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Volumn 4544 LNBI, Issue , 2007, Pages 71-88

A high-throughput bioinformatics platform for mass spectrometry -based proteomics

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; DIAGNOSIS; MASS SPECTROMETRY; PROTEINS; STATISTICAL METHODS;

EID: 34547421706     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-73255-6_9     Document Type: Conference Paper
Times cited : (1)

References (33)
  • 1
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold, R., Mann, M.: Mass spectrometry-based proteomics. Nature 422(6928), 198-207 (2003)
    • (2003) Nature , vol.422 , Issue.6928 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 2
    • 2542640024 scopus 로고    scopus 로고
    • Protein identification by mass spectrometry: Issues to be considered
    • Baldwin, M.A.: Protein identification by mass spectrometry: issues to be considered. Mol. Cell Proteomics 3(1), 1-9 (2004)
    • (2004) Mol. Cell Proteomics , vol.3 , Issue.1 , pp. 1-9
    • Baldwin, M.A.1
  • 3
    • 12344269924 scopus 로고    scopus 로고
    • GO::TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
    • Boyle, E.I., Weng, S., et al.: GO::TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 20(18), 3710-3715 (2004)
    • (2004) Bioinformatics , vol.20 , Issue.18 , pp. 3710-3715
    • Boyle, E.I.1    Weng, S.2
  • 4
    • 7044272787 scopus 로고    scopus 로고
    • Potential for false positive identifications from large databases through tandem mass spectrometry
    • Cargile, B.J., Bundy, J.L., et al.: Potential for false positive identifications from large databases through tandem mass spectrometry. J Proteome Res. 3(5), 1082-1085 (2004)
    • (2004) J Proteome Res , vol.3 , Issue.5 , pp. 1082-1085
    • Cargile, B.J.1    Bundy, J.L.2
  • 5
    • 0034852208 scopus 로고    scopus 로고
    • An introduction to quadrupole-time-of-flight mass spectrometry
    • Chernushevich, I., Loboda, A., et al.: An introduction to quadrupole-time-of-flight mass spectrometry. Journal of Mass Spectrometry 26, 859-865 (2001)
    • (2001) Journal of Mass Spectrometry , vol.26 , pp. 859-865
    • Chernushevich, I.1    Loboda, A.2
  • 6
    • 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 20(9), 1466-1467 (2004)
    • (2004) Bioinformatics , vol.20 , Issue.9 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 7
    • 0037442649 scopus 로고    scopus 로고
    • A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes
    • Fenyo, D., Beavis, R.C.: A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal. Chem. 75(4), 768-774 (2003)
    • (2003) Anal. Chem , vol.75 , Issue.4 , pp. 768-774
    • Fenyo, D.1    Beavis, R.C.2
  • 8
    • 0034582319 scopus 로고    scopus 로고
    • Automated Reduction and Interpretation of High Resolution Electrospray Mass Spectra of Large Molecules
    • Horn, D.M., Zubarev, R.A., et al.: Automated Reduction and Interpretation of High Resolution Electrospray Mass Spectra of Large Molecules. Journal of American Society for Mass Spectrometry 11, 320-322 (2000)
    • (2000) Journal of American Society for Mass Spectrometry , vol.11 , pp. 320-322
    • Horn, D.M.1    Zubarev, R.A.2
  • 9
    • 0344319833 scopus 로고    scopus 로고
    • Identifying biological themes within lists of genes with EASE
    • Hosack, D.A., Dennis, Jr., G., et al.: Identifying biological themes within lists of genes with EASE. Genome Biol, vol. 4(10) (2003)
    • (2003) Genome Biol , vol.4 , Issue.10
    • Hosack, D.A.1    Dennis Jr., G.2
  • 10
    • 4444321495 scopus 로고    scopus 로고
    • Analysis of the Low Molecular Weight Fraction of Serum by LC-Dual ESI-FT-ICR Mass Spectrometry: Precision of Retention Time, Mass, and Ion Abundance
    • Johnson, K.L., Mason, C.J., et al.: Analysis of the Low Molecular Weight Fraction of Serum by LC-Dual ESI-FT-ICR Mass Spectrometry: Precision of Retention Time, Mass, and Ion Abundance. Analytical Chemistry 76, 5097-5103 (2004)
    • (2004) Analytical Chemistry , vol.76 , pp. 5097-5103
    • Johnson, K.L.1    Mason, C.J.2
  • 11
    • 33746930864 scopus 로고    scopus 로고
    • analysis platform utilizing open XML file formats. Molecular Systems Biology
    • Keller, A., Eng, J., et al.: A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Molecular Systems Biology (2005)
    • (2005) A uniform proteomics MS/MS
    • Keller, A.1    Eng, J.2
  • 12
    • 3042818018 scopus 로고    scopus 로고
    • The International Protein Index: An integrated database for proteomics experiments
    • Kersey, P.J., Duarte, J., et al.: The International Protein Index: an integrated database for proteomics experiments. Proteomics 4(7), 1985-1988 (2004)
    • (2004) Proteomics , vol.4 , Issue.7 , pp. 1985-1988
    • Kersey, P.J.1    Duarte, J.2
  • 14
    • 20144365752 scopus 로고    scopus 로고
    • Experimental Peptide Identification Repository (EPIR): An integrated peptide-centric platform for validation and mining of tandem mass spectrometry data
    • Kristensen, D.B., Brand, J.C., et al.: Experimental Peptide Identification Repository (EPIR): an integrated peptide-centric platform for validation and mining of tandem mass spectrometry data. Mol. Cell Proteomics 3(10), 1023-1038 (2004)
    • (2004) Mol. Cell Proteomics , vol.3 , Issue.10 , pp. 1023-1038
    • Kristensen, D.B.1    Brand, J.C.2
  • 15
    • 0344737959 scopus 로고    scopus 로고
    • Automated Statistical Analysis of Protein Abundance Ratios from Data Generated by Stable-Isotope Dilution and Tandem Mass Spectrometry
    • Li, X.-J., Zhang, H., et al.: Automated Statistical Analysis of Protein Abundance Ratios from Data Generated by Stable-Isotope Dilution and Tandem Mass Spectrometry. Analytical Chemistry 75(23), 6648-6657 (2003)
    • (2003) Analytical Chemistry , vol.75 , Issue.23 , pp. 6648-6657
    • Li, X.-J.1    Zhang, H.2
  • 16
    • 0742269626 scopus 로고    scopus 로고
    • Probabilistic Disease Classification of Expression-Dependent Proteomic Data from Mass Spectrometry of Human Serum
    • Lilien, R., Farid, H., et al.: Probabilistic Disease Classification of Expression-Dependent Proteomic Data from Mass Spectrometry of Human Serum. Journal of Computational Biology 10(6), 925-946 (2003)
    • (2003) Journal of Computational Biology , vol.10 , Issue.6 , pp. 925-946
    • Lilien, R.1    Farid, H.2
  • 17
    • 17844394177 scopus 로고    scopus 로고
    • Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry
    • Listgarten, J., Emili, A.: Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol. Cell Proteomics 4(4), 419-434 (2005)
    • (2005) Mol. Cell Proteomics , vol.4 , Issue.4 , pp. 419-434
    • Listgarten, J.1    Emili, A.2
  • 18
    • 31444433469 scopus 로고    scopus 로고
    • Guest Editors' Introduction to the Special Section on Scientific Workflows
    • Ludascher, B., Goble, C.: Guest Editors' Introduction to the Special Section on Scientific Workflows. SIGMOD Rec. 34(3), 4-5 (2005)
    • (2005) SIGMOD Rec , vol.34 , Issue.3 , pp. 4-5
    • Ludascher, B.1    Goble, C.2
  • 19
    • 0346122950 scopus 로고    scopus 로고
    • A Correlation Algorithm for the Automated Quantitative Analysis of Shothun Proteomics
    • MacCoss, M.J., Wu, C.C., et al.: A Correlation Algorithm for the Automated Quantitative Analysis of Shothun Proteomics. Analytical Chemistry 75(24), 6912-6921 (2003)
    • (2003) Analytical Chemistry , vol.75 , Issue.24 , pp. 6912-6921
    • MacCoss, M.J.1    Wu, C.C.2
  • 20
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii, A.I., Keller, A., et al.: A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75(17), 4646-4658 (2003)
    • (2003) Anal. Chem , vol.75 , Issue.17 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2
  • 21
    • 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., et al.: A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol 22(11), 1459-1466 (2004)
    • (2004) Nat. Biotechnol , vol.22 , Issue.11 , pp. 1459-1466
    • Pedrioli, P.G.1    Eng, J.K.2
  • 22
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins, D.N., Pappin, D.J., et al.: Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20(18), 3551-3567 (1999)
    • (1999) Electrophoresis , vol.20 , Issue.18 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.2
  • 23
    • 0037116832 scopus 로고    scopus 로고
    • Use of proteomic patterns in serum to identify ovarian cancer
    • Petricoin, E., Ardekani, A., et al.: Use of proteomic patterns in serum to identify ovarian cancer. Lancet 7(9306), 572-577 (2002)
    • (2002) Lancet , vol.7 , Issue.9306 , pp. 572-577
    • Petricoin, E.1    Ardekani, A.2
  • 24
    • 58149208985 scopus 로고
    • Automated Assignment of Charge States from Resolved Isotopic Peaks for Multiply Charged Ions
    • Senko, M., Beu, S., et al.: Automated Assignment of Charge States from Resolved Isotopic Peaks for Multiply Charged Ions. Journal of American Society for Mass Spectrometry 6, 52-56 (1995)
    • (1995) Journal of American Society for Mass Spectrometry , vol.6 , pp. 52-56
    • Senko, M.1    Beu, S.2
  • 25
    • 31444456909 scopus 로고    scopus 로고
    • A Survey of Data Provenance in e-Science
    • Simmhan, Y., Piale, B., et al.: A Survey of Data Provenance in e-Science. SIGMOD Rec. 34(3), 31-36 (2005)
    • (2005) SIGMOD Rec , vol.34 , Issue.3 , pp. 31-36
    • Simmhan, Y.1    Piale, B.2
  • 27
    • 0025424768 scopus 로고
    • New Developments in Biochemical Mass Spectrometry: Electrospray Ionization
    • Smith, R., Loo, J., et al.: New Developments in Biochemical Mass Spectrometry: Electrospray Ionization. Analytical Chemistry 62, 882-899 (1990)
    • (1990) Analytical Chemistry , vol.62 , pp. 882-899
    • Smith, R.1    Loo, J.2
  • 28
    • 3042765151 scopus 로고    scopus 로고
    • Novel Linear Quadrupole Ion Trap/FT Mass Spectrometer: Performance Characterization and Use in the Comparative Analysis of Histone H3 Post-translational Modifications
    • Syka, J., Marto, J., et al.: Novel Linear Quadrupole Ion Trap/FT Mass Spectrometer: Performance Characterization and Use in the Comparative Analysis of Histone H3 Post-translational Modifications. Journal of Proteomics Research 3, 621-626 (2004)
    • (2004) Journal of Proteomics Research , vol.3 , pp. 621-626
    • Syka, J.1    Marto, J.2
  • 29
    • 0036393898 scopus 로고    scopus 로고
    • DTASelect and Contrast: Tools for assembling and comparing protein identifications from shotgun proteomics
    • Tabb, D.L., McDonald, W.H., et al.: DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J Proteome Res. 1(1), 21-26 (2002)
    • (2002) J Proteome Res , vol.1 , Issue.1 , pp. 21-26
    • Tabb, D.L.1    McDonald, W.H.2
  • 30
    • 0037337307 scopus 로고    scopus 로고
    • A systematic approach to modeling, capturing, and disseminating proteomics experimental data
    • Taylor, C.F., Paton, N.W., et al.: A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat. Biotech 21(3), 247-254 (2003)
    • (2003) Nat. Biotech , vol.21 , Issue.3 , pp. 247-254
    • Taylor, C.F.1    Paton, N.W.2
  • 31
    • 7044241344 scopus 로고    scopus 로고
    • DBParser: Web-based software for shotgun proteomic data analyses
    • Yang, X., Dondeti, V., et al.: DBParser: web-based software for shotgun proteomic data analyses. J Proteome Res. 3(5), 1002-1008 (2004)
    • (2004) J Proteome Res , vol.3 , Issue.5 , pp. 1002-1008
    • Yang, X.1    Dondeti, V.2
  • 32
    • 0038175144 scopus 로고    scopus 로고
    • GoMiner: A resource for biological interpretation of genomic and proteomic data
    • Zeeberg, B.R., Feng, W., et al.: GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol, vol. 4(4) (2003)
    • (2003) Genome Biol , vol.4 , Issue.4
    • Zeeberg, B.R.1    Feng, W.2
  • 33
    • 0032010153 scopus 로고    scopus 로고
    • A Universal Algorithm for Fast and Automated Charge State Deconvolution of Electrospray Mass-to-Charge Ratio Spectra
    • Zhang, Z., Marshall, A.: A Universal Algorithm for Fast and Automated Charge State Deconvolution of Electrospray Mass-to-Charge Ratio Spectra. Journal of American Society for Mass Spectrometry 9, 320-332 (1998)
    • (1998) Journal of American Society for Mass Spectrometry , vol.9 , pp. 320-332
    • Zhang, Z.1    Marshall, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.