MeltDB: A software platform for the analysis and integration of metabolomics experiment data

Bioinformatics

Volumn 24, Issue 23, 2008, Pages 2726-2732

  Neuweger, Heiko ^a   Albaum, Stefan P ^b   Dondrup, Michael ^b   Persicke, Marcus ^a   Watt, Tony ^a,c   Niehaus, Karsten ^c   Stoye, Jens ^a   Goesmann, Alexander ^b  

^a BIELEFELD UNIVERSITY   (Germany)

^b Center for Biotechnology ^*  (Germany)

^c Proteome and Metabolome Research   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER ANALYSIS; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA ANALYSIS; FUNCTIONAL GENOMICS; INFORMATION PROCESSING; METABOLITE; METABOLOMICS; NONHUMAN; PRIORITY JOURNAL; TRANSCRIPTOMICS; XANTHOMONAS CAMPESTRIS;

DATABASE MANAGEMENT SYSTEMS; GENOME, BACTERIAL; METABOLOMICS; PROTEOMICS; SOFTWARE;

NEGIBACTERIA; XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS;

EID: 56649102388     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn452     Document Type: Article

References (35)

1. Barsch,A. et al. (2004) Comprehensive metabolite profiling of sinorhizobium meliloti using gas chromatography-mass spectrometry. Funct. Integr. Genomics, 4, 219-230.
2. Bino,R.J. et al. (2004) Potential of metabolomics as a functional genomics tool. Trends Plant Sci., 9, 418-425.
3. Broeckling,C.D. et al. (2006) Met-idea: Data extraction tool for mass spectrometry-based metabolomics. Anal. Chem., 78, 4334-4341.
4. Dondrup,M. et al. (2003) Emma: A platform for consistent storage and efficient analysis of microarray data. J. Biotechnol., 106 135-146.
5. Dunn,W.B. and Ellis,D.I. (2005) Metabolomics: Current analytical platforms and methodologies. Trends Anal. Chem., 4, 285-294.
6. Ettre,L.S. (1993) Nomenclature for Chromatography (IUPAC Recommendations 1993). Pure Appl. Chem., 65, 819-872.
7. Fiehn,O. (2002) Metabolomics-the link between genotypes and phenotypes. Plant Mol. Biol., 48, 155-171.
8. Fiehn,O. et al. (2008) Quality control for plant metabolomics: reporting msi-compliant studies. Plant J., 53, 691-704.
9. Gamma,E. et al. (1995) Design Patterns. Elements of Reusable Object-Oriented Software. Addison Wesley, Amsterdam.
10. Goesmann,A. et al. (2005) Brigep-the bridge-based genome-transcriptome-proteome browser. Nucleic Acids Res., 33 (Web Server issue), W710-W716.
11. Hyvärinen,A. and Oja,E. (2000) Independent component analysis: algorithms and applications. Neural Netw., 13, 411-430.
12. Jenkins,H. et al. (2005) Toward supportive data collection tools for plant metabolomics. Plant Physiol., 138, 67-77.
13. Jonsson,P. et al. (2005) High-throughput data analysis for detecting and identifying differences between samples in gc/ms-based metabolomic analyses. Anal. Chem., 77, 5635-5642.
14. Kanehisa,M. et al. (2006) From genomics to chemical genomics: New developments in kegg. Nucleic Acids Res., 34(Database issue), D354-D357.
15. Katajamaa,M. et al. (2006) Mzmine: Toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics, 22, 634-636.
16. Kopka,J. et al. (2005) Gmdγsb.db: The golm metabolome database. Bioinformatics, 21, 1635-1638.
17. Lam,H. et al. (2007) Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics, 7, 655-667.
18. Lüdemann,A. et al. (2008) Tagfinder for the quantitative analysis of gas chromatography-mass spectrometry (gc-ms)-based metabolite profiling experiments. Bioinformatics, 24, 732-737.
19. Meyer,F. et al. (2003) Gendb-an open source genome annotation system for prokaryote genomes. Nucleic Acids Res., 31, 2187-2195.
20. Neuweger,H. et al. (2007) Corynecenter - an online resource for the integrated analysis of corynebacterial genome and transcriptome data. BMC Syst. Biol., 1, 55.
21. Orchard,S. et al. (2007) Five years of progress in the standardization of proteomics data 4th annual spring workshop of the hupo-proteomics standards initiative april 23-25, 2007 ecole nationale suprieure (ens), lyon, france. Proteomics, 7, 3436-3440.
22. Pedrioli,P.G.A. et al. (2004) A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol., 22, 1459-1466.
23. Robinson,M.D. et al. (2007) A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments. BMC Bioinformatics, 8, 419.
24. Sansone,S.-A. et al. (2007) The metabolomics standards initiative. Nat. Biotechnol., 25, 846-848.
25. Scholz,M. and Fiehn,O. (2007) Setupx-a public study design database for metabolomic projects. Pac. Symp. Biocomput., 12, 169-180.
26. Smith,C.A. et al. (2005) Metlin: A metabolite mass spectral database. Ther. Drug Monit., 27, 747-751.
27. Smith,C.A. et al. (2006) Xcms: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal. Chem., 78, 779-787.
28. Stein,S.E. (1999) An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data. J. Am. Soc. Mass Spectrom., 10, 770-781.
29. Stein,S. and Scott,D. (1994) Optimization and testing of mass spectra library search algorithms for compound identification. J. Am. Soc. Mass Spectro., 5, 859-866.
30. Steinfath,M. et al. (2008) Metabolite profile analysis: From raw data to regression and classification. Physiol. Plant, 132, 150-161.
31. Steuer,R. et al. (2003) Observing and interpreting correlations in metabolomic networks. Bioinformatics, 19, 1019-1026.
32. Thimm,O. et al. (2004) Mapman: A user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J., 37, 914-939.
33. Unidata (2008) Unidata netcdf. Available at http://www.unidata.ucar.edu/ software/netcdf/ (last accessed date August 25, 2008).
34. Vorhölter,F.-J. et al. (2008) The genome of Xanthomonas campestris pv. campestris b100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis. J. Biotechnol. 134, 33-45.
35. Vos,R.C.H.D. et al. (2007) Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry. Nat. Protoc., 2, 778-791.