메뉴 건너뛰기




Volumn 9, Issue 11, 2014, Pages

Allocator: An interactive web platform for the analysis of metabolomic LC-ESI-MS datasets, enabling semi-automated, user-revised compound annotation and mass isotopomer ratio analysis

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; CARBON 13; DIPEPTIDE; GLUTAMIC ACID;

EID: 84913580305     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0113909     Document Type: Article
Times cited : (26)

References (40)
  • 1
    • 0032168794 scopus 로고    scopus 로고
    • Systematic functional analysis of the yeast genome
    • Oliver SG, Winson MK, Kell DB, Baganz F (1998) Systematic functional analysis of the yeast genome. Trends Biotechnol. 16: 373-378. Available: http://www.ncbi.nlm.nih.gov/pubmed/9744112.
    • (1998) Trends Biotechnol. , vol.16 , pp. 373-378
    • Oliver, S.G.1    Winson, M.K.2    Kell, D.B.3    Baganz, F.4
  • 2
    • 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. Available: http://www.ncbi.nlm.nih.gov/pubmed/11860207.
    • (2002) Plant Mol Biol. , vol.48 , pp. 155-171
    • Fiehn, O.1
  • 4
    • 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, Abagyan R, Siuzdak G (2006) XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem. 78: 779-787. Available: http://www.ncbi.nlm.nih.gov/pubmed/16448051.
    • (2006) Anal Chem. , vol.78 , pp. 779-787
    • Smith, C.A.1    Want, E.J.2    O'Maille, G.3    Abagyan, R.4    Siuzdak, G.5
  • 5
    • 60649089559 scopus 로고    scopus 로고
    • Highly sensitive feature detection for high resolution LC/MS
    • Accessed 20 July 2011
    • Tautenhahn R, Bö ttcher C, Neumann S (2008) Highly sensitive feature detection for high resolution LC/MS. BMC Bioinformatics. 9: 504. Available: http://www.pubmedcentral.nih.gov/articlerender. fcgi?artid52639432&tool5pmcentrez&rendertype5abstract. Accessed 20 July 2011.
    • (2008) BMC Bioinformatics , vol.9 , pp. 504
    • Tautenhahn, R.1    Bö Ttcher, C.2    Neumann, S.3
  • 6
    • 84855402302 scopus 로고    scopus 로고
    • CAMERA: An integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets
    • Accessed 20 February 2012
    • Kuhl C, Tautenhahn R, Bö ttcher C, Larson T (2012) CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of Liquid Chromatography/Mass Spectrometry Data Sets. Anal Chem. 84: 283-289. Available: http://www.ncbi.nlm.nih.gov/pubmed/22111785. Accessed 20 February 2012.
    • (2012) Anal Chem. , vol.84 , pp. 283-289
    • Kuhl, C.1    Tautenhahn, R.2    Bö Ttcher, C.3    Larson, T.4
  • 7
    • 84861915827 scopus 로고    scopus 로고
    • XCMS Online: A web-based platform to process untargeted metabolomic data
    • Tautenhahn R, Patti GJ, Rinehart D, Siuzdak G (2012) XCMS Online: a web-based platform to process untargeted metabolomic data. Anal Chem. 84: 5035-5039. Available: http://www. pubmedcentral.nih.gov/articlerender.fcgi?artid53703953&tool5pmcentrez&rendertype5abstract.
    • (2012) Anal Chem. , vol.84 , pp. 5035-5039
    • Tautenhahn, R.1    Patti, G.J.2    Rinehart, D.3    Siuzdak, G.4
  • 8
    • 33644867564 scopus 로고    scopus 로고
    • MZmine: Toolbox for processing and visualization of mass spectrometry based molecular profile data
    • Accessed 13 November 2013
    • Katajamaa M, Miettinen J, Oresic M (2006) MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics. 22: 634-636. Available: http://www.ncbi.nlm. nih.gov/pubmed/16403790. Accessed 13 November 2013.
    • (2006) Bioinformatics. , vol.22 , pp. 634-636
    • Katajamaa, M.1    Miettinen, J.2    Oresic, M.3
  • 9
    • 77954772536 scopus 로고    scopus 로고
    • MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
    • Accessed 13 November 2013
    • Available: http://www.pubmedcentral.nih.gov/articlerender. fcgi?artid52918584&tool5pmcentrez&rendertype5abstract. Accessed 13 November 2013.
    • (2010) BMC Bioinformatics. , pp. 11
    • Pluskal, T.1    Castillo, S.2    Villar-Briones, A.3    Oresic, M.4
  • 10
    • 84903690538 scopus 로고    scopus 로고
    • MET-COFEA: A liquid chromatography/mass spectrometry data processing platform for metabolite compound feature extraction and annotation
    • Zhang W, Chang J, Lei Z, Huhman D, Sumner LW, et al. (2014) MET-COFEA: A Liquid Chromatography/Mass Spectrometry Data Processing Platform for Metabolite Compound Feature Extraction and Annotation. Anal Chem. 86: 6245-6253. Available: http://www.ncbi.nlm.nih.gov/pubmed/ 24856452.
    • (2014) Anal Chem. , vol.86 , pp. 6245-6253
    • Zhang, W.1    Chang, J.2    Lei, Z.3    Huhman, D.4    Sumner, L.W.5
  • 11
    • 1442326111 scopus 로고    scopus 로고
    • MIRACLE: Mass isotopomer ratio analysis of U-13C-labeled extracts. A new method for accurate quantification of changes in concentrations of intracellular metabolites
    • July
    • Mashego MR, Wu L, Van Dam JC, Ras C, Vinke JL, et al. (2004) MIRACLE: Mass isotopomer ratio analysis of U-13C-labeled extracts. A new method for accurate quantification of changes in concentrations of intracellular metabolites. Biotechnol Bioeng. 85: 620-628. Available: http://www.ncbi. nlm.nih.gov/pubmed/14966803. Accessed 12 July 2014.
    • (2004) Biotechnol Bioeng. , vol.85 , pp. 620-628
    • Mashego, M.R.1    Wu, L.2    Van Dam, J.C.3    Ras, C.4    Vinke, J.L.5
  • 12
    • 78049521558 scopus 로고    scopus 로고
    • Metabolite Identification in Synechococcus sp. PCC 7002 Using Untargeted Stable Isotope Assisted Metabolite Profiling
    • Baran R, Bowen BP, Bouskill NJ, Brodie EL, Yannone SM, et al. (2010) Metabolite Identification in Synechococcus sp. PCC 7002 Using Untargeted Stable Isotope Assisted Metabolite Profiling. Anal Chem. 82: 9034-9042. doi:10.1021/ac1020112.
    • (2010) Anal Chem. , vol.82 , pp. 9034-9042
    • Baran, R.1    Bowen, B.P.2    Bouskill, N.J.3    Brodie, E.L.4    Yannone, S.M.5
  • 13
    • 84904392449 scopus 로고    scopus 로고
    • A novel stable isotope labelling assisted workflow for improved untargeted LC-HRMS based metabolomics research
    • July
    • Bueschl C, Kluger B, Lemmens M, Adam G, Wiesenberger G, et al. (2013) A novel stable isotope labelling assisted workflow for improved untargeted LC-HRMS based metabolomics research. Metabolomics. 10: 754-769. Available: http://link.springer.com/10.1007/s11306-013-0611-0. Accessed 16 July 2014.
    • (2013) Metabolomics. , vol.10 , pp. 754-769
    • Bueschl, C.1    Kluger, B.2    Lemmens, M.3    Adam, G.4    Wiesenberger, G.5
  • 14
    • 84872360941 scopus 로고    scopus 로고
    • Isotopic labeling-assisted metabolomics using LC-MS
    • Accessed 17 January 2014
    • Bueschl C, Krska R, Kluger B, Schuhmacher R (2013) Isotopic labeling-assisted metabolomics using LC-MS. Anal Bioanal Chem. 405: 27-33. Available: http://link.springer.com/article/10.1007/s00216-012-6375-y. Accessed 17 January 2014.
    • (2013) Anal Bioanal Chem. , vol.405 , pp. 27-33
    • Bueschl, C.1    Krska, R.2    Kluger, B.3    Schuhmacher, R.4
  • 15
    • 84872544333 scopus 로고    scopus 로고
    • MzMatch-ISO: An R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data
    • Accessed 6 November 2013
    • Chokkathukalam A, Jankevics A, Creek DJ, Achcar F, Barrett MP, et al. (2013) mzMatch-ISO: An R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data. Bioinformatics. 29: 281-283. Available: http://www.pubmedcentral.nih.gov/articlerender. fcgi?artid53546800&tool5pmcentrez&rendertype5abstract. Accessed 6 November 2013.
    • (2013) Bioinformatics , vol.29 , pp. 281-283
    • Chokkathukalam, A.1    Jankevics, A.2    Creek, D.J.3    Achcar, F.4    Barrett, M.P.5
  • 16
    • 84867374332 scopus 로고    scopus 로고
    • Addressing the current bottlenecks of metabolomics: Isotopic Ratio Outlier Analysis, an isotopic-labeling technique for accurate biochemical profiling
    • De Jong FA, Beecher C (2012) Addressing the current bottlenecks of metabolomics: Isotopic Ratio Outlier Analysis, an isotopic-labeling technique for accurate biochemical profiling. Bioanalysis. 4: 2303-2314. doi:10.4155/bio.12.202.
    • (2012) Bioanalysis. , vol.4 , pp. 2303-2314
    • De Jong, F.A.1    Beecher, C.2
  • 17
    • 84857865811 scopus 로고    scopus 로고
    • MetExtract: A new software tool for the automated comprehensive extraction of metabolite-derived LC/MS signals in metabolomics research
    • Accessed 21 January 2014
    • Bueschl C, Kluger B, Berthiller F, Lirk G, Winkler S, et al. (2012) MetExtract: A new software tool for the automated comprehensive extraction of metabolite-derived LC/MS signals in metabolomics research. Bioinformatics. 28: 736-738. Available: http://www.pubmedcentral.nih.gov/articlerender. fcgi?artid53289915&tool5pmcentrez&rendertype5abstract. Accessed 21 January 2014.
    • (2012) Bioinformatics , vol.28 , pp. 736-738
    • Bueschl, C.1    Kluger, B.2    Berthiller, F.3    Lirk, G.4    Winkler, S.5
  • 18
    • 84893633670 scopus 로고    scopus 로고
    • X13CMS: Global tracking of isotopic labels in untargeted metabolomics
    • Huang X, Chen Y-J, Cho K, Nikolskiy I, Crawford P a, et al. (2014) X13CMS: Global tracking of isotopic labels in untargeted metabolomics. Anal Chem. 86: 1632-1639. Available: http://www.ncbi.nlm. nih.gov/pubmed/24397582.
    • (2014) Anal Chem. , vol.86 , pp. 1632-1639
    • Huang, X.1    Chen, Y.-J.2    Cho, K.3    Nikolskiy, I.4    Crawford, P.5
  • 19
    • 34249309179 scopus 로고    scopus 로고
    • The increasing dominance of teams in production of knowledge
    • Accessed 12 June 2011
    • Wuchty S, Jones BF, Uzzi B (2007) The increasing dominance of teams in production of knowledge. Science. 316: 1036-1039. Available: http://www.ncbi.nlm.nih.gov/pubmed/17431139. Accessed 12 June 2011.
    • (2007) Science. , vol.316 , pp. 1036-1039
    • Wuchty, S.1    Jones, B.F.2    Uzzi, B.3
  • 20
    • 84870629805 scopus 로고    scopus 로고
    • R: A language and environment for statistical computing
    • Accessed 5 November 2014
    • R-Development-Core-Team. (2011) R: A Language and Environment for Statistical Computing: ISBN 3-900051-07-0. The R project for statistical computing Available: http://www.r-project.org/. Accessed 5 November 2014.
    • (2011) The R Project for Statistical Computing
  • 21
    • 84913535611 scopus 로고    scopus 로고
    • Runiversal: Runiversal - Package for converting R objects to Java variables and XML
    • Accessed 5 November 2014
    • Satman MH (2010) Runiversal: Runiversal - Package for converting R objects to Java variables and XML. The Comprehensive R Archive Network Available: http://cran.r-project.org/web/packages/ Runiversal/index.html. Accessed 5 November 2014.
    • (2010) The Comprehensive R Archive Network
    • Satman, M.H.1
  • 22
    • 84862799289 scopus 로고    scopus 로고
    • LC-MS peak annotation and identification with CAMERA
    • Kuhl C, Tautenhahn R (2010) LC-MS Peak Annotation and Identification with CAMERA. Anal Chem. 84: 1-14. Available: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3658281/.
    • (2010) Anal Chem. , vol.84 , pp. 1-14
    • Kuhl, C.1    Tautenhahn, R.2
  • 24
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28: 27-30. Available: http://www.pubmedcentral.nih.gov/articlerender. fcgi?artid5102409&tool5pmcentrez&rendertype5abstract.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 25
    • 77954439868 scopus 로고    scopus 로고
    • MassBank: A public repository for sharing mass spectral data for life sciences
    • Accessed 11 August 2011
    • Horai H, Arita M, Kanaya S, Nihei Y, Ikeda T, et al. (2010) MassBank: a public repository for sharing mass spectral data for life sciences. J Mass Spectrom. 45: 703-714. Available: http://www.ncbi.nlm.nih. gov/pubmed/20623627. Accessed 11 August 2011.
    • (2010) J Mass Spectrom. , vol.45 , pp. 703-714
    • Horai, H.1    Arita, M.2    Kanaya, S.3    Nihei, Y.4    Ikeda, T.5
  • 26
    • 78449296488 scopus 로고    scopus 로고
    • ChemSpider: An online chemical information resource
    • Accessed 27 November 2013
    • Pence H, Williams A (2010) ChemSpider: an online chemical information resource. J Chem Educ. 87: 10-11. Available: http://pubs.acs.org/doi/abs/10.1021/ed100697w. Accessed 27 November 2013.
    • (2010) J Chem Educ. , vol.87 , pp. 10-11
    • Pence, H.1    Williams, A.2
  • 27
    • 34247163207 scopus 로고    scopus 로고
    • Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry
    • Kind T, Fiehn O (2007) Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry. BMC Bioinformatics. 8: 105. Available: http://www.ncbi.nlm.nih.gov/ pubmed/17389044.
    • (2007) BMC Bioinformatics. , vol.8 , pp. 105
    • Kind, T.1    Fiehn, O.2
  • 29
    • 84885566725 scopus 로고    scopus 로고
    • A novel type of N-acetylglutamate synthase is involved in the first step of arginine biosynthesis in Corynebacterium glutamicum
    • Petri K, Walter F, Persicke M, Rü ckert C, Kalinowski J (2013) A novel type of N-acetylglutamate synthase is involved in the first step of arginine biosynthesis in Corynebacterium glutamicum. BMC Genomics. 14: 713. doi:10.1186/1471-2164-14-713.
    • (2013) BMC Genomics. , vol.14 , pp. 713
    • Petri, K.1    Walter, F.2    Persicke, M.3    Rü Ckert, C.4    Kalinowski, J.5
  • 31
    • 78651194741 scopus 로고
    • The Isolation of y-L-Glutamyl Peptides from a Fermentation Broth
    • Vitali RA, Inamine E, Jacob TA (1965) The Isolation of y-L-Glutamyl Peptides from a Fermentation Broth. J Biol Chem. 240: 2508-2511.
    • (1965) J Biol Chem. , vol.240 , pp. 2508-2511
    • Vitali, R.A.1    Inamine, E.2    Jacob, T.A.3
  • 32
    • 0017842777 scopus 로고
    • Gamma-Glutamylpeptide formative activity by Corynebacterium glutamicum by the reverse reaction of the gamma-glutamylpetide hydrolytic enzyme
    • Hasegawa M, Matsubara I (1978) Gamma-Glutamylpeptide formative activity by Corynebacterium glutamicum by the reverse reaction of the gamma-glutamylpetide hydrolytic enzyme. Agric Biol Chem. 42: 371-381.
    • (1978) Agric Biol Chem. , vol.42 , pp. 371-381
    • Hasegawa, M.1    Matsubara, I.2
  • 33
    • 0037295406 scopus 로고    scopus 로고
    • Fragmentation reactions of protonated peptides containing glutamine or glutamic acid
    • Accessed 21 March 2014
    • Harrison AG (2003) Fragmentation reactions of protonated peptides containing glutamine or glutamic acid. J Mass Spectrom. 38: 174-187. Available: http://www.ncbi.nlm.nih.gov/pubmed/12577284. Accessed 21 March 2014.
    • (2003) J Mass Spectrom. , vol.38 , pp. 174-187
    • Harrison, A.G.1
  • 35
    • 33847309176 scopus 로고    scopus 로고
    • Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli
    • Pitera DJ, Paddon CJ, Newman JD, Keasling JD (2007) Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli. Metab Eng. 9: 193-207. doi:10.1016/ j.ymben.2006.11.002.
    • (2007) Metab Eng. , vol.9 , pp. 193-207
    • Pitera, D.J.1    Paddon, C.J.2    Newman, J.D.3    Keasling, J.D.4
  • 36
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Accessed 17 February 2012
    • Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc Ser B. 57: 289-300. Available: http://www.jstor.org/stable/10.2307/ 2346101. Accessed 17 February 2012.
    • (1995) J R Stat Soc Ser B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 37
    • 84907362164 scopus 로고    scopus 로고
    • Metabolic engineering of Corynebacterium glutamicum for L-arginine production
    • Accessed 20 October 2014
    • Park SH, Kim HU, Kim TY, Park JS, Kim S-S, et al. (2014) Metabolic engineering of Corynebacterium glutamicum for L-arginine production. Nat Commun. 5: 4618. Available: http://www.ncbi.nlm.nih.gov/ pubmed/25091334. Accessed 20 October 2014.
    • (2014) Nat Commun. , vol.5 , pp. 4618
    • Park, S.H.1    Kim, H.U.2    Kim, T.Y.3    Park, J.S.4    Kim, S.-S.5
  • 38
    • 84897366826 scopus 로고    scopus 로고
    • MeltDB 2.0-advances of the metabolomics software system
    • Accessed 16 September 2013
    • Kessler N, Neuweger H, Bonte A, Langenkämper G, Niehaus K, et al. (2013) MeltDB 2.0-advances of the metabolomics software system. Bioinformatics. 29: 2452-2459. Available: http://www.ncbi.nlm.nih. gov/pubmed/23918246. Accessed 16 September 2013.
    • (2013) Bioinformatics. , vol.29 , pp. 2452-2459
    • Kessler, N.1    Neuweger, H.2    Bonte, A.3    Langenkämper, G.4    Niehaus, K.5
  • 39
    • 67849106535 scopus 로고    scopus 로고
    • MetaboAnalyst: A web server for metabolomic data analysis and interpretation
    • Accessed 5 July 2011
    • Xia J, Psychogios N, Young N, Wishart DS (2009) MetaboAnalyst: a web server for metabolomic data analysis and interpretation. Nucleic Acids Res. 37: W652-60. Available: http://www.pubmedcentral.nih.govarticlerender.fcgi?artid52703878&tool5pmcentrez&rendertype5abstract. Accessed 5 July 2011.
    • (2009) Nucleic Acids Res. , vol.37 , pp. W652-W660
    • Xia, J.1    Psychogios, N.2    Young, N.3    Wishart, D.S.4
  • 40
    • 0027164654 scopus 로고
    • Isoleucine synthesis in Corynebacterium glutamicum: Molecular analysis of the ilvB-ilvN-ilvC operon
    • Keilhauer C, Eggeling L, Sahm H (1993) Isoleucine synthesis in Corynebacterium glutamicum: molecular analysis of the ilvB-ilvN-ilvC operon. J Bacteriol. 175: 5595-5603.
    • (1993) J Bacteriol. , vol.175 , pp. 5595-5603
    • Keilhauer, C.1    Eggeling, L.2    Sahm, H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.