메뉴 건너뛰기




Volumn 10, Issue 6, 2010, Pages 1230-1249

Using laboratory information management systems as central part of a proteomics data workflow

Author keywords

Bioinformatics; Data management; Laboratory Information Management System; Repository

Indexed keywords

BIOINFORMATICS; DATA ANALYSIS SOFTWARE; DATA BASE; IMAGE ANALYSIS; INFORMATION PROCESSING; INTERNET; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEOMICS; QUANTITATIVE ANALYSIS; REVIEW;

EID: 77949683119     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200900420     Document Type: Review
Times cited : (39)

References (52)
  • 2
    • 67650382229 scopus 로고    scopus 로고
    • Rodriguez, H., Snyder, M., Uhlen, M., Andrews, P. et al., Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: The Amsterdam Principles. J. Proteome. Res. 2009, 8, 3689-3692.
    • Rodriguez, H., Snyder, M., Uhlen, M., Andrews, P. et al., Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: The Amsterdam Principles. J. Proteome. Res. 2009, 8, 3689-3692.
  • 3
    • 34249062964 scopus 로고    scopus 로고
    • The minimum information about a proteomics experiment (MIAPE)
    • Taylor, C. F., Paton, N. W., Lilley, K. S., Binz, P. A. et al., The minimum information about a proteomics experiment (MIAPE). Nat. Biotechnol. 2007, 25, 887-893.
    • (2007) Nat. Biotechnol , vol.25 , pp. 887-893
    • Taylor, C.F.1    Paton, N.W.2    Lilley, K.S.3    Binz, P.A.4
  • 4
    • 55849091359 scopus 로고    scopus 로고
    • Proteomics today: Bioinformatics at its best Proteomics and Bioinformatics - an inseparable couple
    • Hamacher, M., Eisenacher, M., Meyer, H. E., Stephan, C., Proteomics today: bioinformatics at its best Proteomics and Bioinformatics - an inseparable couple. Proteomics 2008, 8, 4616-4617.
    • (2008) Proteomics , vol.8 , pp. 4616-4617
    • Hamacher, M.1    Eisenacher, M.2    Meyer, H.E.3    Stephan, C.4
  • 6
    • 49049106826 scopus 로고    scopus 로고
    • LIMS and the art of MS proteomics
    • Piggee, C., LIMS and the art of MS proteomics. Anal. Chem. 2008, 80, 4801-4806.
    • (2008) Anal. Chem , vol.80 , pp. 4801-4806
    • Piggee, C.1
  • 7
    • 0033631732 scopus 로고    scopus 로고
    • a "howto" guide
    • Implementing LIMS
    • Avery, G., McGee, C., Falk, S., Implementing LIMS: a "howto" guide. Anal. Chem. 2000, 72, 57A-62A.
    • (2000) Anal. Chem , vol.72
    • Avery, G.1    McGee, C.2    Falk, S.3
  • 8
    • 23944526367 scopus 로고    scopus 로고
    • the proteomics identifications database
    • PRIDE
    • 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
  • 9
    • 43049127826 scopus 로고    scopus 로고
    • A resource for target selection for emerging targeted proteomics workflows
    • Deutsch, E. W., Lam, H., Aebersold, R., PeptideAtlas: A resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 2008, 9, 429-434.
    • (2008) EMBO Rep , vol.9 , pp. 429-434
    • Deutsch, E.1    Lam, W.2    Aebersold, H.3    PeptideAtlas, R.4
  • 10
    • 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
  • 11
    • 46249097440 scopus 로고    scopus 로고
    • Robin, X., Hoogland, C., Appel, R. D., Lisacek, F., MIAPE-GelDB, a web-based submission tool and public repository for MIAPE gel electrophoresis documents. J. Proteomics 2008, 71, 249-251.
    • Robin, X., Hoogland, C., Appel, R. D., Lisacek, F., MIAPE-GelDB, a web-based submission tool and public repository for MIAPE gel electrophoresis documents. J. Proteomics 2008, 71, 249-251.
  • 12
    • 34548447191 scopus 로고    scopus 로고
    • available tools and biological applications
    • Public proteomic MS repositories and pipelines
    • Mead, J. A., Shadforth, I. P., Bessant, C., Public proteomic MS repositories and pipelines: available tools and biological applications. Proteomics 2007, 7, 2769-2786.
    • (2007) Proteomics , vol.7 , pp. 2769-2786
    • Mead, J.A.1    Shadforth, I.P.2    Bessant, C.3
  • 13
    • 61349182486 scopus 로고    scopus 로고
    • Recent developments in public proteomic MS repositories and pipelines
    • Mead, J. A., Bianco, L., Bessant, C., Recent developments in public proteomic MS repositories and pipelines. Proteomics 2009, 9, 861-881.
    • (2009) Proteomics , vol.9 , pp. 861-881
    • Mead, J.A.1    Bianco, L.2    Bessant, C.3
  • 14
    • 30744438115 scopus 로고    scopus 로고
    • Computational Proteomics Analysis System (CPAS): An extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments
    • Rauch, A., Bellew, M., Eng, J., Fitzgibbon, M. et al., Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. J. Proteome Res. 2006, 5, 112-121.
    • (2006) J. Proteome Res , vol.5 , pp. 112-121
    • Rauch, A.1    Bellew, M.2    Eng, J.3    Fitzgibbon, M.4
  • 15
    • 33746930864 scopus 로고    scopus 로고
    • A uniform proteomics MS/MS analysis platform utilizing open XML file formats
    • Keller, A., Eng, J., Zhang, N., Li, X. J., Aebersold, R., A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. 2005, 1, 0017.
    • (2005) Mol. Syst. Biol , vol.1 , pp. 0017
    • Keller, A.1    Eng, J.2    Zhang, N.3    Li, X.J.4    Aebersold, R.5
  • 16
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    • Keller, A., Nesvizhskii, A. I., Kolker, E., Aebersold, R., Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 2002, 74, 5383-5392.
    • (2002) Anal. Chem , vol.74 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 17
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii, A. I., Keller, A., Kolker, E., Aebersold, R., A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 2003, 75, 4646-4658.
    • (2003) Anal. Chem , vol.75 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 18
    • 0034789979 scopus 로고    scopus 로고
    • Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry
    • Han, D. K., Eng, J., Zhou, H., Aebersold, R., Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol. 2001, 19, 946-951.
    • (2001) Nat. Biotechnol , vol.19 , pp. 946-951
    • Han, D.K.1    Eng, J.2    Zhou, H.3    Aebersold, R.4
  • 19
    • 33747158479 scopus 로고    scopus 로고
    • Quantitative analysis of acrylamide labeled serum proteins by LC-MS/MS
    • Faca, V., Coram, M., Phanstiel, D., Glukhova, V. et al., Quantitative analysis of acrylamide labeled serum proteins by LC-MS/MS. J. Proteome. Res. 2006, 5, 2009-2018.
    • (2006) J. Proteome. Res , vol.5 , pp. 2009-2018
    • Faca, V.1    Coram, M.2    Phanstiel, D.3    Glukhova, V.4
  • 20
    • 40549090518 scopus 로고    scopus 로고
    • Open-source platform for the analysis of liquid chromatography-mass spectrometry (LC-MS) data
    • Fitzgibbon, M., Law, W., May, D., Detter, A., McIntosh, M., Open-source platform for the analysis of liquid chromatography-mass spectrometry (LC-MS) data. Methods Mol. Biol. 2008, 428, 369-382.
    • (2008) Methods Mol. Biol , vol.428 , pp. 369-382
    • Fitzgibbon, M.1    Law, W.2    May, D.3    Detter, A.4    McIntosh, M.5
  • 21
    • 5344244656 scopus 로고    scopus 로고
    • R Development Core Team:, R Foundation for Statistical Computing, Vienna, Austria
    • R Development Core Team: R: A language and environment for statistical computing., R Foundation for Statistical Computing, Vienna, Austria 2008.
    • (2008) R: A language and environment for statistical computing
  • 22
    • 8344284323 scopus 로고    scopus 로고
    • A common open representation of mass spectrometry data and its application to proteomics research
    • Pedrioli, P. G., Eng, J. K., Hubley, R., Vogelzang, M. et al., A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol. 2004, 22, 1459-1466.
    • (2004) Nat. Biotechnol , vol.22 , pp. 1459-1466
    • Pedrioli, P.G.1    Eng, J.K.2    Hubley, R.3    Vogelzang, M.4
  • 23
    • 67651161991 scopus 로고    scopus 로고
    • Modeling and managing experimental data using FuGE
    • Jones, A. R., Lister, A. L., Hermida, L., Wilkinson, P. et al., Modeling and managing experimental data using FuGE. OMICS 2009, 13, 239-251.
    • (2009) OMICS , vol.13 , pp. 239-251
    • Jones, A.R.1    Lister, A.L.2    Hermida, L.3    Wilkinson, P.4
  • 24
    • 3142702204 scopus 로고    scopus 로고
    • matching proteins with tandem mass spectra
    • TANDEM
    • 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
  • 25
    • 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
  • 26
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • Eng, J. K., McCormack, A. L., Yates, J. R., An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 1994, 5, 976-989.
    • (1994) J. Am. Soc. Mass Spectrom , vol.5 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates, J.R.3
  • 28
    • 0031114483 scopus 로고    scopus 로고
    • GeneCards: Integrating information about genes, proteins and diseases
    • Rebhan, M., Chalifa-Caspi, V., Prilusky, J., Lancet, D., GeneCards: integrating information about genes, proteins and diseases. Trends Genet. 1997, 13, 163.
    • (1997) Trends Genet , vol.13 , pp. 163
    • Rebhan, M.1    Chalifa-Caspi, V.2    Prilusky, J.3    Lancet, D.4
  • 30
    • 0142213547 scopus 로고    scopus 로고
    • Comparison of PDQuest and Progenesis software packages in the analysis of two-dimensional electrophoresis gels
    • Rosengren, A. T., Salmi, J. M., Aittokallio, T., Westerholm, J. et al., Comparison of PDQuest and Progenesis software packages in the analysis of two-dimensional electrophoresis gels. Proteomics 2003, 3, 1936-1946.
    • (2003) Proteomics , vol.3 , pp. 1936-1946
    • Rosengren, A.T.1    Salmi, J.M.2    Aittokallio, T.3    Westerholm, J.4
  • 31
    • 19944432197 scopus 로고    scopus 로고
    • Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
    • Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B. et al., Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell Proteomics 2004, 3, 1154-1169.
    • (2004) Mol. Cell Proteomics , vol.3 , pp. 1154-1169
    • Ross, P.L.1    Huang, Y.N.2    Marchese, J.N.3    Williamson, B.4
  • 32
    • 0038333588 scopus 로고    scopus 로고
    • Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides
    • Gevaert, K., Goethals, M., Martens, L., Van Damme, J. et al., Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat. Biotechnol. 2003, 21, 566-569.
    • (2003) Nat. Biotechnol , vol.21 , pp. 566-569
    • Gevaert, K.1    Goethals, M.2    Martens, L.3    Van Damme, J.4
  • 35
    • 0037337310 scopus 로고    scopus 로고
    • A proteomics strategy to elucidate functional proteinprotein interactions applied to EGF signaling
    • Blagoev, B., Kratchmarova, I., Ong, S. E., Nielsen, M. et al., A proteomics strategy to elucidate functional proteinprotein interactions applied to EGF signaling. Nat. Biotechnol. 2003, 21, 315-318.
    • (2003) Nat. Biotechnol , vol.21 , pp. 315-318
    • Blagoev, B.1    Kratchmarova, I.2    Ong, S.E.3    Nielsen, M.4
  • 36
    • 33845329203 scopus 로고    scopus 로고
    • Functional and quantitative proteomics using SILAC
    • Mann, M., Functional and quantitative proteomics using SILAC. Nat. Rev. Mol. Cell Biol. 2006, 7, 952-958.
    • (2006) Nat. Rev. Mol. Cell Biol , vol.7 , pp. 952-958
    • Mann, M.1
  • 37
    • 0036583926 scopus 로고    scopus 로고
    • Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
    • Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B. et al., Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 2002, 1, 376-386.
    • (2002) Mol. Cell. Proteomics , vol.1 , pp. 376-386
    • Ong, S.E.1    Blagoev, B.2    Kratchmarova, I.3    Kristensen, D.B.4
  • 38
    • 63049091064 scopus 로고    scopus 로고
    • Integration of transcriptome and proteome data from human-pathogenic fungi by using a data warehouse
    • Albrecht, D., Kniemeyer, O., Brakhage, A. A., Berth, M., Guthke, R., Integration of transcriptome and proteome data from human-pathogenic fungi by using a data warehouse. J. Integ. Bioinform. 2007, 4, 52.
    • (2007) J. Integ. Bioinform , vol.4 , pp. 52
    • Albrecht, D.1    Kniemeyer, O.2    Brakhage, A.A.3    Berth, M.4    Guthke, R.5
  • 39
    • 0034213595 scopus 로고    scopus 로고
    • ProFound: An expert system for protein identification using mass spectrometric peptide mapping information
    • Zhang, W., Chait, B. T., ProFound: an expert system for protein identification using mass spectrometric peptide mapping information. Anal. Chem. 2000, 72, 2482-2489.
    • (2000) Anal. Chem , vol.72 , pp. 2482-2489
    • Zhang, W.1    Chait, B.T.2
  • 40
    • 12944269065 scopus 로고
    • Rapid identification of proteins by peptide-mass fingerprinting
    • Pappin, D. J., Hojrup, P., Bleasby, A. J., Rapid identification of proteins by peptide-mass fingerprinting. Curr. Biol. 1993, 3, 327-332.
    • (1993) Curr. Biol , vol.3 , pp. 327-332
    • Pappin, D.J.1    Hojrup, P.2    Bleasby, A.J.3
  • 41
    • 77949753443 scopus 로고    scopus 로고
    • Managing proteomics data: From generation and data warehousing to central data repository
    • Thiele, H., Glandorf, J., Hufnagel, P., Körting, G., Bl .uggel,M., Managing proteomics data: from generation and data warehousing to central data repository. J. Proteom. Bioinform. 2008, 1, 485-507.
    • (2008) J. Proteom. Bioinform , vol.1 , pp. 485-507
    • Thiele, H.1    Glandorf, J.2    Hufnagel, P.3    Körting, G.4    Bl5    uggel, M.6
  • 42
    • 77949689704 scopus 로고    scopus 로고
    • Managing Proteomics Data: From Data Generation and Data Warehousing to Central Data Repository and Journal Reviewing (poster)
    • Amsterdam, The Netherlands
    • Thiele, H., Hufnagel, P., Glandorf, J., Körting, G. et al., Managing Proteomics Data: From Data Generation and Data Warehousing to Central Data Repository and Journal Reviewing (poster) (2008). HUPO World Congress 2008, Amsterdam, The Netherlands.
    • (2008) HUPO World Congress
    • Thiele, H.1    Hufnagel, P.2    Glandorf, J.3    Körting, G.4
  • 43
    • 33749248174 scopus 로고    scopus 로고
    • HUPO Brain Proteome Project: Summary of the pilot phase and introduction of a comprehensive data reprocessing strategy
    • Hamacher, M., Apweiler, R., Arnold, G., Becker, A. et al., HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy. Proteomics 2006, 6, 4890-4898.
    • (2006) Proteomics , vol.6 , pp. 4890-4898
    • Hamacher, M.1    Apweiler, R.2    Arnold, G.3    Becker, A.4
  • 44
    • 33749240944 scopus 로고    scopus 로고
    • Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase
    • Stephan, C., Reidegeld, K. A., Hamacher, M., van Hall, A. et al., Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase. Proteomics 2006, 6, 5015-5029.
    • (2006) Proteomics , vol.6 , pp. 5015-5029
    • Stephan, C.1    Reidegeld, K.A.2    Hamacher, M.3    van Hall, A.4
  • 45
    • 67049100049 scopus 로고    scopus 로고
    • an extensible multiuser platform for management and analysis of proteomics data
    • The proteios software environment
    • Hakkinen, J., Vincic, G., Mansson, O., Warell, K., Levander, F., The proteios software environment: an extensible multiuser platform for management and analysis of proteomics data. J. Proteome. Res. 2009, 8, 3037-3043.
    • (2009) J. Proteome. Res , vol.8 , pp. 3037-3043
    • Hakkinen, J.1    Vincic, G.2    Mansson, O.3    Warell, K.4    Levander, F.5
  • 46
    • 18744366090 scopus 로고    scopus 로고
    • an open source proteomics initiative
    • PROTEIOS
    • Garden, P., Alm, R., Hakkinen, J., PROTEIOS: an open source proteomics initiative. Bioinformatics 2005, 21, 2085-2087.
    • (2005) Bioinformatics , vol.21 , pp. 2085-2087
    • Garden, P.1    Alm, R.2    Hakkinen, J.3
  • 47
    • 39049179322 scopus 로고    scopus 로고
    • Proteomic data exchange and storage: Using Proteios
    • Garden, P., Alm, R., Proteomic data exchange and storage: using Proteios. Methods Mol. Biol. 2007, 367, 241-259.
    • (2007) Methods Mol. Biol , vol.367 , pp. 241-259
    • Garden, P.1    Alm, R.2
  • 48
    • 33947434519 scopus 로고    scopus 로고
    • Automated reporting from gel-based proteomics experiments using the open source Proteios database application
    • Levander, F., Krogh, M., Warell, K., Garden, P. et al., Automated reporting from gel-based proteomics experiments using the open source Proteios database application. Proteomics 2007, 7, 668-674.
    • (2007) Proteomics , vol.7 , pp. 668-674
    • Levander, F.1    Krogh, M.2    Warell, K.3    Garden, P.4
  • 49
    • 41549089987 scopus 로고    scopus 로고
    • An easy-to-use Decoy Database Builder software tool, implementing different decoy strategies for false discovery rate calculation in automated MS/MS protein identifications
    • Reidegeld, K. A., Eisenacher, M., Kohl, M., Chamrad, D. et al., An easy-to-use Decoy Database Builder software tool, implementing different decoy strategies for false discovery rate calculation in automated MS/MS protein identifications. Proteomics 2008, 8, 1129-1137.
    • (2008) Proteomics , vol.8 , pp. 1129-1137
    • Reidegeld, K.A.1    Eisenacher, M.2    Kohl, M.3    Chamrad, D.4
  • 50
    • 0037253267 scopus 로고    scopus 로고
    • A novel experimental design for comparative two-dimensional gel analysis: Two-dimensional difference gel electrophoresis incorporating a pooled internal standard
    • Alban, A., David, S. O., Bjorkesten, L., Andersson, C. et al., A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 2003, 3, 36-44.
    • (2003) Proteomics , vol.3 , pp. 36-44
    • Alban, A.1    David, S.O.2    Bjorkesten, L.3    Andersson, C.4
  • 51
    • 33746704351 scopus 로고    scopus 로고
    • database software supporting genomic expression analyses for systems biology
    • SBEAMS-Microarray
    • Marzolf, B., Deutsch, E. W., Moss, P., Campbell, D. et al., SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. Biomed. Chromatogr. Bioinform. 2006, 7, 286.
    • (2006) Biomed. Chromatogr. Bioinform , vol.7 , pp. 286
    • Marzolf, B.1    Deutsch, E.W.2    Moss, P.3    Campbell, D.4
  • 52
    • 77949680016 scopus 로고    scopus 로고
    • Clark, W, Ed, Europa Science Ltd, Cambridge, UK
    • Clark, W. (Ed.), The Laboratory Informatics Guide 2009, Europa Science Ltd., Cambridge, UK 2009.
    • (2009) The Laboratory Informatics Guide 2009


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.