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Volumn 2, Issue FEB, 2015, Pages

A data preprocessing strategy for metabolomics to reduce the mask effect in data analysis

Author keywords

Biomarkers; Data preprocessing; Differential metabolites; Metabolomics; Pattern recognition

Indexed keywords


EID: 84995547307     PISSN: None     EISSN: 2296889X     Source Type: Journal    
DOI: 10.3389/fmolb.2015.00004     Document Type: Article
Times cited : (88)

References (38)
  • 1
    • 60149111699 scopus 로고    scopus 로고
    • Diagnostics: the prostate-cancer metabolome
    • Abate-Shen, C., and Shen, M. M. (2009). Diagnostics: the prostate-cancer metabolome. Nature 457, 799-800. doi: 10.1038/457799a
    • (2009) Nature , vol.457 , pp. 799-800
    • Abate-Shen, C.1    Shen, M.M.2
  • 2
    • 30744460897 scopus 로고    scopus 로고
    • Large-scale human metabolomics studies: a strategy for data (pre-) processing and validation
    • Bijlsma, S., Bobeldijk, I., Verheij, E. R., Ramaker, R., Kochhar, S., Macdonald, I. A., et al. (2006). Large-scale human metabolomics studies: a strategy for data (pre-) processing and validation. Anal. Chem. 78, 567-574. doi: 10.1021/ac051495j
    • (2006) Anal. Chem , vol.78 , pp. 567-574
    • Bijlsma, S.1    Bobeldijk, I.2    Verheij, E.R.3    Ramaker, R.4    Kochhar, S.5    Macdonald, I.A.6
  • 3
    • 0036913503 scopus 로고    scopus 로고
    • Rapid and noninvasive diagnosis of the presence and severity of coronary heart disease using 1H-NMR-based metabonomics
    • Brindle, J. T., Antti, H., Holmes, E., Tranter, G., Nicholson, J. K., Bethell, H. W., et al. (2002). Rapid and noninvasive diagnosis of the presence and severity of coronary heart disease using 1H-NMR-based metabonomics. Nat. Med. 8, 1439-1444. doi: 10.1038/nm1202-802
    • (2002) Nat. Med , vol.8 , pp. 1439-1444
    • Brindle, J.T.1    Antti, H.2    Holmes, E.3    Tranter, G.4    Nicholson, J.K.5    Bethell, H.W.6
  • 4
    • 33645663178 scopus 로고    scopus 로고
    • Scaling and normalization effects in NMR spectroscopic metabonomic data sets
    • Craig, A., Cloarec, O., Holmes, E., Nicholson, J. K., and Lindon, J. C. (2006). Scaling and normalization effects in NMR spectroscopic metabonomic data sets. Anal. Chem. 78, 2262-2267. doi: 10.1021/ac0519312
    • (2006) Anal. Chem , vol.78 , pp. 2262-2267
    • Craig, A.1    Cloarec, O.2    Holmes, E.3    Nicholson, J.K.4    Lindon, J.C.5
  • 5
    • 84912063200 scopus 로고    scopus 로고
    • Nontargeted modification-specific metabolomics study based on liquid chromatography-high-resolution mass spectrometry
    • Dai, W., Yin, P., Zeng, Z., Kong, H., Tong, H., Xu, Z., et al. (2014). Nontargeted modification-specific metabolomics study based on liquid chromatography-high-resolution mass spectrometry. Anal. Chem. 86, 9146-9153. doi: 10.1021/ac502045j
    • (2014) Anal. Chem , vol.86 , pp. 9146-9153
    • Dai, W.1    Yin, P.2    Zeng, Z.3    Kong, H.4    Tong, H.5    Xu, Z.6
  • 6
    • 40649109368 scopus 로고    scopus 로고
    • Preprocessing, classification modeling and feature selection using flow injection electrospray mass spectrometry metabolite fingerprint data
    • Enot, D. P., Lin, W., Beckmann, M., Parker, D., Overy, D. P., and Draper, J. (2008). Preprocessing, classification modeling and feature selection using flow injection electrospray mass spectrometry metabolite fingerprint data. Nat. Protoc. 3, 446-470. doi: 10.1038/nprot.2007.511
    • (2008) Nat. Protoc , vol.3 , pp. 446-470
    • Enot, D.P.1    Lin, W.2    Beckmann, M.3    Parker, D.4    Overy, D.P.5    Draper, J.6
  • 7
    • 0036007687 scopus 로고    scopus 로고
    • Metabolomics-the link between genotypes and phenotypes
    • Fiehn, O. (2002). Metabolomics-the link between genotypes and phenotypes. Plant Mol. Biol. 48, 155-171. doi: 10.1023/A:1013713905833
    • (2002) Plant Mol. Biol , vol.48 , pp. 155-171
    • Fiehn, O.1
  • 8
    • 84860380628 scopus 로고    scopus 로고
    • Missing values in mass spectrometry based metabolomics: an undervalued step in the data processing pipeline
    • Hrydziuszko, O., and Viant, M. R. (2012). Missing values in mass spectrometry based metabolomics: an undervalued step in the data processing pipeline. Metabolomics 8, S161-S174. doi: 10.1007/s11306-011-0366-4
    • (2012) Metabolomics , vol.8 , pp. S161-S174
    • Hrydziuszko, O.1    Viant, M.R.2
  • 9
    • 2942676743 scopus 로고    scopus 로고
    • Metabolomics and systems biology: making sense of the soup
    • Kell, D. B. (2004). Metabolomics and systems biology: making sense of the soup. Curr. Opin. Microbiol. 7, 296-307. doi: 10.1016/j.mib.2004.04.012
    • (2004) Curr. Opin. Microbiol , vol.7 , pp. 296-307
    • Kell, D.B.1
  • 10
    • 84895918390 scopus 로고    scopus 로고
    • Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery
    • Kell, D. B., and Goodacre, R. (2014). Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery. Drug Discov. Today 19, 171-182. doi: 10.1016/j.drudis.2013.07.014
    • (2014) Drug Discov. Today , vol.19 , pp. 171-182
    • Kell, D.B.1    Goodacre, R.2
  • 11
    • 28444480986 scopus 로고    scopus 로고
    • Metabonomic modeling of drug toxicity
    • Keun, H. C. (2006). Metabonomic modeling of drug toxicity. Pharmacol. Ther. 109, 92-106. doi: 10.1016/j.pharmthera.2005.06.008
    • (2006) Pharmacol. Ther , vol.109 , pp. 92-106
    • Keun, H.C.1
  • 12
    • 0142102568 scopus 로고    scopus 로고
    • Improved analysis of multivariate data by variable stability scaling: application to NMR-based metabolic profiling
    • Keun, H. C., Ebbels, T. M. D., Antti, H., Bollard, M. E., Beckonert, O., Holmes, E., et al. (2003). Improved analysis of multivariate data by variable stability scaling: application to NMR-based metabolic profiling. Anal. Chim. Acta 490, 265-276. doi: 10.1016/S0003-2670(03)00094-1
    • (2003) Anal. Chim. Acta , vol.490 , pp. 265-276
    • Keun, H.C.1    Ebbels, T.M.D.2    Antti, H.3    Bollard, M.E.4    Beckonert, O.5    Holmes, E.6
  • 13
    • 78649841522 scopus 로고    scopus 로고
    • Comparative evaluation of software for retention time alignment of gas chromatography/time-of-flight mass spectrometry-based metabonomic data
    • Koh, Y., Pasikanti, K. K., Yap, C. W., and Chan, E. C. (2010). Comparative evaluation of software for retention time alignment of gas chromatography/time-of-flight mass spectrometry-based metabonomic data. J. Chromatogr. A 1217, 8308-8316. doi: 10.1016/j.chroma.2010.10.101
    • (2010) J. Chromatogr. A , vol.1217 , pp. 8308-8316
    • Koh, Y.1    Pasikanti, K.K.2    Yap, C.W.3    Chan, E.C.4
  • 14
    • 84860359421 scopus 로고    scopus 로고
    • State-of-the art data normalization methods improve NMR-based metabolomic analysis
    • Kohl, S. M., Klein, M. S., Hochrein, J., Oefner, P. J., Spang, R., and Gronwald, W. (2012). State-of-the art data normalization methods improve NMR-based metabolomic analysis. Metabolomics 8, S146-S160. doi: 10.1007/s11306-011-0350-z
    • (2012) Metabolomics , vol.8 , pp. S146-S160
    • Kohl, S.M.1    Klein, M.S.2    Hochrein, J.3    Oefner, P.J.4    Spang, R.5    Gronwald, W.6
  • 15
    • 85039773015 scopus 로고    scopus 로고
    • Tryptophan catabolites as prognostic biomarkers for the severity of chronic liver diseases in potential transplant recipients
    • Lahdou, I. H., Oweira, M., Sadeghi, V., Daniel, G., Fusch, J. C., Schefold, G., et al. (2011). Tryptophan catabolites as prognostic biomarkers for the severity of chronic liver diseases in potential transplant recipients. Transplant Int. 24, 264-264
    • (2011) Transplant Int , vol.24 , pp. 264-264
    • Lahdou, I.H.1    Oweira, M.2    Sadeghi, V.3    Daniel, G.4    Fusch, J.C.5    Schefold, G.6
  • 16
    • 84877617762 scopus 로고    scopus 로고
    • Phytochemical composition of L. analyzed by an integrative GC-MS and LC-MS metabolomics platform
    • Mari, A., Lyon, D., Fragner, L., Montoro, P., Piacente, S., Wienkoop, S., et al. (2013). Phytochemical composition of L. analyzed by an integrative GC-MS and LC-MS metabolomics platform. Metabolomics 9, 599-607. doi: 10.1007/s11306-012-0473-x
    • (2013) Metabolomics , vol.9 , pp. 599-607
    • Mari, A.1    Lyon, D.2    Fragner, L.3    Montoro, P.4    Piacente, S.5    Wienkoop, S.6
  • 17
    • 0036463681 scopus 로고    scopus 로고
    • Metabonomics: a platform for studying drug toxicity and gene function
    • Nicholson, J. K., Connelly, J., Lindon, J. C., and Holmes, E. (2002). Metabonomics: a platform for studying drug toxicity and gene function. Nat. Rev. Drug Discov. 1, 153-161. doi: 10.1038/nrd728
    • (2002) Nat. Rev. Drug Discov , vol.1 , pp. 153-161
    • Nicholson, J.K.1    Connelly, J.2    Lindon, J.C.3    Holmes, E.4
  • 18
    • 12244269071 scopus 로고    scopus 로고
    • High-resolution NMR for metabomics
    • Pelczer, I. (2005). High-resolution NMR for metabomics. Curr. Opin. Drug Discov. Devel. 8, 127-133
    • (2005) Curr. Opin. Drug Discov. Devel , vol.8 , pp. 127-133
    • Pelczer, I.1
  • 19
    • 84910663296 scopus 로고    scopus 로고
    • Development of a GC/Quadrupole-Orbitrap mass spectrometer, part II: new approaches for discovery metabolomics
    • Peterson, A. C., Balloon, A. J., Westphall, M. S., and Coon, J. J. (2014). Development of a GC/Quadrupole-Orbitrap mass spectrometer, part II: new approaches for discovery metabolomics. Anal. Chem. 86, 10044-10051. doi: 10.1021/ac5014755
    • (2014) Anal. Chem , vol.86 , pp. 10044-10051
    • Peterson, A.C.1    Balloon, A.J.2    Westphall, M.S.3    Coon, J.J.4
  • 20
    • 84893302825 scopus 로고    scopus 로고
    • Human plasma stability during handling and storage: impact on NMR metabolomics
    • Pinto, J., Domingues, M. R., Galhano, E., Pita, C., Almeida Mdo, C., Carreira, I. M., et al. (2014). Human plasma stability during handling and storage: impact on NMR metabolomics. Analyst 139, 1168-1177. doi: 10.1039/c3an02188b
    • (2014) Analyst , vol.139 , pp. 1168-1177
    • Pinto, J.1    Domingues, M.R.2    Galhano, E.3    Pita, C.4    Almeida Mdo, C.5    Carreira, I.M.6
  • 21
    • 84905046901 scopus 로고    scopus 로고
    • The current state of drug discovery and a potential role for NMR metabolomics
    • Powers, R. (2014). The current state of drug discovery and a potential role for NMR metabolomics. J. Med. Chem. 57, 5860-5870. doi: 10.1021/jm401803b
    • (2014) J. Med. Chem , vol.57 , pp. 5860-5870
    • Powers, R.1
  • 23
    • 60149091657 scopus 로고    scopus 로고
    • Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression
    • Sreekumar, A., Poisson, L. M., Rajendiran, T. M., Khan, A. P., Cao, Q., Yu, J., et al. (2009). Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature 457, 910-914. doi: 10.1038/nature07762
    • (2009) Nature , vol.457 , pp. 910-914
    • Sreekumar, A.1    Poisson, L.M.2    Rajendiran, T.M.3    Khan, A.P.4    Cao, Q.5    Yu, J.6
  • 24
    • 34347384910 scopus 로고    scopus 로고
    • Normalization method for metabolomics data using optimal selection of multiple internal standards
    • Sysi-Aho, M., Katajamaa, M., Yetukuri, L., and Oresic, M. (2007). Normalization method for metabolomics data using optimal selection of multiple internal standards. BMC Bioinformatics 8:93. doi: 10.1186/1471-2105-8-93
    • (2007) BMC Bioinformatics , vol.8 , pp. 93
    • Sysi-Aho, M.1    Katajamaa, M.2    Yetukuri, L.3    Oresic, M.4
  • 25
    • 33847369007 scopus 로고    scopus 로고
    • Chemometrics in metabonomics
    • Trygg, J., Holmes, E., and Lundstedt, T. (2007). Chemometrics in metabonomics. J. Proteome Res. 6, 469-479. doi: 10.1021/pr060594q
    • (2007) J. Proteome Res , vol.6 , pp. 469-479
    • Trygg, J.1    Holmes, E.2    Lundstedt, T.3
  • 26
    • 33747019547 scopus 로고    scopus 로고
    • Centering, scaling, and transformations: improving the biological information content of metabolomics data
    • van den Berg, R. A., Hoefsloot, H. C. J., Westerhuis, J. A., Smilde, A. K., and van der Werf, M. J. (2006). Centering, scaling, and transformations: improving the biological information content of metabolomics data. BMC Genomics 7:142. doi: 10.1186/1471-2164-7-142
    • (2006) BMC Genomics , vol.7 , pp. 142
    • van den Berg, R.A.1    Hoefsloot, H.C.J.2    Westerhuis, J.A.3    Smilde, A.K.4    van der Werf, M.J.5
  • 27
    • 84896947291 scopus 로고    scopus 로고
    • The sensitivity of metabolomics versus classical regulatory toxicology from a NOAEL perspective
    • van Ravenzwaay, B., Montoya, G. A., Fabian, E., Herold, M., Krennrich, G., Looser, R., et al. (2014). The sensitivity of metabolomics versus classical regulatory toxicology from a NOAEL perspective. Toxicol. Lett. 227, 20-28. doi: 10.1016/j.toxlet.2014.03.004
    • (2014) Toxicol. Lett , vol.227 , pp. 20-28
    • van Ravenzwaay, B.1    Montoya, G.A.2    Fabian, E.3    Herold, M.4    Krennrich, G.5    Looser, R.6
  • 28
    • 79961006349 scopus 로고    scopus 로고
    • Optimized preprocessing of ultra-performance liquid chromatography/mass spectrometry urinary metabolic profiles for improved information recovery
    • Veselkov, K. A., Vingara, L. K., Masson, P., Robinette, S. L., Want, E., Li, J. V., et al. (2011). Optimized preprocessing of ultra-performance liquid chromatography/mass spectrometry urinary metabolic profiles for improved information recovery. Anal. Chem. 83, 5864-5872. doi: 10.1021/ac201065j
    • (2011) Anal. Chem , vol.83 , pp. 5864-5872
    • Veselkov, K.A.1    Vingara, L.K.2    Masson, P.3    Robinette, S.L.4    Want, E.5    Li, J.V.6
  • 29
    • 84912124552 scopus 로고    scopus 로고
    • Continuous water infusion enhances atmospheric pressure chemical ionization of methyl chloroformate derivatives in gas chromatography coupled to time-of-flight mass spectrometry-based metabolomics
    • Wachsmuth, C. J., Dettmer, K., Lang, S. A., Mycielska, M. E., and Oefner, P. J. (2014). Continuous water infusion enhances atmospheric pressure chemical ionization of methyl chloroformate derivatives in gas chromatography coupled to time-of-flight mass spectrometry-based metabolomics. Anal. Chem. 86, 9186-9195. doi: 10.1021/ac502133r
    • (2014) Anal. Chem , vol.86 , pp. 9186-9195
    • Wachsmuth, C.J.1    Dettmer, K.2    Lang, S.A.3    Mycielska, M.E.4    Oefner, P.J.5
  • 30
    • 84885531664 scopus 로고    scopus 로고
    • (1)H NMR-based metabolomics studies on the effect of sesamin in Atlantic salmon (Salmo salar)
    • Wagner, L., Trattner, S., Pickova, J., Gomez-Requeni, P., and Moazzami, A. A. (2014). (1)H NMR-based metabolomics studies on the effect of sesamin in Atlantic salmon (Salmo salar). Food Chem. 147, 98-105. doi: 10.1016/j.foodchem.2013.09.128
    • (2014) Food Chem , vol.147 , pp. 98-105
    • Wagner, L.1    Trattner, S.2    Pickova, J.3    Gomez-Requeni, P.4    Moazzami, A.A.5
  • 31
    • 23944437409 scopus 로고    scopus 로고
    • Biochemical characterization of rat intestine development using high-resolution magic-angle-spinning 1H NMR spectroscopy and multivariate data analysis
    • Wang, Y., Tang, H., Holmes, E., Lindon, J. C., Turini, M. E., Sprenger, N., et al. (2005). Biochemical characterization of rat intestine development using high-resolution magic-angle-spinning 1H NMR spectroscopy and multivariate data analysis. J. Proteome Res. 4, 1324-1329. doi: 10.1021/pr050032r
    • (2005) J. Proteome Res , vol.4 , pp. 1324-1329
    • Wang, Y.1    Tang, H.2    Holmes, E.3    Lindon, J.C.4    Turini, M.E.5    Sprenger, N.6
  • 32
    • 79953740072 scopus 로고    scopus 로고
    • Processing and analysis of GC/LC-MS-based metabolomics data
    • Want, E., and Masson, P. (2011). Processing and analysis of GC/LC-MS-based metabolomics data. Methods Mol. Biol. 708, 277-298. doi: 10.1007/978-1-61737-985-7_17
    • (2011) Methods Mol. Biol , vol.708 , pp. 277-298
    • Want, E.1    Masson, P.2
  • 33
    • 0032517819 scopus 로고    scopus 로고
    • Orthogonal signal correction of near-infrared spectra
    • Wold, S., Antti, H., Lindgren, F., and Ohman, J. (1998). Orthogonal signal correction of near-infrared spectra. Chemometr. Intell. Lab. Syst. 44, 175-185. doi: 10.1016/S0169-7439(98)00109-9
    • (1998) Chemometr. Intell. Lab. Syst , vol.44 , pp. 175-185
    • Wold, S.1    Antti, H.2    Lindgren, F.3    Ohman, J.4
  • 34
    • 84900837560 scopus 로고    scopus 로고
    • MVAPACK: a complete data handling package for NMR metabolomics
    • Worley, B., and Powers, R. (2014). MVAPACK: a complete data handling package for NMR metabolomics. ACS Chem. Biol. 9, 1138-1144. doi: 10.1021/cb4008937
    • (2014) ACS Chem. Biol , vol.9 , pp. 1138-1144
    • Worley, B.1    Powers, R.2
  • 35
    • 8844261879 scopus 로고    scopus 로고
    • Diagnosis of liver cancer using HPLC-based metabonomics avoiding false-positive result from hepatitis and hepatocirrhosis diseases
    • Yang, J., Xu, G., Zheng, Y., Kong, H., Pang, T., Lv, S., et al. (2004). Diagnosis of liver cancer using HPLC-based metabonomics avoiding false-positive result from hepatitis and hepatocirrhosis diseases. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 813, 59-65. doi: 10.1016/j.jchromb.2004.09.032
    • (2004) J. Chromatogr. B Analyt. Technol. Biomed. Life Sci , vol.813 , pp. 59-65
    • Yang, J.1    Xu, G.2    Zheng, Y.3    Kong, H.4    Pang, T.5    Lv, S.6
  • 36
    • 22044449913 scopus 로고    scopus 로고
    • Strategy for metabonomics research based on high-performance liquid chromatography and liquid chromatography coupled with tandem mass spectrometry
    • Yang, J., Xu, G., Zheng, Y., Kong, H., Wang, C., Zhao, X., et al. (2005). Strategy for metabonomics research based on high-performance liquid chromatography and liquid chromatography coupled with tandem mass spectrometry. J. Chromatogr. A 1084, 214-221. doi: 10.1016/j.chroma.2004.10.100
    • (2005) J. Chromatogr. A , vol.1084 , pp. 214-221
    • Yang, J.1    Xu, G.2    Zheng, Y.3    Kong, H.4    Wang, C.5    Zhao, X.6
  • 37
    • 33644835571 scopus 로고    scopus 로고
    • High performance liquid chromatography-mass spectrometry for metabonomics: potential biomarkers for acute deterioration of liver function in chronic hepatitis B
    • Yang, J., Zhao, X., Liu, X., Wang, C., Gao, P., Wang, J., et al. (2006). High performance liquid chromatography-mass spectrometry for metabonomics: potential biomarkers for acute deterioration of liver function in chronic hepatitis B. J. Proteome Res. 5, 554-561. doi: 10.1021/pr050364w
    • (2006) J. Proteome Res , vol.5 , pp. 554-561
    • Yang, J.1    Zhao, X.2    Liu, X.3    Wang, C.4    Gao, P.5    Wang, J.6
  • 38
    • 84893851963 scopus 로고    scopus 로고
    • Serum metabolomics study of polycystic ovary syndrome based on liquid chromatography-mass spectrometry
    • Zhao, X., Xu, F., Qi, B., Hao, S., Li, Y., Li, Y., et al. (2014). Serum metabolomics study of polycystic ovary syndrome based on liquid chromatography-mass spectrometry. J. Proteome Res. 13, 1101-1111. doi: 10.1021/pr401130w
    • (2014) J. Proteome Res , vol.13 , pp. 1101-1111
    • Zhao, X.1    Xu, F.2    Qi, B.3    Hao, S.4    Li, Y.5    Li, Y.6


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