MIDAS: A database-searching algorithm for metabolite identification in metabolomics

Analytical Chemistry

Volumn 86, Issue 19, 2014, Pages 9496-9503

  Wang, Yingfeng ^a   Kora, Guruprasad ^a   Bowen, Benjamin P ^b   Pan, Chongle ^a  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

METABOLITE IDENTIFICATION; METABOLOMICS;

ALGORITHM; CHEMISTRY; FACTUAL DATABASE; METABOLISM; METABOLOME; METABOLOMICS; METHODOLOGY; PROCEDURES; QUALITY CONTROL; STATISTICAL MODEL; STATISTICS AND NUMERICAL DATA; SYNECHOCOCCUS; TANDEM MASS SPECTROMETRY;

ALGORITHMS; BENCHMARKING; DATABASES, FACTUAL; METABOLOME; METABOLOMICS; MODELS, STATISTICAL; RESEARCH DESIGN; SYNECHOCOCCUS; TANDEM MASS SPECTROMETRY;

EID: 84907885060     PISSN: 00032700     EISSN: 15206882     Source Type: Journal    
DOI: 10.1021/ac5014783     Document Type: Article

References (34)

1. Dunn, W. B. Phys. Biol. 2008, 5 011001
2. Ellinger, J. J.; Chylla, R. A.; Ulrich, E. L.; Markley, J. L. Curr. Metabolomics 2013, 1, 1-22
3. Steinhauser, D.; Kopka, J. Experientia, Suppl. 2007, 97, 171-194
4. Theodoridis, G. A.; Gika, H. G.; Want, E. J.; Wilson, I. D. Anal. Chim. Acta 2012, 711, 7-16
5. Scheubert, K.; Hufsky, F.; Bocker, S. J. Cheminf. 2013, 5, 12
6. Smith, C. A.; OMaille, G.; Want, E. J.; Qin, C.; Trauger, S. A.; Brandon, T. R.; Custodio, D. E.; Abagyan, R.; Siuzdak, G. Proc. 9th Int. Congr. Ther. Drug Monit. Clin. Toxicol. 2005, 27, 747-751
7. Tautenhahn, R.; Cho, K.; Uritboonthai, W.; Zhu, Z.; Patti, G. J.; Siuzdak, G. Nat. Biotechnol. 2012, 30, 826-828
8. Wishart, D. S.; Tzur, D.; Knox, C.; Eisner, R.; Guo, A. C. Nucleic Acids Res. 2007, 35, D521-D526
9. Wishart, D. S.; Jewison, T.; Guo, A. C.; Wilson, M.; Knox, C. Nucleic Acids Res. 2013, 41, D801-D807
10. Wishart, D. S.; Knox, C.; Guo, A. C.; Eisner, R.; Young, N. Nucleic Acids Res. 2009, 37, D603-D610
11. Horai, H.; Arita, M.; Kanaya, S.; Nihei, Y.; Ikeda, T. J. Mass Spectrom 2010, 45, 703-714
12. Phinney, K. W.; Ballihaut, G.; Bedner, M.; Benford, B. S.; Camara, J. E. Anal. Chem. 2013, 85, 11732-11738
13. Skogerson, K.; Wohlgemuth, G.; Barupal, D. K.; Fiehn, O. BMC Bioinf. 2011, 12, 321
14. Sadygov, R.; Cociorva, D.; Yates, J. R., III Nat. Methods 2004, 1, 195-202
15. Paizs, B.; Suhai, S. Mass Spectrom Rev. 2005, 24, 508-548
16. Hill, D. W.; Kertesz, T. M.; Fontaine, D.; Friedman, R.; Grant, D. F. Anal. Chem. 2008, 80, 5574-5582
17. Advanced Chemistry Development. Inc. ACD/MS Fragmenter, (2010. http://www.acdlabs.com/products/adh/ms/ms/frag/.
18. Meringer, M. MOLGEN-MSF, 2009. http://www.molgen.de.
19. Kind, T.; Fiehn, O. Bioanal Rev. 2010) 2, 23-60
20. Heinonen, M.; Shen, H.; Zamboni, N.; Rousu, J. Bioinformatics 2012, 28, 2333-2341
21. Schymanski, E. L.; Meringer, M.; Brack, W. Anal. Chem. 2009, 81, 3608-3617
22. Wolf, S.; Schmidt, S.; Muller-Hannemann, M.; Neumann, S. BMC Bioinf. 2010, 11, 148
23. Pan, C.; Park, B. H.; McDonald, W. H.; Carey, P. A.; Banfield, J. F. BMC Bioinf. 2010, 11, 118
24. Landrum, G. RDKit: Open-source cheminformatics, 2013. http://www.rdkit.org.
25. ChemAxon Marvin Beans, (2014. http://www.chemaxon.com.
26. Baran, R.; Bowen, B. P.; Bouskill, N. J.; Brodie, E. L.; Yannone, S. M. Anal. Chem. 2010) 82, 9034-9042
27. Hyatt, D.; Pan, C. Bioinformatics 2012, 28, 1895-1901
28. Wang, Y.; Ahn, T.-H.; Li, Z.; Pan, C. Bioinformatics 2013, 29, 2064-2065
29. Hill, A. W.; Mortishire-Smith, R. J. Rapid Commun. Mass Spectrom. 2005, 19, 3111-3118
30. Heinonen, M.; Rantanen, A.; Mielika, T.; Kokkonen, J.; Kiuru, J. Rapid Commun. Mass Spectrom. 2008, 22, 3043-3052
31. McLafferty, F. W. Anal. Chem. 1959, 31, 82-87
32. Heikamp, K.; Bajorath, J. J. Chem. Inf Model 2011, 51, 1831-1839
33. Wilcoxon, F. Biom. Bull. 1945, 1, 80-83
34. Kangas, L. J.; Metz, T. O.; Isaac, G.; Schrom, B. T.; Ginovska-Pangovska, B. Bioinformatics 2012, 28, 1705-1713