Mass spectral similarity for untargeted metabolomics data analysis of complex mixtures

International Journal of Mass Spectrometry

Volumn 377, Issue 1, 2015, Pages 719-727

  Garg, Neha ^a   Kapono, Clifford A ^b   Lim, Yan Wei ^c   Koyama, Nobuhiro ^a,d   Vermeij, Mark J A ^e   Conrad, Douglas ^f   Rohwer, Forest ^c   Dorrestein, Pieter C ^a,b  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c SAN DIEGO STATE UNIVERSITY   (United States)

^d KITASATO UNIVERSITY   (Japan)

^e UNIVERSITY OF AMSTERDAM   (Netherlands)

^f UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

Complex mixtures; Cytoscape; Database search; Mass spectrometry; Molecular networking; Spectral matching

Indexed keywords

EID: 85028197479     PISSN: 13873806     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijms.2014.06.005     Document Type: Article

References (47)

1. A. Zhang, H. Sun, P. Wang, Y. Han, X. Wang, Modern analytical techniques in metabolomics analysis, Analyst 137 (2012) 293-300.
2. G. J. Patti, O. Yanes, G. Siuzdak, Innovation: metabolomics: the apogee of the omics trilogy, Nat. Rev. Mol. Cell Biol. 13 (2012) 263-269.
3. E. Dudley, M. Yousef, Y. Wang, W. J. Griffiths, Targeted metabolomics and mass spectrometry, Adv. Protein Chem. Struct. Biol. 80 (2010) 45-83.
4. I. D. Wilson, J. K. Nicholson, J. Castro-Perez, J. H. Granger, K. A. Johnson, B. W. Smith, R. S. Plumb, High resolution "ultra performance" liquid chromatography coupled to oa-TOF mass spectrometry as a tool for differential metabolic pathway profiling in functional genomic studies, J. Proteome Res. 4 (2005) 591-598.
5. A. H. Zhang, P. Wang, H. Sun, G. L. Yan, Y. Han, X. J. Wang, High-throughput ultraperformance liquid chromatography-mass spectrometry characterization of metabolites guided by a bioinformatics program, Mol. Biosyst. 9 (2013) 2259-2265.
6. R. G. Kay, B. Gregory, P. B. Grace, S. Pleasance, The application of ultraperformance liquid chromatography/tandem mass spectrometry to the detection and quantitation of apolipoproteins in human serum, Rapid Commun. Mass Spectrom. 21 (2007) 2585-2593.
7. E. Nagele, M. Vollmer, P. Horth, Two-dimensional nano-liquid chromatography-mass spectrometry system for applications in proteomics, J. Chromatogr. A 1009 (2003) 197-205.
8. M. Gaspari, G. Cuda, Nano LC-MS/MS: a robust setup for proteomic analysis, Methods Mol. Biol. 790 (2011) 115-126.
9. B. Brugger, G. Erben, R. Sandhoff, F. T. Wieland, W. D. Lehmann, Quantitative analysis of biological membrane lipids at the low picomole level by nanoelectrospray ionization tandem mass spectrometry, Proc. Natl. Acad. Sci. U. S. A. 94 (1997) 2339-2344.
10. R. Korner, M. Wilm, K. Morand, M. Schubert, M. Mann, Nano electrospray combined with a quadrupole ion trap for the analysis of peptides and protein digests, J. Am. Soc. Mass Spectrom. 7 (1996) 150-156.
11. Z. Takáts, J. M. Wiseman, B. Gologan, R. G. Cooks, Mass spectrometry sampling under ambient conditions with desorption electrospray ionization, Science 306 (2004) 471-473.
12. H. Chen, Z. Pan, N. Talaty, D. Raftery, R. G. Cooks, Combining desorption electrospray ionization mass spectrometry and nuclear magnetic resonance for differential metabolomics without sample preparation, Rapid Commun. Mass Spectrom. 20 (2006) 1577-1584.
13. B. L. Nunn, S. A. Shaffer, A. Scherl, B. Gallis, M. Wu, S. I. Miller, D. R. Goodlett, Comparison of a Salmonella typhimurium proteome defined by shotgun proteomics directly on an LTQ-FT and by proteome pre-fractionation on an LCQ-DUO, Brief. Funct. Genomics Proteomics 5 (2006) 154-168.
14. A. Makarov, E. Denisov, O. Lange, S. Horning, Dynamic range of mass accuracy in LTQ Orbitrap hybrid mass spectrometer, J. Am. Soc. Mass Spectrom. 17 (2006) 977-982.
15. H. Wang, J. Liu, R. G. Cooks, Z. Ouyang, Paper spray for direct analysis of complex mixtures using mass spectrometry, Angew. Chemie. Int. Ed. Engl. 49 (2010) 877-880.
16. J. H. Gross, Direct analysis in real time - a critical review on DART-MS, Anal. Bioanal. Chem. 406 (2014) 63-80.
17. F. M. Fernandez, R. B. Cody, M. D. Green, C. Y. Hampton, R. McGready, S. Sengaloundeth, N. J. White, P. N. Newton, Characterization of solid counterfeit drug samples by desorption electrospray ionization and direct-analysis-inreal-time coupled to time-of-flight mass spectrometry, ChemMedChem 1 (2006) 702-705.
18. J. D. Watrous, P. C. Dorrestein, Imaging mass spectrometry in microbiology, Nat. Rev. Microbiol. 9 (2011) 683-694.
19. L. A. McDonnell, R. M. Heeren, Imaging mass spectrometry, Mass Spectrom. Rev. 26 (2007) 606-643.
20. E. H. Seeley, R. M. Caprioli, Molecular imaging of proteins in tissues by mass spectrometry, Proc. Natl. Acad. Sci. U. S. A. 105 (2008) 18126-18131.
21. C. De Bekker, P. B. Smith, A. D. Patterson, D. P. Hughes, Metabolomics reveals the heterogeneous secretome of two entomopathogenic fungi to ex vivo cultured insect tissues, PLoS ONE 8 (2013) e70609.
22. W. R. Wikoff, A. T. Anfora, J. Liu, P. G. Schultz, S. A. Lesley, E. C. Peters, G. Siuzdak, Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites, Proc. Natl. Acad. Sci. U. S. A. 106 (2009) 3698-3703.
23. K. Ponnusamy, S. Lee, C. H. Lee, Time-dependent correlation of the microbial community and the metabolomics of traditional barley nuruk starter fermentation, Biosci. Biotechnol. Biochem. 77 (2013) 683-690.
24. M. Steinfath, D. Groth, J. Lisec, J. Selbig, Metabolite profile analysis: from raw data to regression and classification, Physiol. Plant 132 (2008) 150-161.
25. J. Xia, N. Psychogios, N. Young, D. S. Wishart, MetaboAnalyst: a web server for metabolomic data analysis and interpretation, Nucleic Acids Res. 37 (2009) W652-W660.
26. C. A. Smith, E. J. Want, G. O'Maille, R. Abagyan, G. Siuzdak, XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification, Anal. Chem. 78 (2006) 779-787.
27. M. Katajamaa, M. Oresic, Processing methods for differential analysis of LC/MS profile data, BMC Bioinform. 6 (2005) 179.
28. M. Katajamaa, J. Miettinen, M. Oresic, MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data, Bioinformatics 22 (2006) 634-636.
29. T. Pluskal, S. Castillo, A. Villar-Briones, M. Oresic, MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometrybased molecular profile data, BMC Bioinform. 11 (2010) 395.
30. C. D. Broeckling, I. R. Reddy, A. L. Duran, X. Zhao, L. W. Sumner, MET-IDEA: data extraction tool for mass spectrometry-based metabolomics, Anal. Chem. 78 (2006) 4334-4341.
31. C. A. Smith, G. O'Maille, E. J. Want, C. Qin, S. A. Trauger, T. R. Brandon, D. E. Custodio, R. Abagyan, G. Siuzdak, METLIN: a metabolite mass spectral database, Ther. Drug Monit. 27 (2005) 747-751.
32. R. Tautenhahn, K. Cho, W. Uritboonthai, Z. Zhu, G. J. Patti, G. Siuzdak, An accelerated workflow for untargeted metabolomics using the METLIN database, Nat. Biotechnol. 30 (2012) 826-828.
33. T. Kind, J. K. Meissen, D. Yang, F. Nocito, A. Vaniya, Y. S. Cheng, J. S. Vandergheynst, O. Fiehn, Qualitative analysis of algal secretions with multiple mass spectrometric platforms, J. Chromatogr. A 1244 (2012) 139-147.
34. T. Kind, K. H. Liu, Y. Lee Do, B. De Felice, J. K. Meissen, O. Fiehn, LipidBlast in silico tandem mass spectrometry database for lipid identification, Nat. Methods 10 (2013) 755-758.
35. S. E. Stein, Chemical substructure identification by mass spectral library searching, J. Am. Soc. Mass Spectrom. 6 (1995) 644-655.
36. D. S. Wishart, T. Jewison, A. C. Guo, M. Wilson, C. Knox, Y. Liu, Y. Djoumbou, R. Mandal, F. Aziat, E. Dong, S. Bouatra, I. Sinelnikov, D. Arndt, J. Xia, P. Liu, F. Yallou, T. Bjorndahl, R. Perez-Pineiro, R. Eisner, F. Allen, V. Neveu, R. Greiner, A. Scalbert, HMDB 3.0 - the human metabolome database in 2013, Nucleic Acids Res. 41 (2013) D801-D807.
37. H. Horai, M. Arita, S. Kanaya, Y. Nihei, T. Ikeda, K. Suwa, Y. Ojima, K. Tanaka, S. Tanaka, K. Aoshima, Y. Oda, Y. Kakazu, M. Kusano, T. Tohge, F. Matsuda, Y. Sawada, M. Y. Hirai, H. Nakanishi, K. Ikeda, N. Akimoto, T. Maoka, H. Takahashi, T. Ara, N. Sakurai, H. Suzuki, D. Shibata, S. Neumann, T. Iida, K. Funatsu, F. Matsuura, T. Soga, R. Taguchi, K. Saito, T. Nishioka, MassBank: a public repository for sharing mass spectral data for life sciences, J. Mass Spectrom. 45 (2010) 703-714.
38. V. V. Phelan, W. T. Liu, K. Pogliano, P. C. Dorrestein, Microbial metabolic exchange - the chemotype-to-phenotype link, Nat. Chem. Biol. 8 (2012) 26-35.
39. J. Watrous, P. Roach, T. Alexandrov, B. S. Heath, J. Y. Yang, R. D. Kersten, M. Van Der Voort, K. Pogliano, H. Gross, J. M. Raaijmakers, B. S. Moore, J. Laskin, N. Bandeira, P. C. Dorrestein, Mass spectral molecular networking of living microbial colonies, Proc. Natl. Acad. Sci. U. S. A. 109 (2012) E1743-E1752.
40. A. Guthals, J. D. Watrous, P. C. Dorrestein, N. Bandeira, The spectral networks paradigminhigh throughput mass spectrometry, Mol. Biosyst. 8 (2012) 2535-2544.
41. J. Y. Yang, L. M. Sanchez, C. M. Rath, X. Liu, P. D. Boudreau, N. Bruns, E. Glukhov, A. Wodtke, R. De Felicio, A. Fenner, W. R. Wong, R. G. Linington, L. Zhang, H. M. Debonsi, W. H. Gerwick, P. C. Dorrestein, Molecular networking as a dereplication strategy, J. Nat. Prod. 76 (2013) 1686-1699.
42. A. M. Frank, N. Bandeira, Z. Shen, S. Tanner, S. P. Briggs, R. D. Smith, P. A. Pevzner, Clustering millions of tandem mass spectra, J. Proteome Res. 7 (2008) 113-122.
43. L. M. Niemi, K. A. Stencel, M. J. Murphy, M. M. Schultz, Quantitative determination of antidepressants and their select degradates by liquid chromatography/electrospray ionization tandem mass spectrometry in biosolids destined for land application, Anal. Chem. 85 (2013) 7279-7286.
44. C. B. Archer, F. M. Cunningham, M. W. Greaves, Actions of platelet activating factor (PAF) homologues and their combinations on neutrophil chemokinesis and cutaneous inflammatory responses in man, J. Invest. Dermatol. 91 (1988) 82-85.
45. R. M. Kramer, G. M. Patton, C. R. Pritzker, D. Deykin, Metabolism of plateletactivating factor in human platelets. Transacylase-mediated synthesis of 1-O-alkyl-2-arachidonoyl-sn-glycero-3-phosphocholine, J. Biol. Chem. 259 (1984) 13316-13320.
46. M. Ohno, K. Fujita, H. Nakai, S. Kobayashi, K. Inoue, S. Nojima, An enantioselective synthesis of platelet-activating factors, their enantiomers, and their analogues from D- and L-tartaric acids, Chem. Pharm. Bull. (Tokyo) 33 (1985) 572-582.
47. M. E. Smoot, K. Ono, J. Ruscheinski, P. L. Wang, T. Ideker, Cytoscape 2.8: new features for data integration and network visualization, Bioinformatics 27 (2011) 431-432.