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Volumn 1277, Issue , 2015, Pages 123-136

Preprocessing of raw metabonomic data

(1)  Vettukattil, Riyas a  

a NONE

Author keywords

Baseline correction; Binning; Denoising; Metabolomics; Metabonomics; Normalization; Peak alignment; Peak extraction; Preprocessing; Scaling; Smoothing

Indexed keywords

ANALYTIC METHOD; ARTICLE; BIOMICS; COMPUTER PROGRAM; DATA ANALYSIS; DATA PROCESSING; METABONOMICS; PRIORITY JOURNAL; ALGORITHM; METABOLOMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRINCIPAL COMPONENT ANALYSIS; PROCEDURES; STANDARD; STATISTICS;

EID: 84922883053     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-2377-9_10     Document Type: Article
Times cited : (18)

References (22)
  • 1
    • 1942470073 scopus 로고    scopus 로고
    • Metabolomics by numbers: Acquiring and understanding global metabolite data
    • Goodacre R, Vaidyanathan S, Dunn WB et al (2004) Metabolomics by numbers: acquiring and understanding global metabolite data. Trends Biotechnol 22: 245-252.
    • (2004) Trends Biotechnol , vol.22 , pp. 245-252
    • Goodacre, R.1    Vaidyanathan, S.2    Dunn, W.B.3
  • 2
    • 33645663178 scopus 로고    scopus 로고
    • Scaling and normalization effects in NMR spectroscopic metabonomic data sets
    • Craig A, Cloarec O, Holmes E et al (2006) Scaling and normalization effects in NMR spectroscopic metabonomic data sets. Anal Chem 78: 2262-2267.
    • (2006) Anal Chem , vol.78 , pp. 2262-2267
    • Craig, A.1    Cloarec, O.2    Holmes, E.3
  • 3
    • 34347405493 scopus 로고    scopus 로고
    • Data processing for mass spectrometry-based metabolomics
    • Katajamaa M, Oresic M (2007) Data processing for mass spectrometry-based metabolomics. J Chromatogr A 1158: 318-328.
    • (2007) J Chromatogr A , vol.1158 , pp. 318-328
    • Katajamaa, M.1    Oresic, M.2
  • 4
    • 79960144635 scopus 로고    scopus 로고
    • Algorithms and tools for the preprocessing of LC-MS metabolomics data
    • Castillo S, Gopalacharyulu P, Yetukuri L et al (2011) Algorithms and tools for the preprocessing of LC-MS metabolomics data. Chemometr Intell Lab Syst 108: 23-32.
    • (2011) Chemometr Intell Lab Syst , vol.108 , pp. 23-32
    • Castillo, S.1    Gopalacharyulu, P.2    Yetukuri, L.3
  • 5
    • 78649334547 scopus 로고    scopus 로고
    • Alignment of high resolution magic angle spinning magnetic resonance spectra using warping methods
    • Giskeodegard GF, Bloemberg TG, Postma G et al (2010) Alignment of high resolution magic angle spinning magnetic resonance spectra using warping methods. Anal Chim Acta 683: 1-11.
    • (2010) Anal Chim Acta , vol.683 , pp. 1-11
    • Giskeodegard, G.F.1    Bloemberg, T.G.2    Postma, G.3
  • 6
    • 51949100510 scopus 로고    scopus 로고
    • Robust algorithms for automated chemical shift calibration of 1D 1H NMR spectra of blood serum
    • Pearce JT, Athersuch TJ, Ebbels TM et al (2008) Robust algorithms for automated chemical shift calibration of 1D 1H NMR spectra of blood serum. Anal Chem 80: 7158-7162.
    • (2008) Anal Chem , vol.80 , pp. 7158-7162
    • Pearce, J.T.1    Athersuch, T.J.2    Ebbels, T.M.3
  • 7
    • 33845590667 scopus 로고    scopus 로고
    • Adaptive binning: An improved binning method for metabolomics data using the undecimated wavelet transform
    • Davis RA, Charlton AJ, Godward J et al (2007) Adaptive binning: an improved binning method for metabolomics data using the undecimated wavelet transform. Chemometr Intell Lab Syst 85: 144-154.
    • (2007) Chemometr Intell Lab Syst , vol.85 , pp. 144-154
    • Davis, R.A.1    Charlton, A.J.2    Godward, J.3
  • 8
    • 43949089850 scopus 로고    scopus 로고
    • NMR-based characterization of metabolic alterations in hypertension using an adaptive, intelligent binning algorithm
    • De Meyer T, Sinnaeve D, Van Gasse B et al (2008) NMR-based characterization of metabolic alterations in hypertension using an adaptive, intelligent binning algorithm. Anal Chem 80: 3783-3790.
    • (2008) Anal Chem , vol.80 , pp. 3783-3790
    • De Meyer, T.1    Sinnaeve, D.2    Van Gasse, B.3
  • 9
    • 33745728718 scopus 로고    scopus 로고
    • Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. Application in 1H NMR metabonomics
    • Dieterle F, Ross A, Schlotterbeck G et al (2006) Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. Application in 1H NMR metabonomics. Anal Chem 78: 4281-4290.
    • (2006) Anal Chem , vol.78 , pp. 4281-4290
    • Dieterle, F.1    Ross, A.2    Schlotterbeck, G.3
  • 10
    • 34748839546 scopus 로고    scopus 로고
    • Proposed minimum reporting standards for data analysis in metabolomics
    • Goodacre R, Broadhurst D, Smilde A et al (2007) Proposed minimum reporting standards for data analysis in metabolomics. Metabolomics 3: 231-241.
    • (2007) Metabolomics , vol.3 , pp. 231-241
    • Goodacre, R.1    Broadhurst, D.2    Smilde, A.3
  • 11
    • 33747019547 scopus 로고    scopus 로고
    • Centering, scaling, and transformations: Improving the biological information content of metabolomics data
    • van den Berg RA, Hoefsloot HC, Westerhuis JA et al (2006) Centering, scaling, and transformations: improving the biological information content of metabolomics data. BMC Genomics 7: 142.
    • (2006) BMC Genomics , vol.7
    • van den Berg, R.A.1    Hoefsloot, H.C.2    Westerhuis, J.A.3
  • 12
    • 72449164088 scopus 로고    scopus 로고
    • Icoshift: A versatile tool for the rapid alignment of 1D NMR spectra
    • Savorani F, Tomasi G, Engelsen SB (2010) icoshift: A versatile tool for the rapid alignment of 1D NMR spectra. J Magn Reson 202: 190-202.
    • (2010) J Magn Reson , vol.202 , pp. 190-202
    • Savorani, F.1    Tomasi, G.2    Engelsen, S.B.3
  • 13
    • 84857124407 scopus 로고    scopus 로고
    • Bioinformatics tools for mass spectroscopy-based metabolomic data processing and analysis
    • Sugimoto M, Kawakami M, Robert M et al (2012) Bioinformatics tools for mass spectroscopy-based metabolomic data processing and analysis. Curr Bioinformatics 7: 96-108.
    • (2012) Curr Bioinformatics , vol.7 , pp. 96-108
    • Sugimoto, M.1    Kawakami, M.2    Robert, M.3
  • 14
    • 84912525352 scopus 로고    scopus 로고
    • Databases and software for NMR-based metabolomics
    • Ellinger JJ, Chylla RA, Ulrich EL et al (2013) Databases and software for NMR-based metabolomics. Curr Metabolomics 1, doi: 10. 2174/2213235X11301010028.
    • (2013) Curr Metabolomics
    • Ellinger, J.J.1    Chylla, R.A.2    Ulrich, E.L.3
  • 15
    • 77950408373 scopus 로고    scopus 로고
    • CDK-Taverna: An open workflow environment for cheminformatics
    • Kuhn T, Willighagen EL, Zielesny A et al (2010) CDK-Taverna: an open workflow environment for cheminformatics. BMC Bioinformatics 11: 159.
    • (2010) BMC Bioinformatics , vol.11
    • Kuhn, T.1    Willighagen, E.L.2    Zielesny, A.3
  • 16
    • 68549083763 scopus 로고    scopus 로고
    • ChromA: Signalbased retention time alignment for chromatography-mass spectrometry data
    • Hoffmann N, Stoye J (2009) ChromA: signalbased retention time alignment for chromatography-mass spectrometry data. Bioinformatics 25: 2080-2081.
    • (2009) Bioinformatics , vol.25 , pp. 2080-2081
    • Hoffmann, N.1    Stoye, J.2
  • 17
    • 77956520033 scopus 로고    scopus 로고
    • Chromaligner: A web server for chromatogram alignment
    • Wang SY, Ho TJ, Kuo CH et al (2010) Chromaligner: a web server for chromatogram alignment. Bioinformatics 26: 2338-2339.
    • (2010) Bioinformatics , vol.26 , pp. 2338-2339
    • Wang, S.Y.1    Ho, T.J.2    Kuo, C.H.3
  • 18
    • 71749118213 scopus 로고    scopus 로고
    • A novel R-package graphic user interface for the analysis of metabonomic profiles
    • Izquierdo-Garcia JL, Rodriguez I, Kyriazis A et al (2009) A novel R-package graphic user interface for the analysis of metabonomic profiles. BMC Bioinformatics 10: 363.
    • (2009) BMC Bioinformatics , vol.10
    • Izquierdo-Garcia, J.L.1    Rodriguez, I.2    Kyriazis, A.3
  • 19
    • 65249132985 scopus 로고    scopus 로고
    • MetAlign: Interface-driven, versatile metabolomics tool for hyphenated full-scan mass spectrometry data preprocessing
    • Lommen A (2009) MetAlign: interface-driven, versatile metabolomics tool for hyphenated full-scan mass spectrometry data preprocessing. Anal Chem 81: 3079-3086.
    • (2009) Anal Chem , vol.81 , pp. 3079-3086
    • Lommen, A.1
  • 20
    • 79952124278 scopus 로고    scopus 로고
    • metaXCMS: Second-order analysis of untargeted metabolomics data
    • Tautenhahn R, Patti GJ, Kalisiak E et al (2011) metaXCMS: second-order analysis of untargeted metabolomics data. Anal Chem 83: 696-700.
    • (2011) Anal Chem , vol.83 , pp. 696-700
    • Tautenhahn, R.1    Patti, G.J.2    Kalisiak, E.3
  • 21
    • 32444446805 scopus 로고    scopus 로고
    • XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification
    • Smith CA, Want EJ, O'Maille G et al (2006) XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem 78: 779-787.
    • (2006) Anal Chem , vol.78 , pp. 779-787
    • Smith, C.A.1    Want, E.J.2    O'Maille, G.3
  • 22
    • 50049096775 scopus 로고    scopus 로고
    • XCMS2: Processing tandem mass spectrometry data for metabolite identification and structural characterization
    • Benton HP, Wong DM, Trauger SA et al (2008) XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization. Anal Chem 80: 6382-6389.
    • (2008) Anal Chem , vol.80 , pp. 6382-6389
    • Benton, H.P.1    Wong, D.M.2    Trauger, S.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.