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Volumn 72, Issue 10, 2011, Pages 1020-1027

A legume specific protein database (LegProt) improves the number of identified peptides, confidence scores and overall protein identification success rates for legume proteomics

Author keywords

Glycine max; Legume proteomics; Lotus japonica; Lupinus albus; Medicago sativa; Medicago truncatula; Phaseolus vulgaris; Pisum sativum; Protein database; Tandem mass spectrometry

Indexed keywords

PEPTIDE; VEGETABLE PROTEIN;

EID: 79958093889     PISSN: 00319422     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.phytochem.2011.01.026     Document Type: Article
Times cited : (25)

References (45)
  • 1
    • 34548017391 scopus 로고    scopus 로고
    • Genomic organization and evolutionary insights on GRP and NCR genes, two large nodule-specific gene families in Medicago truncatula
    • DOI 10.1094/MPMI-20-9-1138
    • B. Alunni, Z. Kevei, M. Redondo-Nieto, A. Kondorosi, P. Mergaert, and E. Kondorosi Genomic organization and evolutionary insights on GRP and NCR genes, two large nodule-specific gene families in Medicago truncatula Mol. Plant Microbe Interact. 20 2007 1138 1148 (Pubitemid 47281780)
    • (2007) Molecular Plant-Microbe Interactions , vol.20 , Issue.9 , pp. 1138-1148
    • Alunni, B.1    Kevei, Z.2    Redondo-Nieto, M.3    Kondorosi, A.4    Mergaert, P.5    Kondorosi, E.6
  • 5
    • 36749037110 scopus 로고    scopus 로고
    • Comparative proteomics analysis of differentially expressed proteins in chickpea extracellular matrix during dehydration stress
    • DOI 10.1074/mcp.M700015-MCP200
    • D. Bhushan, A. Pandey, M.K. Choudhary, A. Datta, S. Chakraborty, and N. Chakraborty Comparative proteomics analysis of differentially expressed proteins in chickpea extracellular matrix during dehydration stress Mol. Cell. Proteomics 6 2007 1868 1884 (Pubitemid 350201865)
    • (2007) Molecular and Cellular Proteomics , vol.6 , Issue.11 , pp. 1868-1884
    • Bhushan, D.1    Pandey, A.2    Choudhary, M.K.3    Datta, A.4    Chakraborty, S.5    Chakraborty, N.6
  • 7
    • 60349108930 scopus 로고    scopus 로고
    • Dissecting the proteome of pea mature seeds reveals the phenotypic plasticity of seed protein composition
    • M. Bourgeois, F. Jacquin, V. Savois, N. Sommerer, V. Labas, C. Henry, and J. Burstin Dissecting the proteome of pea mature seeds reveals the phenotypic plasticity of seed protein composition Proteomics 9 2009 254 271
    • (2009) Proteomics , vol.9 , pp. 254-271
    • Bourgeois, M.1    Jacquin, F.2    Savois, V.3    Sommerer, N.4    Labas, V.5    Henry, C.6    Burstin, J.7
  • 8
    • 60349105480 scopus 로고    scopus 로고
    • A label-free internal standard method for the differential analysis of bioactive lupin proteins using nano HPLC-chip coupled with ion trap mass spectrometry
    • F. Brambilla, D. Resta, I. Isak, M. Zanotti, and A. Arnoldi A label-free internal standard method for the differential analysis of bioactive lupin proteins using nano HPLC-chip coupled with ion trap mass spectrometry Proteomics 9 2009 272 286
    • (2009) Proteomics , vol.9 , pp. 272-286
    • Brambilla, F.1    Resta, D.2    Isak, I.3    Zanotti, M.4    Arnoldi, A.5
  • 11
    • 67049132397 scopus 로고    scopus 로고
    • Mascot-derived false positive peptide identifications revealed by manual analysis of tandem mass spectra
    • Y. Chen, J. Zhang, G. Xing, and Y. Zhao Mascot-derived false positive peptide identifications revealed by manual analysis of tandem mass spectra J. Proteome Res. 8 2009 3141 3147
    • (2009) J. Proteome Res. , vol.8 , pp. 3141-3147
    • Chen, Y.1    Zhang, J.2    Xing, G.3    Zhao, Y.4
  • 13
    • 77956416196 scopus 로고    scopus 로고
    • Medicago truncatula proteomics
    • F. Colditz, and H.P. Braun Medicago truncatula proteomics J. Proteomics 73 2010 1974 1985
    • (2010) J. Proteomics , vol.73 , pp. 1974-1985
    • Colditz, F.1    Braun, H.P.2
  • 14
    • 0033180478 scopus 로고    scopus 로고
    • Medicago truncatula - A model in the making!
    • DOI 10.1016/S1369-5266(99)80053-3
    • D.R. Cook Medicago truncatula - a model in the making! Curr. Opin. Plant Biol. 2 1999 301 304 (Pubitemid 29365677)
    • (1999) Current Opinion in Plant Biology , vol.2 , Issue.4 , pp. 301-304
    • Cook, D.R.1
  • 15
  • 17
    • 0242365841 scopus 로고    scopus 로고
    • Species-specific protein sequence and fold optimizations
    • M. Dumontier, K. Michalickova, and C. Hogue Species-specific protein sequence and fold optimizations BMC Bioinf. 3 2002 39
    • (2002) BMC Bioinf. , vol.3 , pp. 39
    • Dumontier, M.1    Michalickova, K.2    Hogue, C.3
  • 18
    • 0034095972 scopus 로고    scopus 로고
    • The current state of two-dimensional electrophoresis with immobilized pH gradients
    • DOI 10.10 02/(SI CI)1522-26 83(20000 401)21:6<10 37::AID-EL PS10 37>3.0.CO;2-V
    • A. Gorg, C. Obermaier, G. Boguth, A. Harder, B. Scheibe, R. Wildgruber, and W. Weiss The current state of two-dimensional electrophoresis with immobilized pH gradients Electrophoresis 21 2000 1037 1053 (Pubitemid 30230771)
    • (2000) Electrophoresis , vol.21 , Issue.6 , pp. 1037-1053
    • Gorg, A.1    Obermaier, C.2    Boguth, G.3    Harder, A.4    Scheibe, B.5    Wildgruber, R.6    Weiss, W.7
  • 19
    • 10644230916 scopus 로고    scopus 로고
    • Current two-dimensional electrophoresis technology for proteomics
    • DOI 10.1002/pmic.200401031
    • A. Görg, W. Weiss, and M.J. Dunn Current two-dimensional electrophoresis technology for proteomics Proteomics 4 2004 3665 3685 (Pubitemid 39657447)
    • (2004) Proteomics , vol.4 , Issue.12 , pp. 3665-3685
    • Gorg, A.1    Weiss, W.2    Dunn, M.J.3
  • 20
    • 0037353554 scopus 로고    scopus 로고
    • Legumes: Importance and constraints to greater use
    • DOI 10.1104/pp.017004
    • P.H. Graham, and C.P. Vance Legumes: importance and constraints to greater use Plant Physiol. 131 2003 872 877 (Pubitemid 36405303)
    • (2003) Plant Physiology , vol.131 , Issue.3 , pp. 872-877
    • Graham, P.H.1    Vance, C.P.2
  • 21
    • 3042814319 scopus 로고    scopus 로고
    • Proteome reference maps of Medicago truncatula embryogenic cell cultures generated from single protoplasts
    • DOI 10.1002/pmic.200300803
    • N. Imin, F. De Jong, U. Mathesius, G. van Noorden, N.A. Saeed, X.D. Wang, R.J. Rose, and B.G. Rolfe Proteome reference maps of Medicago truncatula embryogenic cell cultures generated from single protoplasts Proteomics 4 2004 1883 1896 (Pubitemid 38880349)
    • (2004) Proteomics , vol.4 , Issue.7 , pp. 1883-1896
    • Imin, N.1    De Jong, F.2    Mathesius, U.3    Van Noorden, G.4    Saeed, N.A.5    Wang, X.-D.6    Rose, R.J.7    Rolfe, B.G.8
  • 23
    • 63349106787 scopus 로고    scopus 로고
    • Soybean proteomics and its application to functional analysis
    • S. Komatsu, and N. Ahsan Soybean proteomics and its application to functional analysis J. Proteomics 72 2009 325 336
    • (2009) J. Proteomics , vol.72 , pp. 325-336
    • Komatsu, S.1    Ahsan, N.2
  • 25
    • 28644445655 scopus 로고    scopus 로고
    • A two-dimensional electrophoresis proteomic reference map and systematic identification of 1367 proteins from a cell suspension culture of the model legume Medicago truncatula
    • DOI 10.1074/mcp.D500005-MCP200
    • Z. Lei, A.M. Elmer, B.S. Watson, R.A. Dixon, P.J. Mendes, and L.W. Sumner A two-dimensional electrophoresis proteomic reference map and systematic identification of 1367 proteins from a cell suspension culture of the model legume Medicago truncatula Mol. Cell. Proteomics 4 2005 1812 1825 (Pubitemid 41749273)
    • (2005) Molecular and Cellular Proteomics , vol.4 , Issue.11 , pp. 1812-1825
    • Lei, Z.1    Elmer, A.M.2    Watson, B.S.3    Dixon, R.A.4    Mendes, P.J.5    Sumner, L.W.6
  • 26
    • 0035525061 scopus 로고    scopus 로고
    • Establishment of a root proteome reference map for the model legume Medicago truncatula using the expressed sequence tag database for peptide mass fingerprinting
    • U. Mathesius, G. Keijzers, S.H. Natera, J.J. Weinman, M.A. Djordjevic, and B.G. Rolfe Establishment of a root proteome reference map for the model legume Medicago truncatula using the expressed sequence tag database for peptide mass fingerprinting Proteomics 1 2001 1424 1440 (Pubitemid 33587898)
    • (2001) Proteomics , vol.1 , Issue.11 , pp. 1424-1440
    • Mathesius, U.1    Keijzers, G.2    Natera, S.H.A.3    Weinman, J.J.4    Djordjevic, M.A.5    Rolfe, B.G.6
  • 27
    • 0038663127 scopus 로고    scopus 로고
    • A novel family in Medicago truncatula consisting of more than 300 nodule-specific genes coding for small, secreted polypeptides with conserved cysteine motifs
    • DOI 10.1104/pp.102.018192
    • P. Mergaert, K. Nikovics, Z. Kelemen, N. Maunoury, D. Vaubert, A. Kondorosi, and E. Kondorosi A novel family in Medicago truncatula consisting of more than 300 nodule-specific genes coding for small, secreted polypeptides with conserved cysteine motifs Plant Physiol. 132 2003 161 173 (Pubitemid 36590408)
    • (2003) Plant Physiology , vol.132 , Issue.1 , pp. 161-173
    • Mergaert, P.1    Nikovics, K.2    Kelemen, Z.3    Maunoury, N.4    Vaubert, D.5    Kondorosi, A.6    Kondorosi, E.7
  • 28
    • 39049153858 scopus 로고    scopus 로고
    • Proteomics approach to identify dehydration responsive nuclear proteins from chickpea (Cicer arietinum L.)
    • DOI 10.1074/mcp.M700314-MCP200
    • A. Pandey, S. Chakraborty, A. Datta, and N. Chakraborty Proteomics approach to identify dehydration responsive nuclear proteins from chickpea (Cicer arietinum L.) Mol. Cell. Proteomics 7 2008 88 107 (Pubitemid 351248236)
    • (2008) Molecular and Cellular Proteomics , vol.7 , Issue.1 , pp. 88-107
    • Pandey, A.1    Chakraborty, S.2    Datta, A.3    Chakraborty, N.4
  • 29
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • D.N. Perkins, D.J. Pappin, D.M. Creasy, and J.S. Cottrell Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 20 1999 3551 3567 (Pubitemid 30007252)
    • (1999) Electrophoresis , vol.20 , Issue.18 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.C.2    Creasy, D.M.3    Cottrell, J.S.4
  • 30
    • 0036007665 scopus 로고    scopus 로고
    • Computational gene finding in plants
    • DOI 10.1023/A:1013770123580
    • M. Pertea, and S.L. Salzberg Computational gene finding in plants Plant Mol. Biol. 48 2002 39 48 (Pubitemid 34128491)
    • (2002) Plant Molecular Biology , vol.48 , Issue.1-2 , pp. 39-48
    • Pertea, M.1    Salzberg, S.L.2
  • 31
    • 0026299159 scopus 로고
    • Alfalfa and the nitrogen cycle in the Corn Belt
    • T.A. Peterson, and M.P. Russelle Alfalfa and the nitrogen cycle in the Corn Belt J. Soil Water Conserv. 46 1991 229 235
    • (1991) J. Soil Water Conserv. , vol.46 , pp. 229-235
    • Peterson, T.A.1    Russelle, M.P.2
  • 32
    • 0036211102 scopus 로고    scopus 로고
    • Characterisation by proteomics of peribacteroid space and peribacteroid membrane preparations from pea (Pisum sativum) symbiosomes
    • DOI 10.10 02/161 5-9861(20 0203)2:3<32 5::AID-PROT3 25>3.0.CO;2-W
    • G. Saalbach, P. Pinar Erik, and S. Stefanie Wienkoop Characterisation by proteomics of peribacteroid space and peribacteroid membrane preparations from pea (Pisum sativum) symbiosomes Proteomics 2 2002 325 337 (Pubitemid 34269986)
    • (2002) Proteomics , vol.2 , Issue.3 , pp. 325-337
    • Saalbach, G.1    Erik, P.2    Wienkoop, S.3
  • 34
    • 30344450374 scopus 로고    scopus 로고
    • RNA polyadenylation in prokaryotes and organelles; different tails tell different tales
    • DOI 10.1080/07352680500391337, PII N6P747G60G1N1162
    • S. Slomovic, V. Portnoy, V. Liveanu, and G. Schuster RNA polyadenylation in prokaryotes and organelles; different tails tell different tales Crit. Rev. Plant Sci. 25 2006 65 77 (Pubitemid 43068155)
    • (2006) Critical Reviews in Plant Sciences , vol.25 , Issue.1 , pp. 65-77
    • Slomovic, S.1    Portnoy, V.2    Liveanu, V.3    Schuster, G.4
  • 35
    • 34347383999 scopus 로고    scopus 로고
    • Proteomics of ionically bound and soluble extracellular proteins in Medicago truncatula leaves
    • DOI 10.1002/pmic.200600953
    • N.C. Soares, R. Francisco, C.P. Ricardo, and P.A. Jackson Proteomics of ionically bound and soluble extracellular proteins in Medicago truncatula leaves Proteomics 7 2007 2070 2082 (Pubitemid 47022957)
    • (2007) Proteomics , vol.7 , Issue.12 , pp. 2070-2082
    • Soares, N.C.1    Francisco, R.2    Ricardo, C.P.3    Jackson, P.A.4
  • 36
    • 0002359805 scopus 로고    scopus 로고
    • The molecular genetic linkage map of the model legume Medicago truncatula: An essential tool for comparative legume genomics and the isolation of agronomically important genes
    • P. Thoquet, M. Gherardi, E. Journet, A. Kereszt, J. Ane, J. Prosperi, and T. Huguet The molecular genetic linkage map of the model legume Medicago truncatula: an essential tool for comparative legume genomics and the isolation of agronomically important genes BMC Plant Biol. 2 2002 1 13
    • (2002) BMC Plant Biol. , vol.2 , pp. 1-13
    • Thoquet, P.1    Gherardi, M.2    Journet, E.3    Kereszt, A.4    Ane, J.5    Prosperi, J.6    Huguet, T.7
  • 40
    • 0037353383 scopus 로고    scopus 로고
    • Mapping the proteome of barrel medic (Medicago truncatula)
    • DOI 10.1104/pp.102.019034
    • B.S. Watson, V.S. Asirvatham, L. Wang, and L.W. Sumner Mapping the proteome of barrel medic (Medicago truncatula) Plant Physiol. 131 2003 1104 1123 (Pubitemid 36405301)
    • (2003) Plant Physiology , vol.131 , Issue.3 , pp. 1104-1123
    • Watson, B.S.1    Asirvatham, V.S.2    Wang, L.3    Sumner, L.W.4
  • 41
    • 3242773845 scopus 로고    scopus 로고
    • Proteomics of Medicago sativa cell walls
    • DOI 10.1016/j.phytochem.2004.04.026, PII S0031942204001839
    • B.S. Watson, Z. Lei, R.A. Dixon, and L.W. Sumner Proteomics of Medicago sativa cell walls Phytochemistry 65 2004 1709 1720 (Pubitemid 38969917)
    • (2004) Phytochemistry , vol.65 , Issue.12 , pp. 1709-1720
    • Watson, B.S.1    Lei, Z.2    Dixon, R.A.3    Sumner, L.W.4
  • 42
    • 0036744340 scopus 로고    scopus 로고
    • The proteomics of senescence in leaves of white clover, Trifolium repens (L.)
    • K.A. Wilson, M.T. McManus, M.E. Gordon, and T.W. Jordan The proteomics of senescence in leaves of white clover, Trifolium repens (L.) Proteomics 2 2002 1114 1122
    • (2002) Proteomics , vol.2 , pp. 1114-1122
    • Wilson, K.A.1    McManus, M.T.2    Gordon, M.E.3    Jordan, T.W.4
  • 43
  • 44
    • 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
  • 45
    • 33845459217 scopus 로고    scopus 로고
    • The Medicago truncatula small protein proteome and peptidome
    • DOI 10.1021/pr060336t
    • K. Zhang, C. McKinlay, C.H. Hocart, and M.A. Djordjevic The Medicago truncatula small protein proteome and peptidome J. Proteome Res. 5 2006 3355 3367 (Pubitemid 44904327)
    • (2006) Journal of Proteome Research , vol.5 , Issue.12 , pp. 3355-3367
    • Zhang, K.1    McKinlay, C.2    Hocart, C.H.3    Djordjevic, M.A.4


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