Analysis of metabolomics datasets with high-performance computing and metabolite atlases

Metabolites

Volumn 5, Issue 3, 2015, Pages 431-442

  Yao, Yushu ^a   Sun, Terence ^a   Wang, Tony ^a   Ruebel, Oliver ^a   Northen, Trent ^a   Bowen, Benjamin P ^a  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

Biology; Data analysis; IPython; LC MS; Metabolite atlas; Metabolomics; MS MS; Python; SciDB

Indexed keywords

ARTICLE; DATA ANALYSIS SOFTWARE; DATA BASE; INFORMATION PROCESSING; INFORMATION SYSTEM; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METABOLOMICS; MOLECULAR GENETICS;

EID: 85016892194     PISSN: None     EISSN: 22181989     Source Type: Journal    
DOI: 10.3390/metabo5030431     Document Type: Article

References (34)

1. Baran, R., Bowen, B.P., Bouskill, N.J., Brodie, E.L., Yannone, S.M., Northen, T.R. Metabolite Identification in Synechococcus sp. PCC 7002 Using Untargeted Stable Isotope Assisted Metabolite Profiling. Anal. Chem. 2010, 82, 9034–9042
2. Evans, A.M., DeHaven, C.D., Barrett, T., Mitchell, M., Milgram, E. Integrated, nontargeted ultrahigh performance liquid chromatography/electrospray ionization tandem mass spectrometry platform for the identification and relative quantification of the small-molecule complement of biological systems. Anal. Chem. 2009, 81, 6656–6667
3. MSI Board Members; Sansone, S.-A., Fan, T., Goodacre, R., Griffin, J.L., Hardy, N.W., Kaddurah-Daouk, R., Kristal, B.S., Lindon, J., Mendes, P., et al. The metabolomics standards initiative. Nat. Biotechnol. 2007, 25, 846–848
4. Sansone, S.-A., Schober, D., Atherton, H.J., Fiehn, O., Jenkins, H., Rocca-Serra, P., Rubtsov, D.V., Spasić, I., Soldatova, L., Taylor, C., et al. Metabolomics standards initiative: Ontology working group work in progress. Metabolomics 2007, 3, 249–256
5. Castle, A.L., Fiehn, O., Kaddurah-Daouk, R., Lindon, J.C. Metabolomics Standards Workshop and the development of international standards for reporting metabolomics experimental results. Brief. Bioinform. 2006, 7, 159–165
6. Giacomoni, F., le Corguillé, G., Monsoor, M., Landi, M., Pericard, P., Pétéra, M., Duperier, C., Tremblay-Franco, M., Martin, J.-F., Jacob, D., et al. Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics 2015, 31, 1493–1495
7. Carroll, A.J., Badger, M.R., Harvey Millar, A. The MetabolomeExpress Project: Enabling web-based processing, analysis and transparent dissemination of GC/MS metabolomics datasets. BMC Bioinform. 2010, 11, 376
8. Xia, J., Psychogios, N., Young, N., Wishart, D.S. MetaboAnalyst: A web server for metabolomic data analysis and interpretation. Nucleic Acids Res. 2009, 37, W652–W660
9. Ara, T., Enomoto, M., Arita, M., Ikeda, C., Kera, K., Yamada, M., Nishioka, T., Ikeda, T., Nihei, Y., Shibata, D., et al. Metabolonote: A wiki-based database for managing hierarchical metadata of metabolome analyses. Front. Bioeng. Biotechnol. 2015, 3, 38
10. Bowen, B.P., Northen, T.R. Dealing with the unknown: Metabolomics and metabolite atlases. J. Am. Soc. Mass Spectrom. 2010, 21, 1471–1476
11. Smith, C.A., Want, E.J., O’Maille, G., Abagyan, R., Siuzdak, G. XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal. Chem. 2006, 78, 779–787
12. Katajamaa, M., Miettinen, J., Oresic, M. MZmine: Toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics 2006, 22, 634–636
13. Scholz, M., Fiehn, O. SetupX—a public study design database for metabolomic projects. Pacific Symposium on Biocomputing 2007: Maui, Hawaii, 3–7 January 2007; Altman, R., Ed., World Scientific Publishing Co. Pte. Ltd.: Singapore, 2007; pp. 169–180
14. Stonebraker, M., Brown, P., Zhang, D., Becla, J. SciDB: A Database Management System for Applications with Complex Analytics. Comput. Sci. Eng. 2013, 15, 54–62
15. Pérez, F., Granger, B.E. IPython: A System for Interactive Scientific Computing. Comput. Sci. Eng. 2007, 9, 21–29
16. Yao, Y., Bowen, B., Baron, D., Poznanski, D. SciDB for High Performance Array-structured Science Data at NERSC. Comput. Sci. Eng. 2015, 17, 44–52
17. Martens, L., Chambers, M., Sturm, M., Kessner, D., Levander, F., Shofstahl, J., Tang, W.H., Römpp, A., Neumann, S., Pizarro, A.D., et al. mzML—a Community Standard for Mass Spectrometry Data. Mol. Cell. Proteomics 2010, doi:10.1074/mcp.R110.000133
18. Kessner, D., Chambers, M., Burke, R., Agus, D., Mallick, P. ProteoWizard: Open source software for rapid proteomics tools development. Bioinformatics 2008, 24, 2534–2536
19. Forcier, J., Bissex, P., Chun, W. Python Web Development with Django; Addison-Wesley Professional: Boston, MA, USA, 2008
20. Metabolite Atlas. Available online: http://metatlas.nersc.gov (accessed on 16 July 2015).
21. Wang, Y., Kora, G., Bowen, B.P., Pan, C. MIDAS: A Database-Searching Algorithm for Metabolite Identification in Metabolomics. Anal. Chem. 2014, 86, 9496–9503
22. Wolf, S., Schmidt, S., Mueller-Hannemann, M., Neumann, S. In silico fragmentation for computer assisted identification of metabolite mass spectra. BMC Bioinform. 2010, 11, 148
23. Jenkins, H., Hardy, N., Beckmann, M., Draper, J., Smith, A.R., Taylor, J., Fiehn, O., Goodacre, R., Bino, R.J., Hall, R., et al. A proposed framework for the description of plant metabolomics experiments and their results. Nat. Biotechnol. 2004, 22, 1601–1606
24. Steinbeck, C., Conesa, P., Haug, K., Mahendraker, T., Williams, M., Maguire, E., Rocca-Serra, P., Sansone, S.-A., Salek, R.M., Griffin, J.L. MetaboLights: Towards a new COSMOS of metabolomics data management. Metabolomics 2012, 8, 757–760
25. Horai, H., Arita, M., Kanaya, S., Nihei, Y., Ikeda, T., Suwa, K., Ojima, Y., Tanaka, K., Tanaka, S., Aoshima, K., et al. MassBank: A public repository for sharing mass spectral data for life sciences. J. Mass Spectrom. 2010, 45, 703–714
26. Goecks, J., Nekrutenko, A., Taylor, J. Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010, 11, R86
27. Herzog, R., Schuhmann, K., Schwudke, D., Sampaio, J.L., Bornstein, S.R., Schroeder, M., Shevchenko, A. LipidXplorer: A Software for Consensual Cross-Platform Lipidomics. PLoS ONE 2012, 7, e29851
28. Williams, J.D., Weiner, B.E., Ormand, J.R., Brunner, J., Thornquest, A.D., Burinsky, D.J. Automated molecular weight assignment of electrospray ionization mass spectra. Rapid Commun. Mass Spectrom. 2001, 15, 2446–2455
29. Mendes, P. Emerging bioinformatics for the metabolome. Brief. Bioinform. 2002, 3, 134–145
30. Spinellis, D. Git. IEEE Softw. 2012, 29, 100–101
31. Thung, F., Bissyande, T.F., Lo, D., Jiang, L. Network Structure of Social Coding in GitHub. In Proceedings of the 2013 17th European Conference on Software Maintenance and Reengineering, Genova, Italy, 5–8 March 2013; pp. 323–326
32. NBViewer. Available online: http://nbviewer.ipython.org (accessed on 16 July 2015).
33. Karp, P.D., Paley, S., Romero, P. The Pathway Tools software. Bioinformatics 2002, 18 (Suppl. 1), S225–S232
34. The Systems Biology Knowledgebase. Available online: http://kbase.us (accessed on 16 July 2015).