MET-IDEA version 2.06; improved efficiency and additional functions for mass spectrometry-based metabolomics data processing

Metabolomics

Volumn 8, Issue , 2012, Pages 105-110

  Lei, Zhentian ^a   Li, Haiquan ^a,b   Chang, Junil ^a   Zhao, Patrick X ^a   Sumner, Lloyd W ^a  

^a PLANT BIOLOGY DIVISION   (United States)

^b UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

Author keywords

Data Processing; GC MS; LC MS; Mass spectrometry; MET IDEA; Metabolomics; Visualization

Indexed keywords

ARTICLE; CAPILLARY ELECTROPHORESIS; COMPUTER PROGRAM; DATA ANALYSIS SOFTWARE; DATA PROCESSING; FUNCTIONAL GENOMICS; GAS CHROMATOGRAPHY; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METABOLOMICS; METABOLOMICS ION BASED DATA EXTRACTION ALGORITHM; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; ROOT HAIR; SENSITIVITY ANALYSIS; SOYBEAN; SYSTEMS BIOLOGY;

EID: 84862830090     PISSN: 15733882     EISSN: 15733890     Source Type: Journal    
DOI: 10.1007/s11306-012-0397-5     Document Type: Article

References (25)

1. Baran, R., Kochi, H., Saito, N., Suematsu, M., Soga, T., Nishioka, T., et al. (2006). MathDAMP: A package for differential analysis of metabolite profiles. BMC Bioinformatics, 7(530), doi: 10. 1186/1471-2105-7-530.
2. Benkeblia, N., Shinano, T., & Osaki, M. (2007). Metabolite profiling and assessment of metabolome compartmentation of soybean leaves using non-aqueous fractionation and GC-MS analysis. Metabolomics, 3(3), 297-305.
3. Brechenmacher, L., Lei, Z., Libault, M., Findley, S., Sugawara, M., Sadowsky, M. J., et al. (2010). Soybean metabolites regulated in root hairs in response to the symbiotic bacterium Bradyrhizobium japonicum. Plant Physiology, 153(4), 1808-1822. doi: 10. 1104/pp. 110. 157800.
4. Broeckling, C. D., Reddy, I. R., Duran, A. L., Zhao, X. J., & Sumner, L. W. (2006). MET-IDEA: data extraction tool for mass spectrometry-based metabolomics. Analytical Chemistry, 78(13), 4334-4341. doi: 10. 1021/ac0521596.
5. Broeckling, C. D., Broz, A. K., Bergelson, J., Manter, D. K., & Vivanco, J. M. (2008). Root exudates regulate soil fungal community composition and diversity. Applied and Environmental Microbiology, 74(3), 738-744. doi: 10. 1128/aem. 02188-07.
6. Dolan, J. W. (2009). Integration problems. LCGC North America, 27(10), 892-899.
7. Duran, A. L., Yang, J., Wang, L. J., & Sumner, L. W. (2003). Metabolomics spectral formatting, alignment and conversion tools (MSFACTs). Bioinformatics, 19(17), 2283-2293. doi: 10. 1093/bioinformatics/btg315.
8. Farag, M. A. (2008). Headspace analysis of volatile compounds in leaves from the Juglandaceae (Walnut) family. Journal of Essential Oil Research, 20(4), 323-327.
9. Farag, M. A. (2009). Chemical composition and biological activities of Asimina triloba leaf essential oil. Pharmaceutical Biology, 47(10), 982-986. doi: 10. 1080/13880200902967995.
10. Farag, M. A., Ryu, C. M., Sumner, L. W., & Pare, P. W. (2006). GC-MS SPME profiling of rhizobacterial volatiles reveals prospective inducers of growth promotion and induced systemic resistance in plants. Phytochemistry, 67(20), 2262-2268. doi: 10. 1016/j. phytochem. 2006. 07. 021.
11. Farag, M. A., Huhman, D. V., Dixon, R. A., & Sumner, L. W. (2008). Metabolomics reveals novel pathways and differential mechanistic and elicitor-specific responses in phenylpropanoid and isoflavonoid biosynthesis in Medicago truncatula cell cultures. Plant Physiology, 146(2), 387-402. doi: 10. 1104/pp. 107. 108431.
12. Farag, M. A., Deavours, B. E., de Fatima, A., Naoumkina, M., Dixon, R. A., & Sumner, L. W. (2009). Integrated metabolite and transcript profiling identify a biosynthetic mechanism for hispidol in Medicago truncatula cell cultures. Plant Physiology, 151(3), 1096-1113. doi: 10. 1104/pp. 109. 141481.
13. FDA. (2001). Guidance for industry: Bioanalytical method validation. Rockville, MD: FDA, pp. 1-25.
14. Fiehn, O., Wohlgemuth, G., Scholz, M. (2005). Setup and annotation of metabolomic experiments by integrating biological and mass spectrometric metadata. In B. Ludascher, L. Raschid (Eds.), Data Integration in the Life Sciences, Proceedings (vol. 3615, pp. 224-239, Lecture Notes in Computer Science). Berlin: Springer-Verlag.
15. Florida_DEP. (2011). CM-018-1. 7 Laboratory policy regarding manual chromatographic peak integration. pp. 1-5. http://www. dep. state. fl. us/labs/cgi-bin/sop/sop1. asp?sect=CHEMISTRY.
16. Hamzehzarghani, H., Paranidharan, V., Abu-Nada, Y., Kushalappa, A. C., Mamer, O., & Somers, D. (2008). Metabolic profiling to discriminate wheat near isogenic lines, with quantitative trait loci at chromosome 2DL, varying in resistance to Fusarium head blight. Canadian Journal of Plant Science, 88(4), 789-797.
17. Hiller, K., Hangebrauk, J., Jager, C., Spura, J., Schreiber, K., & Schomburg, D. (2009). MetaboliteDetector: Comprehensive analysis tool for targeted and nontargeted GC/MS based metabolome analysis. Analytical Chemistry, 81(9), 3429-3439. doi: 10. 1021/ac802689c.
18. Katajamaa, M., Miettinen, J., & Oresic, M. (2006). MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics, 22(5), 634-636. doi: 10. 1093/bioinformatics/btk039.
19. Kopka, J., Schauer, N., Krueger, S., Birkemeyer, C., Usadel, B., Bergmuller, E., et al. (2005). GMD@CSB. DB: the Golm metabolome database. Bioinformatics, 21(8), 1635-1638. doi: 10. 1093/bioinformatics/bti236.
20. Lisec, J., Schauer, N., Kopka, J., Willmitzer, L., & Fernie, A. R. (2006). Gas chromatography mass spectrometry-based metabolite profiling in plants. Nature Protocols, 1(1), 387-396. doi: 10. 1038/nprot. 2006. 59.
21. Lommen, A. (2009). MetAlign: interface-driven, versatile metabolomics tool for hyphenated full-scan mass spectrometry data preprocessing. Analytical Chemistry, 81(8), 3079-3086. doi: 10. 1021/ac900036d.
22. Luedemann, A., Strassburg, K., Erban, A., & Kopka, J. (2008). TagFinder for the quantitative analysis of gas chromatography-mass spectrometry (GC-MS)-based metabolite profiling experiments. Bioinformatics, 24(5), 732-737. doi: 10. 1093/bioinformatics/btn023.
23. Naoumkina, M., Vaghchhipawala, S., Tang, Y. H., Ben, Y. X., Powell, R. J., & Dixon, R. A. (2008). Metabolic and genetic perturbations accompany the modification of galactomannan in seeds of Medicago truncatula expressing mannan synthase from guar (Cyamopsis tetragonoloba L.). Plant Biotechnology Journal, 6(6), 619-631. doi: 10. 1111/j. 1467-7652. 2008. 00345. x.
24. Smith, C. A., Want, E. J., O'Maille, G., Abagyan, R., & Siuzdak, G. (2006). XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Analytical Chemistry, 78(3), 779-787. doi: 10. 1021/ac051437y.
25. Xu, P., Chen, F., Mannas, J. P., Feldman, T., Sumner, L. W., & Roossinck, M. J. (2008). Virus infection improves drought tolerance. New Phytologist, 180(4), 911-921. doi: 10. 1111/j. 1469-8137. 2008. 02627. x.