메뉴 건너뛰기




Volumn 11, Issue 6, 2011, Pages 1114-1124

Generic workflow for quality assessment of quantitative label-free LC-MS analysis

Author keywords

Bioinformatics; Label free quantification; LC MS; Quality control

Indexed keywords

ARTICLE; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; HUMAN; HUMAN CELL; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PRIORITY JOURNAL; QUALITY CONTROL; QUANTITATIVE ANALYSIS; RELIABILITY; WORKFLOW;

EID: 79952304665     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201000493     Document Type: Article
Times cited : (28)

References (25)
  • 1
    • 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
  • 2
    • 34250657012 scopus 로고    scopus 로고
    • Quantitative proteome analysis using isotope-coded affinity tags and mass spectrometry
    • Shiio, Y., Aebersold, R., Quantitative proteome analysis using isotope-coded affinity tags and mass spectrometry. Nat. Protoc. 2006, 1, 139-145.
    • (2006) Nat. Protoc. , vol.1 , pp. 139-145
    • Shiio, Y.1    Aebersold, R.2
  • 3
    • 12444345515 scopus 로고    scopus 로고
    • Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by ms/ms
    • Thompson, A., Schafer, J., Kuhn, K., Kienle, S. et al., Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by ms/ms. Anal. Chem. 2003, 75, 1895-1904.
    • (2003) Anal. Chem. , vol.75 , pp. 1895-1904
    • Thompson, A.1    Schafer, J.2    Kuhn, K.3    Kienle, S.4
  • 4
    • 19944432197 scopus 로고    scopus 로고
    • Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
    • Ross, P. L., Huang, Y. L. 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.L.N.2    Marchese, J.N.3    Williamson, B.4
  • 5
    • 42049094894 scopus 로고    scopus 로고
    • Computational methods for the comparative quantification of proteins in label-free LCn-MS experiments
    • Wong, J. W. H., Sullivan, M. J., Cagney, G., Computational methods for the comparative quantification of proteins in label-free LCn-MS experiments. Brief. Bioinform. 2008, 9, 156-165.
    • (2008) Brief. Bioinform. , vol.9 , pp. 156-165
    • Wong, J.W.H.1    Sullivan, M.J.2    Cagney, G.3
  • 6
    • 27644543078 scopus 로고    scopus 로고
    • Comparison of label-free methods for quantifying human proteins by shotgun proteomics
    • Old, W. M., Meyer-Arendt, K., Aveline-Wolf, L., Pierce, K. G. et al., Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol. Cell. Proteomics 2005, 4 1487-1502.
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 1487-1502
    • Old, W.M.1    Meyer-Arendt, K.2    Aveline-Wolf, L.3    Pierce, K.G.4
  • 8
    • 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 2005, 4, 419-434.
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 419-434
    • Listgarten, J.1    Emili, A.2
  • 9
    • 67349208911 scopus 로고    scopus 로고
    • Bioinformatics analysis of mass spectrometry-based proteomics data sets
    • Kumar, C., Mann, M., Bioinformatics analysis of mass spectrometry-based proteomics data sets. FEBS Lett. 2009, 583, 1703-1712.
    • (2009) FEBS Lett. , vol.583 , pp. 1703-1712
    • Kumar, C.1    Mann, M.2
  • 10
    • 62549154087 scopus 로고    scopus 로고
    • Retention time alignment algorithms for LC/MS data must consider non-linear shifts
    • Podwojski, K., Fritsch, A., Chamrad, D. C., Paul, W. et al., Retention time alignment algorithms for LC/MS data must consider non-linear shifts. Bioinformatics 2009, 25, 758-764.
    • (2009) Bioinformatics , vol.25 , pp. 758-764
    • Podwojski, K.1    Fritsch, A.2    Chamrad, D.C.3    Paul, W.4
  • 11
    • 71049194213 scopus 로고    scopus 로고
    • Development and evaluation of normalization methods for label-free relative quantification of endogenous peptides
    • Kultima, K., Nilsson, A., Scholz, B., Rossbach, U. L. et al., Development and evaluation of normalization methods for label-free relative quantification of endogenous peptides. Mol. Cell. Proteomics 2009, 8, 2285-2295.
    • (2009) Mol. Cell. Proteomics , vol.8 , pp. 2285-2295
    • Kultima, K.1    Nilsson, A.2    Scholz, B.3    Rossbach, U.L.4
  • 12
    • 38649095599 scopus 로고    scopus 로고
    • An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data
    • Mueller, L. N., Brusniak, M. Y., Mani, D. R., Aebersold, R., An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J. Proteome Res. 2008, 7, 51-61.
    • (2008) J. Proteome Res. , vol.7 , pp. 51-61
    • Mueller, L.N.1    Brusniak, M.Y.2    Mani, D.R.3    Aebersold, R.4
  • 13
    • 54349106196 scopus 로고    scopus 로고
    • Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements
    • Lange, E., Tautenhahn, R., Neumann, S., Groepl, C., Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements. BMC Bioinformatics 2008, 9, 375.
    • (2008) BMC Bioinformatics , vol.9 , pp. 375
    • Lange, E.1    Tautenhahn, R.2    Neumann, S.3    Groepl, C.4
  • 14
    • 70349617072 scopus 로고    scopus 로고
    • Comparative analysis to guide quality improvements in proteomics
    • Mann, M., Comparative analysis to guide quality improvements in proteomics. Nat. Methods 2009, 6, 717-719.
    • (2009) Nat. Methods , vol.6 , pp. 717-719
    • Mann, M.1
  • 15
    • 67049100049 scopus 로고    scopus 로고
    • The Proteios software environment: an extensible multiuser platform for management and analysis of proteomics data
    • Häkkinen, J., Vincic, G., Månsson, O., Wårell, 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
    • Häkkinen, J.1    Vincic, G.2    Månsson, O.3    Wårell, K.4    Levander, F.5
  • 16
    • 29244448703 scopus 로고    scopus 로고
    • Parts per million mass accuracy on an orbitrap mass spectrometer via lock mass injection into a c-trap
    • Olsen, J. V., de Godoy, L. M. F., Li, G. Q., Macek, B. et al., Parts per million mass accuracy on an orbitrap mass spectrometer via lock mass injection into a c-trap. Mol. Cell. Proteomics 2005, 4, 2010-2021.
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 2010-2021
    • Olsen, J.V.1    de Godoy, L.M.F.2    Li, G.Q.3    Macek, B.4
  • 17
    • 54949129419 scopus 로고    scopus 로고
    • ProteoWizard: open source software for rapid proteomics tools development
    • Kessner, D., Chambers, M., Burke, R., Agusand, 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    Agusand, D.4    Mallick, P.5
  • 18
    • 42249108173 scopus 로고    scopus 로고
    • OpenMS - an open-source software framework for mass spectrometry
    • Sturm, M., Bertsch, A., Groepl, C., Hildebrandt, A. et al., OpenMS - an open-source software framework for mass spectrometry. BMC Bioinformatics 2008, 9, 1.
    • (2008) BMC Bioinformatics , vol.9 , pp. 1
    • Sturm, M.1    Bertsch, A.2    Groepl, C.3    Hildebrandt, A.4
  • 19
    • 79952286581 scopus 로고    scopus 로고
    • Nonlinear Dynamics, Progenesis LC-MS Tutorial for LC-MS version 2.5.
    • Nonlinear Dynamics, Progenesis LC-MS Tutorial for LC-MS version 2.5.
  • 20
    • 33747180294 scopus 로고    scopus 로고
    • A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS
    • Bellew, M., Coram, M., Fitzgibbon, M., Igra, M. et al., A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics 2006, 22, 1902-1909.
    • (2006) Bioinformatics , vol.22 , pp. 1902-1909
    • Bellew, M.1    Coram, M.2    Fitzgibbon, M.3    Igra, M.4
  • 21
    • 34547156610 scopus 로고    scopus 로고
    • A platform for accurate mass and time analyses of mass spectrometry data
    • May, D., Fitzgibbon, M., Liu, Y., Holzman, T. et al., A platform for accurate mass and time analyses of mass spectrometry data. J. Proteome Res. 2007, 6, 2685-2694.
    • (2007) J. Proteome Res. , vol.6 , pp. 2685-2694
    • May, D.1    Fitzgibbon, M.2    Liu, Y.3    Holzman, T.4
  • 22
    • 35348965139 scopus 로고    scopus 로고
    • SuperHirn - a novel tool for high-resolution LC-MS-based peptide/protein profiling
    • Mueller, L. N., Rinner, O., Schmidt, A., Letarte, S. et al., SuperHirn - a novel tool for high-resolution LC-MS-based peptide/protein profiling. Proteomics 2007, 7, 3470-3480.
    • (2007) Proteomics , vol.7 , pp. 3470-3480
    • Mueller, L.N.1    Rinner, O.2    Schmidt, A.3    Letarte, S.4
  • 23
    • 84949527882 scopus 로고    scopus 로고
    • Design and Analysis of Experiments.
    • Wiley, Hoboken, New Jersey USA.
    • Montgomery, D. C., Design and Analysis of Experiments, Wiley, Hoboken, New Jersey USA 2005.
    • (2005)
    • Montgomery, D.C.1
  • 25
    • 40549126588 scopus 로고    scopus 로고
    • Alignment of LC-MS images, with applications to biomarker discovery and protein identification
    • Vandenbogaert, M., Li-Thiao-Te, S., Kaltenbach, H. M., Zhang, R. X. et al., Alignment of LC-MS images, with applications to biomarker discovery and protein identification. Proteomics 2008, 8, 650-672.
    • (2008) Proteomics , vol.8 , pp. 650-672
    • Vandenbogaert, M.1    Li-Thiao-Te, S.2    Kaltenbach, H.M.3    Zhang, R.X.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.