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Volumn 13, Issue 9, 2013, Pages 1457-1466

Management and dissemination of MS proteomic data with PROTICdb: Example of a quantitative comparison between methods of protein extraction

Author keywords

Bioinformatics; Database; MS; Protein extraction; Quantification

Indexed keywords

ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; DATA BASE; EVOLUTION; EXTRACTION; INFORMATION PROCESSING; INFORMATION RETRIEVAL; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXTRACTION; PROTEOMICS; QUANTITATIVE ANALYSIS;

EID: 84876466311     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201200564     Document Type: Article
Times cited : (21)

References (31)
  • 2
    • 0041859590 scopus 로고    scopus 로고
    • The Make 2D-DB II package: conversion of federated two-dimensional gel electrophoresis databases into a relational format and interconnection of distributed databases
    • Mostaguir, K., Hoogland, C., Binz, P.-A., Appel, R. D., The Make 2D-DB II package: conversion of federated two-dimensional gel electrophoresis databases into a relational format and interconnection of distributed databases. Proteomics 2003, 3, 1441-1444.
    • (2003) Proteomics , vol.3 , pp. 1441-1444
    • Mostaguir, K.1    Hoogland, C.2    Binz, P.-A.3    Appel, R.D.4
  • 3
    • 20044393867 scopus 로고    scopus 로고
    • PROTICdb: a web-based application to store, track, query, and compare plant proteome data
    • Ferry-Dumazet, H., Houel, G., Montalent, P., Moreau, L. et al., PROTICdb: a web-based application to store, track, query, and compare plant proteome data. Proteomics 2005, 5, 2069-2081.
    • (2005) Proteomics , vol.5 , pp. 2069-2081
    • Ferry-Dumazet, H.1    Houel, G.2    Montalent, P.3    Moreau, L.4
  • 4
    • 65349174459 scopus 로고    scopus 로고
    • PROTEOMER: a workflow-optimized laboratory information management system for 2-D electrophoresis-centered proteomics
    • Nebrich, G., Herrmann, M., Hartl, D., Diedrich, M. et al., PROTEOMER: a workflow-optimized laboratory information management system for 2-D electrophoresis-centered proteomics. Proteomics 2009, 9, 1795-1808.
    • (2009) Proteomics , vol.9 , pp. 1795-1808
    • Nebrich, G.1    Herrmann, M.2    Hartl, D.3    Diedrich, M.4
  • 5
    • 78650979357 scopus 로고    scopus 로고
    • MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data
    • Joshi, H. J., Hirsch-Hoffmann, M., Baerenfaller, K., Gruissem, W. et al., MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data. Plant Physiol. 2011, 155, 259-270.
    • (2011) Plant Physiol. , vol.155 , pp. 259-270
    • Joshi, H.J.1    Hirsch-Hoffmann, M.2    Baerenfaller, K.3    Gruissem, W.4
  • 7
    • 84876467322 scopus 로고    scopus 로고
    • AT_CHLORO: a chloroplast protein database dedicated to sub-plastidial localization
    • Bruley, C., Dupierris, V., Salvi, D., Rolland, N., Ferro, M., AT_CHLORO: a chloroplast protein database dedicated to sub-plastidial localization. Front. Plant Sci. 2012, 3, 205.
    • (2012) Front. Plant Sci. , vol.3 , pp. 205
    • Bruley, C.1    Dupierris, V.2    Salvi, D.3    Rolland, N.4    Ferro, M.5
  • 8
    • 75549090366 scopus 로고    scopus 로고
    • PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update
    • Durek, P., Schmidt, R., Heazlewood, J. L., Jones, A. et al., PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update. Nucleic Acids Res. 2010, 38, D828-D834.
    • (2010) Nucleic Acids Res. , vol.38
    • Durek, P.1    Schmidt, R.2    Heazlewood, J.L.3    Jones, A.4
  • 9
    • 84876472005 scopus 로고    scopus 로고
    • P(3)DB: an integrated database for plant protein phosphorylation
    • Yao, Q., Bollinger, C., Gao, J., Xu, D. et al., P(3)DB: an integrated database for plant protein phosphorylation. Front. Plant Sci. 2012, 3, 206.
    • (2012) Front. Plant Sci. , vol.3 , pp. 206
    • Yao, Q.1    Bollinger, C.2    Gao, J.3    Xu, D.4
  • 11
    • 23944526367 scopus 로고    scopus 로고
    • PRIDE: the proteomics identifications database
    • Martens, L., Hermjakob, H., Jones, P., Adamski, M. et al., PRIDE: the proteomics identifications database. Proteomics 2005, 5, 3537-3545.
    • (2005) Proteomics , vol.5 , pp. 3537-3545
    • Martens, L.1    Hermjakob, H.2    Jones, P.3    Adamski, M.4
  • 12
    • 84857980282 scopus 로고    scopus 로고
    • Analysis of high accuracy, quantitative proteomics data in the {MaxQB} database
    • Schaab, C., Geiger, T., Stoehr, G., Cox, J. et al., Analysis of high accuracy, quantitative proteomics data in the {MaxQB} database. Mol. Cell. Proteomics 2012, 11, doi: 10.1074/mcp.M111.014068.
    • (2012) Mol. Cell. Proteomics , vol.11
    • Schaab, C.1    Geiger, T.2    Stoehr, G.3    Cox, J.4
  • 13
    • 39049188304 scopus 로고    scopus 로고
    • The PROTICdb database for 2-DE proteomics
    • Langella, O., Zivy, M., Joets, J., The PROTICdb database for 2-DE proteomics. Methods Mol. Biol. 2007, 355, 279-303.
    • (2007) Methods Mol. Biol. , vol.355 , pp. 279-303
    • Langella, O.1    Zivy, M.2    Joets, J.3
  • 14
    • 33747833111 scopus 로고    scopus 로고
    • Taverna: a tool for building and running workflows of services
    • Hull, D., Wolstencroft, K., Stevens, R., Goble, C. et al., Taverna: a tool for building and running workflows of services. Nucleic Acids Res. 2006, 34, W729-W732.
    • (2006) Nucleic Acids Res. , vol.34
    • Hull, D.1    Wolstencroft, K.2    Stevens, R.3    Goble, C.4
  • 15
  • 16
    • 0020687849 scopus 로고
    • Removal of sodium dodecyl sulfate from proteins by ion-pair extraction
    • Konigsberg, W. H., Henderson, L., Removal of sodium dodecyl sulfate from proteins by ion-pair extraction. Methods Enzymol. 1983, 91, 254-259.
    • (1983) Methods Enzymol. , vol.91 , pp. 254-259
    • Konigsberg, W.H.1    Henderson, L.2
  • 17
    • 77954691758 scopus 로고    scopus 로고
    • A simple and efficient method for processing of cell lysates for two-dimensional gel electrophoresis
    • Xavier, T., Ganesan, T. S., Menon, K. N., A simple and efficient method for processing of cell lysates for two-dimensional gel electrophoresis. Electrophoresis 2010, 31, 2429-2435.
    • (2010) Electrophoresis , vol.31 , pp. 2429-2435
    • Xavier, T.1    Ganesan, T.S.2    Menon, K.N.3
  • 18
    • 54949129419 scopus 로고    scopus 로고
    • ProteoWizard: open source software for rapid proteomics tools development
    • Kessner, D., Chambers, M., Burke, R., Agus, D., Mallick, P., ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 2008, 24, 2534-2536.
    • (2008) Bioinformatics , vol.24 , pp. 2534-2536
    • Kessner, D.1    Chambers, M.2    Burke, R.3    Agus, D.4    Mallick, P.5
  • 19
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: matching proteins with tandem mass spectra
    • Craig, R., Beavis, R. C., TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20, 1466-1467.
    • (2004) Bioinformatics , vol.20 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 20
    • 80051817160 scopus 로고    scopus 로고
    • MassChroQ: a versatile tool for mass spectrometry quantification
    • Valot, B., Langella, O., Nano, E., Zivy, M., MassChroQ: a versatile tool for mass spectrometry quantification. Proteomics 2011, 11, 3572-3577.
    • (2011) Proteomics , vol.11 , pp. 3572-3577
    • Valot, B.1    Langella, O.2    Nano, E.3    Zivy, M.4
  • 21
    • 35948989284 scopus 로고    scopus 로고
    • The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
    • Smith, B., Ashburner, M., Rosse, C., Bard, J. et al., The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 2007, 25, 1251-1255.
    • (2007) Nat. Biotechnol. , vol.25 , pp. 1251-1255
    • Smith, B.1    Ashburner, M.2    Rosse, C.3    Bard, J.4
  • 22
    • 38549134393 scopus 로고    scopus 로고
    • The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations
    • Avraham, S., Tung, C.-W., Ilic, K., Jaiswal, P. et al., The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Res. 2008, 36, D449-D454.
    • (2008) Nucleic Acids Res. , vol.36
    • Avraham, S.1    Tung, C.-W.2    Ilic, K.3    Jaiswal, P.4
  • 23
    • 49449097859 scopus 로고    scopus 로고
    • The PSI-MOD community standard for representation of protein modification data
    • Montecchi-Palazzi, L., Beavis, R., Binz, P.-A., Chalkley, R. J. et al., The PSI-MOD community standard for representation of protein modification data. Nat. Biotechnol. 2008, 26, 864-866.
    • (2008) Nat. Biotechnol. , vol.26 , pp. 864-866
    • Montecchi-Palazzi, L.1    Beavis, R.2    Binz, P.-A.3    Chalkley, R.J.4
  • 24
    • 84870721324 scopus 로고    scopus 로고
    • File formats commonly used in mass spectrometry proteomics
    • Deutsch, E. W., File formats commonly used in mass spectrometry proteomics. Mol. Cell. Proteomics 2012, 11, 1612-1621.
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. 1612-1621
    • Deutsch, E.W.1
  • 25
    • 33748087472 scopus 로고    scopus 로고
    • The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI)
    • Taylor, C. F., Hermjakob, H., Julian, R. K., Garavelli, J. S. et al., The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI). OMICS 2006, 10, 145-151.
    • (2006) OMICS , vol.10 , pp. 145-151
    • Taylor, C.F.1    Hermjakob, H.2    Julian, R.K.3    Garavelli, J.S.4
  • 26
    • 38449100072 scopus 로고    scopus 로고
    • The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases
    • Côté, R. G., Jones, P., Martens, L., Kerrien, S. et al., The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. BMC Bioinformatics 2007, 8, 401.
    • (2007) BMC Bioinformatics , vol.8 , pp. 401
    • Côté, R.G.1    Jones, P.2    Martens, L.3    Kerrien, S.4
  • 28
    • 84855410433 scopus 로고    scopus 로고
    • BioMart: a data federation framework for large collaborative projects
    • doi: 10.1093/database/bar038.
    • Zhang, J., Haider, S., Baran, J., Cros, A. et al., BioMart: a data federation framework for large collaborative projects. Database 2011, doi: 10.1093/database/bar038.
    • (2011) Database
    • Zhang, J.1    Haider, S.2    Baran, J.3    Cros, A.4
  • 29
    • 84858314394 scopus 로고    scopus 로고
    • BioMart: driving a paradigm change in biological data management
    • doi: 10.1093/database/bar049.
    • Kasprzyk, A., BioMart: driving a paradigm change in biological data management. Database 2011, doi: 10.1093/database/bar049.
    • (2011) Database
    • Kasprzyk, A.1
  • 30
    • 46249112468 scopus 로고    scopus 로고
    • The World-2DPAGE Constellation to promote and publish gel-based proteomics data through the ExPASy server
    • Hoogland, C., Mostaguir, K., Appel, R. D., Lisacek, F., The World-2DPAGE Constellation to promote and publish gel-based proteomics data through the ExPASy server. J. Proteomics 2008, 71, 245-248.
    • (2008) J. Proteomics , vol.71 , pp. 245-248
    • Hoogland, C.1    Mostaguir, K.2    Appel, R.D.3    Lisacek, F.4
  • 31
    • 77949676526 scopus 로고    scopus 로고
    • A guided tour of the trans-proteomic pipeline
    • Deutsch, E. W., Mendoza, L., Shteynberg, D., Farrah, T. et al., A guided tour of the trans-proteomic pipeline. Proteomics 2010, 10, 1150-1159.
    • (2010) Proteomics , vol.10 , pp. 1150-1159
    • Deutsch, E.W.1    Mendoza, L.2    Shteynberg, D.3    Farrah, T.4


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