Mass spectral metabonomics beyond elemental formula: Chemical database querying by matching experimental with computational fragmentation spectra

Analytical Chemistry

Volumn 80, Issue 14, 2008, Pages 5574-5582

  Hill, Dennis W ^a   Kertesz, Tzipporah M ^a   Fontaine, Dan ^a   Friedman, Robert ^a   Grant, David F ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINS; DATABASE SYSTEMS; EXPERIMENTS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; MASS SPECTROMETERS; MASS SPECTROMETRY; NUCLEAR MAGNETIC RESONANCE; ORGANIC COMPOUNDS; TESTING;

ANALYTICAL CHALLENGES; BIO FLUIDS; CHEMICAL DATABASES; CHEMICAL IDENTIFICATIONS; CHEMICAL STRUCTURES; CID SPECTRUMS; ELEMENTAL FORMULAS; INDUCED DISSOCIATIONS; MASS SPECTRAL; MASS SPECTROSCOPIES; METABONOMICS; MONOISOTOPIC; STRUCTURAL IDENTIFICATIONS; STRUCTURAL INFORMATIONS;

CHEMICAL COMPOUNDS;

ORGANIC COMPOUND;

ARTICLE; CHEMICAL ANALYSIS; CHEMICAL STRUCTURE; COMPUTER PROGRAM; FRAGMENTATION REACTION; MASS SPECTROMETRY; MOLECULAR WEIGHT; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; SPECTRUM; STRUCTURE ANALYSIS; COMPUTER; FACTUAL DATABASE; METHODOLOGY;

COMPUTERS; DATABASES, FACTUAL; MASS SPECTROMETRY; MOLECULAR WEIGHT; SOFTWARE;

EID: 49049121462     PISSN: 00032700     EISSN: None     Source Type: Journal    
DOI: 10.1021/ac800548g     Document Type: Article

References (30)

1. Grigorov, M. G. Bioinformatics 2006, 22, 1424-1430.
2. Hood, L.; Heath, J. R.; Phelps, M. E.; Lin, B. Science 2004, 306, 640-643.
3. Nicholson, J. K.; Lindon, J. C.; Holmes, E. Xenobiotica 1999, 29, 1181-1189.
4. German, J. B.; Hammock, B. D.; Watkins, S. M. Metabolomics 2005, 1, 3-9.
5. Dunn, W. B.; Bailey, N. J.; Johnson, H. E. Analyst 2005, 130, 606-625.
6. Wishart, D. S. Briefings Bioinf. 2007, 8, 279-293.
7. Ding, J.; Sorensen, C. M.; Zhang, Q.; Jiang, H.; Jaitly, N.; Livesay, E. A.; Shen, Y.; Smith, R. D.; Metz, T. O. Anal. Chem. 2007, 79, 6081-6093.
8. Denkert, C.; Budczies, J.; Kind, T.; Weichert, W.; Tablack, P.; Sehouli, J.; Niesporek, S.; Konsgen, D.; Dietel, M.; Fiehn, O. Cancer Res. 2006, 66, 10795-10804.
9. Benecke, C.; Grund, R.; Hohberger, R.; Kerber, A.; Laue, R.; Wieland, T. Anal. Chim. Acta 1995, 314, 141-147.
10. Hill, A. W.; Mortishire-Smith, R. J. Rapid Commun. Mass Spectrom. 2005, 19, 3111-3118.
11. Plumb, R. S.; Johnson, K. A.; Rainville, P.; Smith, B. W.; Wilson, I. D.; CastroPerez, J. M.; Nicholson, J. K. Rapid Commun. Mass Spectrom. 2006, 20, 1989-1994.
12. McLafferty, F. W.; Hertel, R. H.; Villwock, R. D. Org. Mass Spectrom. 1974, 9, 690-702.
13. McLafferty, F. W.; Stauffer, D. A.; Loh, S. Y.; Wesdemiotis, C. J. Am. Soc. Mass Spectrom. 1999, 10, 1229-1240.
14. Kienhuis, P. G.; Geerdink, R. B. J. Chromatogr., A 2002, 974, 161-168.
15. McLafferty, F. W.; Turecek, F. Interpretation of Mass Spectra, 4th ed.; University Science Books: Sausalito, CA, 1993.
16. Tetko, I. V.; Tanchuk, V. Y.; Villa, A. E. J. Chem. Inf. Comput. Sci. 2001, 41, 1407-1421.
17. Yang, D.; Beylot, M.; Agarwal, K. C.; Soloviev, M. V.; Brunengraber, H. Anal. Biochem. 1993, 212, 277-282.
18. Ghosh, S.; Grant, D. F.; Dey, D. K.; Hill, D. W. BMC Bioinf. 2008, 9, 38.
19. Chen, J.; Swamidass, S. J.; Dou, Y.; Bruand, J.; Baldi, P. Bioinformatics 2005, 21, 4133-4139.
20. Wishart, D. S.; Tzur, D.; Knox, C.; Eisner, R.; Guo, A. C.; Young, N.; Cheng, D.; Jewell, K.; Arndt, D.; Sawhney, S.; Fung, C.; Nikolai, L.; Lewis, M.; Coutouly, M. A.; Forsythe, I.; Tang, P.; Shrivastava, S.; Jeroncic, K.; Stothard, P.; Amegbey, G.; Block, D.; Hau, D. D.; Wagner, J.; Miniaci, J.; Clements, M.; Gebremedhin, M.; Guo, N.; Zhang, Y.; Duggan, G. E.; Macinnis, G. D.; Weljie, A. M.; Dowlatabadi, R.; Bamforth, F.; Clive, D.; Greiner, R.; Li, L.; Marrie, T.; Sykes, B. D.; Vogel, H. J.; Querengesser, L. Nucleic Acids Res. 2007, 35, D521-D526.
21. Irwin, J. J.; Shoichet, B. K. J. Chem. Inf. Model. 2005, 45, 177-182.
22. Kanehisa, M.; Goto, S.; Hattori, M.; Aoki-Kinoshita, K. F.; Itoh, M.; Kawashima, S.; Katayama, T.; Araki, M.; Hirakawa, M. Nucleic Acids Res. 2006, 34, D354-D357.
23. Polettini, A.; Gottardo, R.; Pascali, J. P.; Tagliaro, F. Anal. Chem. 2008, 80, 3050-3057.
24. Berthod, A.; Carda-Broch, S. J. Chromatogr., A 2004, 1037, 3-14.
25. Klopman, G.; Zhu, H. Mini-Rev. Med. Chem. 2005, 5, 127-133.
26. Wiczling, P.; Kawczak, P.; Nasal, A.; Kaliszan, R. Anal. Chem. 2006, 78, 239-249.
27. Wang, R. X.; Fu, Y.; Lai, L. H. J. Chem. Inf. Comput. Sci. 1997, 37, 615-621.
28. Kind, T.; Fiehn, O. BMC Bioinf. 2006, 7, 234.
29. Kind, T.; Fiehn, O. BMC Bioinf. 2007, 8, 105.
30. Brown, S. C.; Kruppa, G.; Dasseux, J. L. Mass Spectrom. Rev. 2005, 24, 223-231.