메뉴 건너뛰기




Volumn 12, Issue 11, 2013, Pages 3388-3397

Proteogenomic analysis of bradyrhizobium japonicum USDA110 using genosuite, an automated multi-algorithmic pipeline

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CYTOCHROME P450;

EID: 84886054819     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M112.027169     Document Type: Article
Times cited : (37)

References (50)
  • 6
    • 84860575662 scopus 로고    scopus 로고
    • Proteogenomic analysis of bacteria and archaea: A 46 organism case study
    • Venter, E., Smith, R. D., and Payne, S. H. (2011) Proteogenomic analysis of bacteria and archaea: A 46 organism case study. PLoS. One. 6, e27587.
    • (2011) PLoS. One , vol.6
    • Venter, E.1    Smith, R.D.2    Payne, S.H.3
  • 7
    • 0029645432 scopus 로고
    • Mining genomes: Correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases
    • Yates, J. R. 3rd, Eng, J. K., and McCormack, A. L. (1995) Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. Anal. Chem. 67, 3202-3210.
    • (1995) Anal. Chem. , vol.67 , pp. 3202-3210
    • Yates III, J.R.1    Eng, J.K.2    McCormack, A.L.3
  • 8
    • 0942287072 scopus 로고    scopus 로고
    • Proteogenomic mapping as a complementary method to perform genome annotation
    • DOI 10.1002/pmic.200300511
    • Jaffe, J. D., Berg, H. C., and Church, G. M. (2004) Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics 4, 59-77. (Pubitemid 38140875)
    • (2004) Proteomics , vol.4 , Issue.1 , pp. 59-77
    • Jaffe, J.D.1    Berg, H.C.2    Church, G.M.3
  • 10
    • 84857006793 scopus 로고    scopus 로고
    • High-throughput proteogenomics of Ruegeria pomeroyi: Seeding a better genomic annotation for the whole marine Roseobacter clade
    • Christie-Oleza, J. A., Miotello, G., and Armengaud, J. (2012) High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade. BMC. Genomics 13, 73.
    • (2012) BMC. Genomics , vol.13 , pp. 73
    • Christie-Oleza, J.A.1    Miotello, G.2    Armengaud, J.3
  • 14
    • 77957237701 scopus 로고    scopus 로고
    • Proteogenomics to discover the full coding content of genomes: A computational perspective
    • Castellana, N., and Bafna, V. (2010) Proteogenomics to discover the full coding content of genomes: A computational perspective. J. Proteomics 73, 2124-2135.
    • (2010) J. Proteomics , vol.73 , pp. 2124-2135
    • Castellana, N.1    Bafna, V.2
  • 15
    • 77949768663 scopus 로고    scopus 로고
    • Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines
    • Yu, W., Taylor, J. A., Davis, M. T., Bonilla, L. E., Lee, K. A., Auger, P. L., Farnsworth, C. C., Welcher, A. A., and Patterson, S. D. (2010) Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines. Proteomics 10, 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
  • 18
    • 34147132825 scopus 로고    scopus 로고
    • Identifying bacterial genes and endosymbiont DNA with Glimmer
    • DOI 10.1093/bioinformatics/btm009
    • Delcher, A. L., Bratke, K. A., Powers, E. C., and Salzberg, S. L. (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673-679. (Pubitemid 46554717)
    • (2007) Bioinformatics , vol.23 , Issue.6 , pp. 673-679
    • Delcher, A.L.1    Bratke, K.A.2    Powers, E.C.3    Salzberg, S.L.4
  • 20
    • 77950679651 scopus 로고    scopus 로고
    • An integrated proteomics and transcriptomics reference data set provides new insights into the Bradyrhizobium japonicum bacteroid metabolism in soybean root nodules
    • Delmotte, N., Ahrens, C. H., Knief, C., Qeli, E., Koch, M., Fischer, H. M., Vorholt, J. A., Hennecke, H., and Pessi, G. (2010) An integrated proteomics and transcriptomics reference data set provides new insights into the Bradyrhizobium japonicum bacteroid metabolism in soybean root nodules. Proteomics 10, 1391-1400.
    • (2010) Proteomics , vol.10 , pp. 1391-1400
    • Delmotte, N.1    Ahrens, C.H.2    Knief, C.3    Qeli, E.4    Koch, M.5    Fischer, H.M.6    Vorholt, J.A.7    Hennecke, H.8    Pessi, G.9
  • 22
    • 79955864497 scopus 로고    scopus 로고
    • Mass wiz: A novel scoring algorithm with target-decoy based analysis pipeline for tandem mass spectrometry
    • Yadav, A. K., Kumar, D., and Dash, D. (2011) Mass Wiz: A novel scoring algorithm with target-decoy based analysis pipeline for tandem mass spectrometry. J. Proteome. Res. 10, 2154-2160.
    • (2011) J. Proteome. Res. , vol.10 , pp. 2154-2160
    • Yadav, A.K.1    Kumar, D.2    Dash, D.3
  • 24
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: Matching proteins with tandem mass spectra
    • DOI 10.1093/bioinformatics/bth092
    • Craig, R., and Beavis, R. C. (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20, 1466-1467. (Pubitemid 38931421)
    • (2004) Bioinformatics , vol.20 , Issue.9 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 25
    • 27544511899 scopus 로고    scopus 로고
    • InsPecT: Identification of posttranslationally modified peptides from tandem mass spectra
    • DOI 10.1021/ac050102d
    • Tanner, S., Shu, H., Frank, A., Wang, L. C., Zandi, E., Mumby, M., Pevzner, P. A., and Bafna, V. (2005) Ins PecT: identification of post translation ally modified peptides from tandem mass spectra. Anal. Chem. 77, 4626-4639. (Pubitemid 41542287)
    • (2005) Analytical Chemistry , vol.77 , Issue.14 , pp. 4626-4639
    • Tanner, S.1    Shu, H.2    Frank, A.3    Wang, L.-C.4    Zandi, E.5    Mumby, M.6    Pevzner, P.A.7    Bafna, V.8
  • 26
    • 63049120021 scopus 로고    scopus 로고
    • Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines
    • Jones, A. R., Siepen, J. A., Hubbard, S. J., and Paton, N. W. (2009) Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines. Proteomics 9, 1220-1229.
    • (2009) Proteomics , vol.9 , pp. 1220-1229
    • Jones, A.R.1    Siepen, J.A.2    Hubbard, S.J.3    Paton, N.W.4
  • 27
    • 38649083118 scopus 로고    scopus 로고
    • Assigning significance to peptides identified by tandem mass spectrometry using decoy databases
    • DOI 10.1021/pr700600n
    • Kä ll, L., Storey, J. D., MacCoss, M. J., and Noble, W. S. (2008) Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J. Proteome. Res. 7, 29-34. (Pubitemid 351171110)
    • (2008) Journal of Proteome Research , vol.7 , Issue.1 , pp. 29-34
    • Kall, L.1    Storey, J.D.2    MacCoss, M.J.3    Noble, W.S.4
  • 28
    • 0032519353 scopus 로고    scopus 로고
    • GeneMark.Hmm: New solutions for gene finding
    • DOI 10.1093/nar/26.4.1107
    • Lukashin, A. V., and Borodovsky, M. (1998) GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res. 26, 1107-1115. (Pubitemid 28291669)
    • (1998) Nucleic Acids Research , vol.26 , Issue.4 , pp. 1107-1115
    • Lukashin, A.V.1    Borodovsky, M.2
  • 34
    • 35748972060 scopus 로고    scopus 로고
    • Semi-supervised learning for peptide identification from shotgun proteomics datasets
    • DOI 10.1038/nmeth1113, PII NMETH1113
    • Kä ll, L., Canterbury, J. D., Weston, J., Noble, W. S., and MacCoss, M. J. (2007) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat. Methods 4, 923-925. (Pubitemid 350042380)
    • (2007) Nature Methods , vol.4 , Issue.11 , pp. 923-925
    • Kall, L.1    Canterbury, J.D.2    Weston, J.3    Noble, W.S.4    MacCoss, M.J.5
  • 35
    • 67049118923 scopus 로고    scopus 로고
    • Accurate and sensitive peptide identification with mascot percolator
    • Brosch, M., Yu, L., Hubbard, T., and Choudhary, J. (2009) Accurate and sensitive peptide identification with Mascot Percolator. J. Proteome. Res. 8, 3176-3181.
    • (2009) J. Proteome. Res. , vol.8 , pp. 3176-3181
    • Brosch, M.1    Yu, L.2    Hubbard, T.3    Choudhary, J.4
  • 36
    • 84870040445 scopus 로고    scopus 로고
    • Learning from decoys to improve the sensitivity and specificity of proteomics database search results
    • Yadav, A. K., Kumar, D., and Dash, D. (2012) Learning from decoys to improve the sensitivity and specificity of proteomics database search results. PLoS. One 7, e50651.
    • (2012) PLoS. One , vol.7
    • Yadav, A.K.1    Kumar, D.2    Dash, D.3
  • 37
    • 79953725441 scopus 로고    scopus 로고
    • FDR analysis: A tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines
    • Wedge, D. C., Krishna, R., Blackhurst, P., Siepen, J. A., Jones, A. R., and Hubbard, S. J. (2011) FDR Analysis: A tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines. J. Proteome. Res. 10, 2088-2094.
    • (2011) J. Proteome. Res. , vol.10 , pp. 2088-2094
    • Wedge, D.C.1    Krishna, R.2    Blackhurst, P.3    Siepen, J.A.4    Jones, A.R.5    Hubbard, S.J.6
  • 38
    • 34547838618 scopus 로고    scopus 로고
    • 54 regulon, and identification of a ferredoxin gene (fdxN) for symbiotic nitrogen fixation
    • DOI 10.1007/s00438-007-0246-9
    • Hauser, F., Pessi, G., Friberg, M., Weber, C., Rusca, N., Lindemann, A., Fischer, H. M., and Hennecke, H. (2007) Dissection of the Bradyrhizobium japonicum NifA-sigma54 regulon, and identification of a ferredoxin gene (fdxN) for symbiotic nitrogen fixation. Mol. Genet. Genomics 278, 255-271. (Pubitemid 47247268)
    • (2007) Molecular Genetics and Genomics , vol.278 , Issue.3 , pp. 255-271
    • Hauser, F.1    Pessi, G.2    Friberg, M.3    Weber, C.4    Rusca, N.5    Lindemann, A.6    Fischer, H.-M.7    Hennecke, H.8
  • 40
    • 84055199940 scopus 로고    scopus 로고
    • Complete genome sequence of the soybean symbiont bradyrhizobium japonicum strain usda6t
    • Kaneko, T. (2011) Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T. Genes 2, 763-787.
    • (2011) Genes , vol.2 , pp. 763-787
    • Kaneko, T.1
  • 42
    • 0035143664 scopus 로고    scopus 로고
    • Potential symbiosis-specific genes uncovered by sequencing a 410-kilobase DNA region of the Bradyrhizobium japonicum chromosome
    • DOI 10.1128/JB.183.4.1405-1412.2001
    • Gö ttfert, M., Rö thlisberger, S., Kü ndig, C., Beck, C., Marty, R., and Hennecke, H. (2001) Potential symbiosis-specific genes uncovered by sequencing a 410-kilobase DNA region of the Bradyrhizobium japonicum chromosome. J. Bacteriol. 183, 1405-1412. (Pubitemid 32107737)
    • (2001) Journal of Bacteriology , vol.183 , Issue.4 , pp. 1405-1412
    • Gottfert, M.1    Rothlisberger, S.2    Kundig, C.3    Beck, C.4    Marty, R.5    Hennecke, H.6
  • 44
    • 0032985668 scopus 로고    scopus 로고
    • The Bradyrhizobium japonicum nolA gene encodes three functionally distinct proteins
    • Loh, J., Stacey, M. G., Sadowsky, M. J., and Stacey, G. (1999) The Bradyrhizobium japonicum nolA gene encodes three functionally distinct proteins. J. Bacteriol. 181, 1544-1554. (Pubitemid 29110815)
    • (1999) Journal of Bacteriology , vol.181 , Issue.5 , pp. 1544-1554
    • Loh, J.1    Stacey, M.G.2    Sadowsky, M.J.3    Stacey, G.4
  • 45
    • 33750127867 scopus 로고    scopus 로고
    • GAPP: A fully automated software for the confident identification of human peptides from tandem mass spectra
    • DOI 10.1021/pr060205s
    • Shadforth, I., Xu, W., Crowther, D., and Bessant, C. (2006) GAPP: A fully automated software for the confident identification of human peptides from tandem mass spectra. J. Proteome. Res. 5, 2849-2852. (Pubitemid 44595185)
    • (2006) Journal of Proteome Research , vol.5 , Issue.10 , pp. 2849-2852
    • Shadforth, I.1    Xu, W.2    Crowther, D.3    Bessant, C.4
  • 47
    • 11144310562 scopus 로고    scopus 로고
    • Estimation of the number of authentic orphan genes in bacterial genomes
    • Fukuchi, S., and Nishikawa, K. (2004) Estimation of the number of authentic orphan genes in bacterial genomes. DNA Res. 11, 219-231, 311-313.
    • (2004) DNA Res. , vol.11 , Issue.219-231 , pp. 311-313
    • Fukuchi, S.1    Nishikawa, K.2
  • 48
    • 77957836421 scopus 로고    scopus 로고
    • Protein acetylation in archaea, bacteria, and eukaryotes
    • Soppa, J. (2010) Protein acetylation in archaea, bacteria, and eukaryotes. Archaea. 2010, 1-9.
    • (2010) Archaea, 2010 , pp. 1-9
    • Soppa, J.1
  • 49
    • 77954013335 scopus 로고    scopus 로고
    • Bacterial protein acetylation: The dawning of a new age
    • Hu, L. I., Lima, B. P., and Wolfe, A. J. (2010) Bacterial protein acetylation: The dawning of a new age. Mol. Microbiol. 77, 15-21.
    • (2010) Mol. Microbiol , vol.77 , pp. 15-21
    • Hu, L.I.1    Lima, B.P.2    Wolfe, A.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.