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Volumn 16, Issue 1, 2015, Pages

Metabolome searcher: A high throughput tool for metabolite identification and metabolic pathway mapping directly from mass spectrometry and using genome restriction

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULES; DATA VISUALIZATION; DATABASE SYSTEMS; DRUG PRODUCTS; GENES; HTML; HYPERTEXT SYSTEMS; MASS SPECTROMETRY; METABOLITES; QUERY PROCESSING; VISUALIZATION; WEBSITES;

EID: 84924165442     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-015-0462-y     Document Type: Article
Times cited : (24)

References (44)
  • 1
    • 84886206077 scopus 로고
    • Lactic fermentation of dairy foods and their biological significance
    • Kilara A, Shahani KM. Lactic fermentation of dairy foods and their biological significance. J Dairy Sci. 1978;61:1793-800.
    • (1978) J Dairy Sci , vol.61 , pp. 1793-1800
    • Kilara, A.1    Shahani, K.M.2
  • 2
    • 33947295962 scopus 로고
    • Microbially induced flavours and fermented food flavour in fermented dairy products
    • Sandine WE, Elliker PR. Microbially induced flavours and fermented food flavour in fermented dairy products. J Agr Food Chem. 1970;18:557-62.
    • (1970) J Agr Food Chem , vol.18 , pp. 557-562
    • Sandine, W.E.1    Elliker, P.R.2
  • 3
    • 0032475934 scopus 로고    scopus 로고
    • An investigation of the metabolism of valine to isobutyl alcohol in Saccharomyces cerevisiae
    • Dickinson JR, Harrison SJ, Hewlins MJE. An investigation of the metabolism of valine to isobutyl alcohol in Saccharomyces cerevisiae. J Biol Chem. 1998;273(40):25751-6.
    • (1998) J Biol Chem , vol.273 , Issue.40 , pp. 25751-25756
    • Dickinson, J.R.1    Harrison, S.J.2    Hewlins, M.J.E.3
  • 4
    • 0030613543 scopus 로고    scopus 로고
    • A 13C nuclear magnetic resonance investigation of the metabolism of leucine to isoamyl alcohol in Saccharomyces cerevisiae
    • Dickinson JR, Lanterman MM, Danner DJ, Pearson BM, Sanz P, Harrison SJ, et al. A 13C nuclear magnetic resonance investigation of the metabolism of leucine to isoamyl alcohol in Saccharomyces cerevisiae. J Biol Chem. 1997;272(43):26871-8.
    • (1997) J Biol Chem , vol.272 , Issue.43 , pp. 26871-26878
    • Dickinson, J.R.1    Lanterman, M.M.2    Danner, D.J.3    Pearson, B.M.4    Sanz, P.5    Harrison, S.J.6
  • 6
    • 42149167253 scopus 로고    scopus 로고
    • Integrating biological processes to facilitate the generation of 'Biofuel'
    • Singh OV, Harvey SP. Integrating biological processes to facilitate the generation of 'Biofuel'. J Ind Microbiol Biotechnol. 2008;35(5):291-2.
    • (2008) J Ind Microbiol Biotechnol , vol.35 , Issue.5 , pp. 291-292
    • Singh, O.V.1    Harvey, S.P.2
  • 7
    • 40949099059 scopus 로고    scopus 로고
    • Technological options for biological fuel ethanol
    • Vertes AA, Inui M, Yukawa H. Technological options for biological fuel ethanol. J Mol Microbiol Biotechnol. 2008;15(1):16-30.
    • (2008) J Mol Microbiol Biotechnol , vol.15 , Issue.1 , pp. 16-30
    • Vertes, A.A.1    Inui, M.2    Yukawa, H.3
  • 8
    • 35448987277 scopus 로고    scopus 로고
    • Dietary supplements and health: the research agenda
    • Coates PM. Dietary supplements and health: the research agenda. Novartis Found Symp. 2007;282:202-7. discussion 207-218.
    • (2007) Novartis Found Symp , vol.282 , pp. 202-207
    • Coates, P.M.1
  • 9
    • 33750624074 scopus 로고    scopus 로고
    • Metallo-beta-lactamases: novel weaponry for antibiotic resistance in bacteria
    • Crowder MW, Spencer J, Vila AJ. Metallo-beta-lactamases: novel weaponry for antibiotic resistance in bacteria. Acc Chem Res. 2006;39(10):721-8.
    • (2006) Acc Chem Res , vol.39 , Issue.10 , pp. 721-728
    • Crowder, M.W.1    Spencer, J.2    Vila, A.J.3
  • 10
    • 33749064352 scopus 로고    scopus 로고
    • Novel ways of preventing antibiotic-resistant infections: what might the future hold?
    • Roghmann MC, McGrail L. Novel ways of preventing antibiotic-resistant infections: what might the future hold? Am J Infect Control. 2006;34(8):469-75.
    • (2006) Am J Infect Control , vol.34 , Issue.8 , pp. 469-475
    • Roghmann, M.C.1    McGrail, L.2
  • 11
    • 33646818699 scopus 로고    scopus 로고
    • Antibiotic resistance in bacteria and its future for novel antibiotic development
    • Yoneyama H, Katsumata R. Antibiotic resistance in bacteria and its future for novel antibiotic development. Biosci Biotechnol Biochem. 2006;70(5):1060-75.
    • (2006) Biosci Biotechnol Biochem , vol.70 , Issue.5 , pp. 1060-1075
    • Yoneyama, H.1    Katsumata, R.2
  • 12
    • 29144490206 scopus 로고    scopus 로고
    • P-Ser-HPr-a link between carbon metabolism and the virulence of some pathogenic bacteria
    • Deutscher J, Herro R, Bourand A, Mijakovic I, Poncet S. P-Ser-HPr-a link between carbon metabolism and the virulence of some pathogenic bacteria. Biochim Biophys Acta. 2005;1754(1-2):118-25.
    • (2005) Biochim Biophys Acta , vol.1754 , Issue.1-2 , pp. 118-125
    • Deutscher, J.1    Herro, R.2    Bourand, A.3    Mijakovic, I.4    Poncet, S.5
  • 13
    • 0942276378 scopus 로고    scopus 로고
    • A pyrophosphatase regulating polyphosphate metabolism in acidocalcisomes is essential for Trypanosoma brucei virulence in mice
    • Lemercier G, Espiau B, Ruiz FA, Vieira M, Luo S, Baltz T, et al. A pyrophosphatase regulating polyphosphate metabolism in acidocalcisomes is essential for Trypanosoma brucei virulence in mice. J Biol Chem. 2004;279(5):3420-5.
    • (2004) J Biol Chem , vol.279 , Issue.5 , pp. 3420-3425
    • Lemercier, G.1    Espiau, B.2    Ruiz, F.A.3    Vieira, M.4    Luo, S.5    Baltz, T.6
  • 14
    • 66149122278 scopus 로고    scopus 로고
    • Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p
    • Moxley JF, Jewett MC, Antoniewicz MR, Villas-Boas SG, Alper H, Wheeler RT, et al. Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. Proc Natl Acad Sci U S A. 2009;106(16):6477-82.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , Issue.16 , pp. 6477-6482
    • Moxley, J.F.1    Jewett, M.C.2    Antoniewicz, M.R.3    Villas-Boas, S.G.4    Alper, H.5    Wheeler, R.T.6
  • 15
    • 0031831305 scopus 로고    scopus 로고
    • In search of higher energy: metabolism-dependent behaviour in bacteria
    • Taylor BL, Zhulin IB. In search of higher energy: metabolism-dependent behaviour in bacteria. Mol Microbiol. 1998;28(4):683-90.
    • (1998) Mol Microbiol , vol.28 , Issue.4 , pp. 683-690
    • Taylor, B.L.1    Zhulin, I.B.2
  • 16
    • 67749104100 scopus 로고    scopus 로고
    • Metabolites in safety testing: metabolite identification strategies in discovery and development
    • Nedderman AN. Metabolites in safety testing: metabolite identification strategies in discovery and development. Biopharm Drug Dispos. 2009;30(4):153-62.
    • (2009) Biopharm Drug Dispos , vol.30 , Issue.4 , pp. 153-162
    • Nedderman, A.N.1
  • 17
    • 0346494819 scopus 로고    scopus 로고
    • MetaCyc: a multiorganism database of metabolic pathways and enzymes
    • Database issue
    • Krieger CJ, Zhang P, Mueller LA, Wang A, Paley S, Arnaud M, et al. MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 2004;32(Database issue):D438-42.
    • (2004) Nucleic Acids Res , vol.32 , pp. D438-D442
    • Krieger, C.J.1    Zhang, P.2    Mueller, L.A.3    Wang, A.4    Paley, S.5    Arnaud, M.6
  • 18
    • 33745148973 scopus 로고    scopus 로고
    • C.: Identification of the catabolic pathway of leucine-to-2-methylbutyric acid by Lactococcus lactis
    • Ganesan B, Dobrowolski P, Weimer B. C.: Identification of the catabolic pathway of leucine-to-2-methylbutyric acid by Lactococcus lactis. Appl Environ Microbiol. 2006;72(6):4264-73.
    • (2006) Appl Environ Microbiol , vol.72 , Issue.6 , pp. 4264-4273
    • Ganesan, B.1    Dobrowolski, P.2    Weimer, B.3
  • 19
    • 0033984722 scopus 로고    scopus 로고
    • The metabolic network of Lactococcus lactis: distribution of 14 C-labelled substrates between catabolic and anabolic pathways
    • Novak L, Loubierre P. The metabolic network of Lactococcus lactis: distribution of 14 C-labelled substrates between catabolic and anabolic pathways. J Bacteriol. 2000;182(4):1136-43.
    • (2000) J Bacteriol , vol.182 , Issue.4 , pp. 1136-1143
    • Novak, L.1    Loubierre, P.2
  • 20
    • 67649834742 scopus 로고    scopus 로고
    • Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics
    • Brown M, Dunn WB, Dobson P, Patel Y, Winder CL, Francis-McIntyre S, et al. Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics. Analyst. 2009;134(7):1322-32.
    • (2009) Analyst , vol.134 , Issue.7 , pp. 1322-1332
    • Brown, M.1    Dunn, W.B.2    Dobson, P.3    Patel, Y.4    Winder, C.L.5    Francis-McIntyre, S.6
  • 22
    • 22244458870 scopus 로고    scopus 로고
    • Dihydrocaffeoyl polyamines (kukoamine and allies) in potato (Solanum tuberosum) tubers detected during metabolite profiling
    • Parr AJ, Mellon FA, Colquhoun IJ, Davies HV. Dihydrocaffeoyl polyamines (kukoamine and allies) in potato (Solanum tuberosum) tubers detected during metabolite profiling. J Agric Food Chem. 2005;53(13):5461-6.
    • (2005) J Agric Food Chem , vol.53 , Issue.13 , pp. 5461-5466
    • Parr, A.J.1    Mellon, F.A.2    Colquhoun, I.J.3    Davies, H.V.4
  • 23
    • 6444243156 scopus 로고    scopus 로고
    • Metabolomics: an emerging post-genomic tool for nutrition
    • Whitfield PD, German AJ, Noble PJ. Metabolomics: an emerging post-genomic tool for nutrition. Br J Nutr. 2004;92(4):549-55.
    • (2004) Br J Nutr , vol.92 , Issue.4 , pp. 549-555
    • Whitfield, P.D.1    German, A.J.2    Noble, P.J.3
  • 25
    • 80054699758 scopus 로고    scopus 로고
    • MetSign: a computational platform for high-resolution mass spectrometry-based metabolomics
    • Wei X, Sun W, Shi X, Koo I, Wang B, Zhang J, et al. MetSign: a computational platform for high-resolution mass spectrometry-based metabolomics. Anal Chem. 2011;83(20):7668-75.
    • (2011) Anal Chem , vol.83 , Issue.20 , pp. 7668-7675
    • Wei, X.1    Sun, W.2    Shi, X.3    Koo, I.4    Wang, B.5    Zhang, J.6
  • 26
    • 77954772536 scopus 로고    scopus 로고
    • MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
    • Pluskal T, Castillo S, Villar-Briones A, Oresic M. MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics. 2010;11(1):395.
    • (2010) BMC Bioinformatics , vol.11 , Issue.1 , pp. 395
    • Pluskal, T.1    Castillo, S.2    Villar-Briones, A.3    Oresic, M.4
  • 27
    • 84860009126 scopus 로고    scopus 로고
    • LC-MS Data Processing with MAVEN: A Metabolomic Analysis and Visualization Engine
    • Clasquin MF, Melamud E, Rabinowitz JD. LC-MS Data Processing with MAVEN: A Metabolomic Analysis and Visualization Engine. Curr Protoc Bioinformatics. 2012;37:14.11.11- 23.
    • (2012) Curr Protoc Bioinformatics , vol.37 , pp. 141111-141123
    • Clasquin, M.F.1    Melamud, E.2    Rabinowitz, J.D.3
  • 28
    • 50049096775 scopus 로고    scopus 로고
    • XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization
    • Benton HP, Wong DM, Trauger SA, Siuzdak G. XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization. Anal Chem. 2008;80(16):6382-9.
    • (2008) Anal Chem , vol.80 , Issue.16 , pp. 6382-6389
    • Benton, H.P.1    Wong, D.M.2    Trauger, S.A.3    Siuzdak, G.4
  • 31
    • 84903699923 scopus 로고    scopus 로고
    • An R package to analyse LC/MS metabolomic data: MAIT (Metabolite Automatic Identification Toolkit)
    • Fernández-Albert F, Llorach R, Andrés-Lacueva C, Perera A. An R package to analyse LC/MS metabolomic data: MAIT (Metabolite Automatic Identification Toolkit). Bioinformatics. 2014;30(13):1937-9.
    • (2014) Bioinformatics , vol.30 , Issue.13 , pp. 1937-1939
    • Fernández-Albert, F.1    Llorach, R.2    Andrés-Lacueva, C.3    Perera, A.4
  • 33
    • 84861915827 scopus 로고    scopus 로고
    • XCMS Online: a web-based platform to process untargeted metabolomic data
    • Tautenhahn R, Patti GJ, Rinehart D, Siuzdak G. XCMS Online: a web-based platform to process untargeted metabolomic data. Anal Chem. 2012;84(11):5035-9.
    • (2012) Anal Chem , vol.84 , Issue.11 , pp. 5035-5039
    • Tautenhahn, R.1    Patti, G.J.2    Rinehart, D.3    Siuzdak, G.4
  • 34
    • 68949163674 scopus 로고    scopus 로고
    • Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour 'rules'
    • Draper J, Enot DP, Parker D, Beckmann M, Snowdon S, Lin W, et al. Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour 'rules'. BMC Bioinformatics. 2009;10:227.
    • (2009) BMC Bioinformatics , vol.10 , pp. 227
    • Draper, J.1    Enot, D.P.2    Parker, D.3    Beckmann, M.4    Snowdon, S.5    Lin, W.6
  • 37
    • 33645506527 scopus 로고    scopus 로고
    • Matrix effects on accurate mass measurements of low-molecular weight compounds using liquid chromatography-electrospray-quadrupole time-of-flight mass spectrometry
    • Calbiani F, Careri M, Elviri L, Mangia A, Zagnoni I. Matrix effects on accurate mass measurements of low-molecular weight compounds using liquid chromatography-electrospray-quadrupole time-of-flight mass spectrometry. J Mass Spectrom. 2006;41(3):289-94.
    • (2006) J Mass Spectrom , vol.41 , Issue.3 , pp. 289-294
    • Calbiani, F.1    Careri, M.2    Elviri, L.3    Mangia, A.4    Zagnoni, I.5
  • 38
    • 0036671264 scopus 로고    scopus 로고
    • Adduct formation in electrospray ionization. Part 1: common acidic pharmaceuticals
    • Kevin Schug HMM. Adduct formation in electrospray ionization. Part 1: common acidic pharmaceuticals. J Sep Sci. 2002;25(12):759-66.
    • (2002) J Sep Sci , vol.25 , Issue.12 , pp. 759-766
    • Kevin Schug, H.M.M.1
  • 39
    • 0037805576 scopus 로고    scopus 로고
    • The KEGG database
    • Kanehisa M. The KEGG database. Novartis Found Symp. 2002;247:91-101. discussion 101-103, 119-128, 244-152.
    • (2002) Novartis Found Symp , vol.247 , pp. 91-101
    • Kanehisa, M.1
  • 40
    • 25144438177 scopus 로고    scopus 로고
    • Accelerated throughput metabolic route screening in early drug discovery using high-resolution liquid chromatography/quadrupole time-of-flight mass spectrometry and automated data analysis
    • Mortishire-Smith RJ, O'Connor D, Castro-Perez JM, Kirby J. Accelerated throughput metabolic route screening in early drug discovery using high-resolution liquid chromatography/quadrupole time-of-flight mass spectrometry and automated data analysis. Rapid Commun Mass Spectrom. 2005;19(18):2659-70.
    • (2005) Rapid Commun Mass Spectrom , vol.19 , Issue.18 , pp. 2659-2670
    • Mortishire-Smith, R.J.1    O'Connor, D.2    Castro-Perez, J.M.3    Kirby, J.4
  • 41
    • 27844568286 scopus 로고    scopus 로고
    • Mass spectrometric studies on brain metabolism, using stable isotopes
    • Ando S, Tanaka Y. Mass spectrometric studies on brain metabolism, using stable isotopes. Mass Spectrom Rev. 2005;24(6):865-86.
    • (2005) Mass Spectrom Rev , vol.24 , Issue.6 , pp. 865-886
    • Ando, S.1    Tanaka, Y.2
  • 43
    • 33747154732 scopus 로고    scopus 로고
    • In vivo 15N-enrichment of metabolites in suspension cultured cells and its application to metabolomics
    • Harada K, Fukusaki E, Bamba T, Sato F, Kobayashi A. In vivo 15N-enrichment of metabolites in suspension cultured cells and its application to metabolomics. Biotechnol Prog. 2006;22(4):1003-11.
    • (2006) Biotechnol Prog , vol.22 , Issue.4 , pp. 1003-1011
    • Harada, K.1    Fukusaki, E.2    Bamba, T.3    Sato, F.4    Kobayashi, A.5
  • 44
    • 15044341146 scopus 로고    scopus 로고
    • NMR analysis of plant nitrogen metabolism
    • Mesnard F, Ratcliffe RG. NMR analysis of plant nitrogen metabolism. Photosynth Res. 2005;83(2):163-80.
    • (2005) Photosynth Res , vol.83 , Issue.2 , pp. 163-180
    • Mesnard, F.1    Ratcliffe, R.G.2


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