Ion annotation-assisted analysis of LC-MS based metabolomic experiment
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- 作者：Rency S Varghese (1)
Bin Zhou (1)
Mohammad R Nezami Ranjbar (1) (2)
Yi Zhao (3)
Habtom W Ressom (1) - 刊名：Proteome Science
- 出版年：2012
- 出版时间：June 2012
- 年：2012
- 卷：10
- 期：1-supp
- 全文大小：640KB
- 参考文献：1. Chen C, Gonzalez FJ, Idle JR: LC-MS-Based Metabolomics in Drug Metabolism. / Drug Metabolism Reviews 2007, 39:581鈥?97. CrossRef
2. Jonsson P, Gullberg J, Nordstr枚m A, Kusano M, Kowalczyk M, Sj枚str枚m M, Moritz T: A Strategy for Identifying Differences in Large Series of Metabolomic Samples Analyzed by GC/MS. / Analytical Chemistry 2004, 76:1738鈥?745. CrossRef
3. Tikunov Y, Lommen A, de Vos CH, Verhoeven HA, Bino RJ, Hall RD, Bovy AG: A novel approach for nontargeted data analysis for metabolomics. Large-scale profiling of tomato fruit volatiles. / Plant Physiol 2005, 139:1125鈥?137. CrossRef
4. Smith CA, Want EJ, 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鈥?87. CrossRef
5. Xia J, Psychogios N, Young N, Wishart DS: MetaboAnalyst: a web server for metabolomic data analysis and interpretation. / Nucleic Acids Res 2009, 37:W652鈥?60. CrossRef
6. Pluskal T, Castillo S, Villar-Briones A, Oresic M: MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. / BMC Bioinformatics 2010, 11:395. CrossRef
7. Katajamaa M, Oresic M: Processing methods for differential analysis of LC/MS profile data. / BMC Bioinformatics 2005, 6:179. CrossRef
8. Katajamaa M, Oresic M: Data processing for mass spectrometry-based metabolomics. / J Chromatogr A 2007, 1158:318鈥?28. CrossRef
9. Scheltema R, Decuypere S, Dujardin J, Watson D, Jansen R, Breitling R: Simple data-reduction method for high-resolution LC-MS data in metabolomics. / Bioanalysis 2009, 1:1551鈥?557. CrossRef
10. Tautenhahn R, B枚ttcher C, Neumann S: Annotation of LC/ESI-MS Mass Signals. In / Bioinformatics Research and Development. / Volume 4414. Edited by: Hochreiter S, Wagner R. Springer Berlin/Heidelberg; 2007:371鈥?80. Lecture Notes in Computer Science CrossRef
11. Bocker S, Letzel MC, Liptak Z, Pervukhin A: SIRIUS: decomposing isotope patterns for metabolite identification. / Bioinformatics 2009, 25:218鈥?24. CrossRef
12. Jaitly N, Mayampurath A, Littlefield K, Adkins JN, Anderson GA, Smith RD: Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data. / BMC Bioinformatics 2009, 10:87. CrossRef
13. Horn DM, Zubarev RA, McLafferty FW: Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. / J Am Soc Mass Spectrom 2000, 11:320鈥?32. CrossRef
14. Storey J: False discovery rates. In / International Encyclopedia of Statistical Science. 1st edition. Edited by: Lovric M. Springer; 2011:1673.
15. Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, Hau DD, Psychogios N, Dong E, Bouatra S, / et al.: HMDB: a knowledgebase for the human metabolome. / Nucl Acids Res 2009, 37:D603鈥?10. CrossRef
16. Smith CA, Maille GO, Want EJ, Qin C, Trauger SA, Brandon TR, Custodio DE, Abagyan R, Siuzdak G: METLIN: A Metabolite Mass Spectral Database. / Therapeutic Drug Monitoring 2005, 27:747鈥?51. CrossRef
17. Fahy E, Sud M, Cotter D, Subramaniam S: LIPID MAPS online tools for lipid research. / Nucleic Acids Res 2007, 35:W606鈥?12. CrossRef
18. Cui Q, Lewis IA, Hegeman AD, Anderson ME, Li J, Schulte CF, Westler WM, Eghbalnia HR, Sussman MR, Markley JL: Metabolite identification via the Madison Metabolomics Consortium Database. / Nat Biotechnol 2008, 26:162鈥?64. CrossRef
19. McNaught AD, Wilkinson A: / IUPAC:Compendium of Chemical Terminology. 2nd edition. Oxford:Blackwell Science; 1997.
20. Huang N, Siegel M, Kruppa G, Laukien F: Automation of a Fourier transform ion cyclotron resonance mass spectrometer for acquisition, analysis, and e-mailing of high-resolution exact-mass electrospray ionization mass spectral data. / Journal of the American Society for Mass Spectrometry 1999, 10:1166鈥?173. CrossRef
21. Keller BO, Sui J, Young AB, Whittal RM: Interferences and contaminants encountered in modern mass spectrometry. / Analytica Chimica Acta 2008, 627:71鈥?1. CrossRef
22. Tautenhahn R, B枚ttcher C, Neumann S: / Annotation of LC/ESI-MS Mass Signals in Bioinformatics Research and Development. / Volume 4414. Edited by: Hochreiter S, Wagner R. Springer Berlin/Heidelberg; 2007:371鈥?80. - 作者单位：Rency S Varghese (1)
Bin Zhou (1)
Mohammad R Nezami Ranjbar (1) (2)
Yi Zhao (3)
Habtom W Ressom (1)
1. Department of Oncology, Georgetown University, Kragujevac, DC, USA
2. Department of Electrical and Computer Engineering, Virginia Tech, Falls Church, VA, USA
3. Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University, Kragujevac, DC, USA
文摘
Background Analysis of multiple LC-MS based metabolomic studies is carried out to determine overlaps and differences among various experiments. For example, in large metabolic biomarker discovery studies involving hundreds of samples, it may be necessary to conduct multiple experiments, each involving a subset of the samples due to technical limitations. The ions selected from each experiment are analyzed to determine overlapping ions. One of the challenges in comparing the ion lists is the presence of a large number of derivative ions such as isotopes, adducts, and fragments. These derivative ions and the retention time drifts need to be taken into account during comparison. Results We implemented an ion annotation-assisted method to determine overlapping ions in the presence of derivative ions. Following this, each ion is represented by the monoisotopic mass of its cluster. This mass is then used to determine overlaps among the ions selected across multiple experiments. Conclusion The resulting ion list provides better coverage and more accurate identification of metabolites compared to the traditional method in which overlapping ions are selected on the basis of individual ion mass.