protein identification using mass spectrometric information
    • Fenyö D., Qin J., Chait B.T. Protein identification using mass spectrometric information. Electrophoresis 1998, 19:998-1005.
    • (1998) Electrophoresis , vol.19 , pp. 998-1005
    • Fenyö, D.1    Qin, J.2    Chait, B.T.3
  • 25
    • 0035582244 scopus 로고    scopus 로고
    • An automated multidimensional protein identification technology for shotgun proteomics
    • Wolters D.A., Washburn M.P., Yates J.R. An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem 2001, 73:5683-5690.
    • (2001) Anal Chem , vol.73 , pp. 5683-5690
    • Wolters, D.A.1    Washburn, M.P.2    Yates, J.R.3
  • 26
    • 33750631580 scopus 로고    scopus 로고
    • Efficient fractionation and improved protein identification by peptide OFFGEL electrophoresis
    • Horth P., Miller C.A., Preckel T., Wenz C. Efficient fractionation and improved protein identification by peptide OFFGEL electrophoresis. Mol Cell Proteomics 2006, 5:1968-1974.
    • (2006) Mol Cell Proteomics , vol.5 , pp. 1968-1974
    • Horth, P.1    Miller, C.A.2    Preckel, T.3    Wenz, C.4
  • 27
    • 28544435850 scopus 로고    scopus 로고
    • Enhanced characterization of complex proteomic samples using LC-MALDI MS/MS: exclusion of redundant peptides from MS/MS analysis in replicate runs
    • Chen H.S., Rejtar T., Andreev V., Moskovets E., Karger B.L. Enhanced characterization of complex proteomic samples using LC-MALDI MS/MS: exclusion of redundant peptides from MS/MS analysis in replicate runs. Anal Chem 2005, 77:7816-7825.
    • (2005) Anal Chem , vol.77 , pp. 7816-7825
    • Chen, H.S.1    Rejtar, T.2    Andreev, V.3    Moskovets, E.4    Karger, B.L.5
  • 28
    • 84860573550 scopus 로고    scopus 로고
    • Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel targets involved in plant cell wall biosynthesis
    • Parsons H.T., Christiansen K., Knierim B., Carroll A., Ito J., Batth T.S., et al. Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel targets involved in plant cell wall biosynthesis. Plant Physiol 2012, 159:12-26.
    • (2012) Plant Physiol , vol.159 , pp. 12-26
    • Parsons, H.T.1    Christiansen, K.2    Knierim, B.3    Carroll, A.4    Ito, J.5    Batth, T.S.6
  • 29
    • 0035237935 scopus 로고    scopus 로고
    • Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry. I. Profiling an unfractionated tryptic digest
    • Spahr C.S., Davis M.T., McGinley M.D., Robinson J.H., Bures E.J., Beierle J., et al. Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry. I. Profiling an unfractionated tryptic digest. Proteomics 2001, 1:93-107.
    • (2001) Proteomics , vol.1 , pp. 93-107
    • Spahr, C.S.1    Davis, M.T.2    McGinley, M.D.3    Robinson, J.H.4    Bures, E.J.5    Beierle, J.6
  • 30
    • 84873028352 scopus 로고    scopus 로고
    • The green proteome: challenges in plant proteomics
    • Heazlewood J.L. The green proteome: challenges in plant proteomics. Front Plant Sci 2011, 2. 10.3389/fpls.2011.00006.
    • (2011) Front Plant Sci , vol.2
    • Heazlewood, J.L.1
  • 31
    • 79961212595 scopus 로고    scopus 로고
    • Improvements in proteomic metrics of low abundance proteins through proteome equalization using ProteoMiner prior to MudPIT
    • Fonslow B.R., Carvalho P.C., Academia K., Freeby S., Xu T., Nakorchevsky A., et al. Improvements in proteomic metrics of low abundance proteins through proteome equalization using ProteoMiner prior to MudPIT. J Proteome Res 2011, 10:3690-3700.
    • (2011) J Proteome Res , vol.10 , pp. 3690-3700
    • Fonslow, B.R.1    Carvalho, P.C.2    Academia, K.3    Freeby, S.4    Xu, T.5    Nakorchevsky, A.6
  • 32
    • 57449099068 scopus 로고    scopus 로고
    • Precision proteomics: the case for high resolution and high mass accuracy
    • Mann M., Kelleher N.L. Precision proteomics: the case for high resolution and high mass accuracy. Proc Natl Acad Sci U S A 2008, 105:18132-18138.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 18132-18138
    • Mann, M.1    Kelleher, N.L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.