The task in the critical assessment of small molecule identification (CASMI) contest category 2 was to determine the identification of (initially) unknown compounds for which high-resolution tandem mass spectra were published. We focused on computer-assisted methods that tried to correctly identify the compound automatically and entered the contest with MetFrag and MetFusion to score candidate structures retrieved from the PubChem structure database. MetFrag was combined with the metabolite-likeness score, which helped to improve the performance for the natural product challenges. We present the results, discuss the performance, and give details of how to interpret the MetFrag and MetFusion output.
References
[1]
Wolf, S.; Schmidt, S.; Müller-Hannemann, M.; Neumann, S. In silico fragmentation for computer assisted identification of metabolite mass spectra. BMC Bioinforma. 2010, 11, 148, doi:10.1186/1471-2105-11-148.
[2]
Schymanski, E.L.; Gallampois, C.M.J.; Krauss, M.; Meringer, M.; Neumann, S.; Schulze, T.; Wolf, S.; Brack, W. Consensus structure elucidation combining GC/EI-MS, structure generation, and calculated properties. Anal. Chem. 2012, 84, 3287–3295, doi:10.1021/ac203471y.
[3]
Bolton, Evan E.; Wang, Y.; Thiessen, Paul A.; Bryant, Stephen H.; Wheeler, Ralph A.; Spellmeyer, David C. Chapter 12 PubChem: Integrated Platform of Small Molecules and Biological Activities. Elsevier 2008, 4, 217–241.
[4]
Horai, H.; Arita, M.; Kanaya, S.; Nihei, Y.; Ikeda, T.; Suwa, K.; Ojima, Y.; Tanaka, K.; Tanaka, S.; Aoshima, K.; et al. MassBank: A public repository for sharing mass spectral data for life sciences. J. Mass. Spectrom. 2010, 45, 703–714, doi:10.1002/jms.1777.
[5]
Gerlich, M.; Neumann, S. MetFusion: Integration of compound identification strategies. J. Mass Spectrom. 2013, 48, 291–298, doi:10.1002/jms.3123.
[6]
Smith, C.; Want, E.; 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, 779–787, doi:10.1021/ac051437y.
[7]
Kazmi, S.; Ghosh, S.; Shin, D.; Hill, D.; Grant, D. Alignment of high resolution mass spectra: Development of a heuristic approach for metabolomics. Metabolomics 2006, 2, 75–83, doi:10.1007/s11306-006-0021-7.
[8]
Heller, S.; McNaught, A.; Stein, S.; Tchekhovskoi, D.; Pletnev, I. InChI-the worldwide chemical structure identifier standard. J. Cheminf. 2013, 5, 7, doi:10.1186/1758-2946-5-7.
[9]
Bolton, E.E.; Wang, Y.; Thiessen, P.A.; Bryant, S.H.; Wheeler, R.A.; Spellmeyer, D.C. Chapter 12 PubChem: Integrated platform of small molecules and biological activities. Ann. Rep. Comput. Chem. 2008, 4, 217–241, doi:10.1016/S1574-1400(08)00012-1.
[10]
Kind, T.; Fiehn, O. Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry. BMC Bioinformatics 2007, 8, 105, doi:10.1186/1471-2105-8-105.
[11]
Peironcely, J.E.; Reijmers, T.; Coulier, L.; Bender, A.; Hankemeier, T. Understanding and classifying metabolite space and metabolite-likeness. PLoS One 2011, 6, e28966.
[12]
Liaw, A.; Wiener, M. Classification and regression by randomforest. R News 2002, 2, 18–22.
Irwin, J.J.; Sterling, T.; Mysinger, M.M.; Bolstad, E.S.; Coleman, R.G. ZINC: A free tool to discover chemistry for biology. J. Chem. Inf. Model 2012, 52, 1757–1768, doi:10.1021/ci3001277.
[15]
Steinbeck, C.; Han, Y.; Kuhn, S.; Horlacher, O.; Luttmann, E.; Willighagen, E. The chemistry development kit (CDK): An open-source java library for chemo-and bioinformatics. J. Chem. Inf. Comput. Sci. 2003, 43, 493–500, doi:10.1021/ci025584y.
[16]
Schymanski, E.L.; Neumann, S. CASMI: And the winner is …. Metabolites 2013, 3, 412–439, doi:10.3390/metabo3020412.
[17]
Allwood, J.W.; Weber, R.J.; Zhou, J.; He, S.; Viant, M.R.; Dunn, W.B. CASMI–The small molecule identification process from a Birmingham perspective. Metabolites 2013, 3, 397–411, doi:10.3390/metabo3020397.
[18]
Gerlich, M.; Neumann, S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 27 1999, 1, 29–34.
[19]
Meringer, M.; Schymanski, E.L. Small molecule identification with MOLGEN and mass spectrometry. Metabolites 2013, 3, 440–462, doi:10.3390/metabo3020440.
