We present results of the SIRIUS 2 submission to the 2012 CASMI contest. Only results for Category 1 (molecular formula identification) were submitted. The SIRIUS method and the parameters used are briefly described, followed by detailed analysis of the results and a discussion of cases where SIRIUS 2 was unable to come up with the correct molecular formula. SIRIUS 2 returns consistently high quality results, with the exception of fragmentation pattern analysis of time-of-flight data. We then discuss possibilities for further improving SIRIUS 2 in the future.
References
[1]
McLafferty, F.W.; Zhang, M.Y.; Stauffer, D.B.; Loh, S.Y. Comparison of algorithms and databases for matching unknown mass spectra. J. Am. Soc. Mass Spectrom. 1998, 9, 92–95, doi:10.1016/S1044-0305(97)00235-3.
[2]
Oberacher, H.; Pavlic, M.; Libiseller, K.; Schubert, B.; Sulyok, M.; Schuhmacher, R.; Csaszar, E.; K？feler, H.C. On the inter-instrument and inter-laboratory transferability of a tandem mass spectral reference library: 1. Results of an Austrian multicenter study. J. Mass Spectrom. 2009, 44, 485–493, doi:10.1002/jms.1545.
[3]
Gerlich, M.; Neumann, S. MetFusion: Integration of compound identification strategies. J. Mass Spectrom. 2013, 48, 291–298, doi:10.1002/jms.3123.
[4]
Kangas, L.J.; Metz, T.O.; Isaac, G.; Schrom, B.T.; Ginovska-Pangovska, B.; Wang, L.; Tan, L.; Lewis, R.R.; Miller, J.H. In silico identification software (ISIS): A machine learning approach to tandem mass spectral identification of lipids. Bioinformatics 2012, 28, 1705–1713, doi:10.1093/bioinformatics/bts194.
[5]
Heinonen, M.; Shen, H.; Zamboni, N.; Rousu, J. Metabolite identification and molecular fingerprint prediction via machine learning. Bioinformatics 2012, 28, 2333–2341, doi:10.1093/bioinformatics/bts437.
[6]
B？cker, S.; Letzel, M.; Lipták, Z.; Pervukhin, A. SIRIUS: Decomposing isotope patterns for metabolite identification. Bioinformatics 2009, 25, 218–224, doi:10.1093/bioinformatics/btn603.
[7]
Rasche, F.; Friedrich-Schiller-Universit？t Jena, Germany. Analysis of Metabolite Tandem Mass Spectra. Diplomarbeit, 2008.
[8]
B？cker, S.; Letzel, M.; Lipták, Z.; Pervukhin, A. Decomposing Metabolomic Isotope Patterns. In Proceedings of Workshop on Algorithms in Bioinformatics (WABI 2006), Zurich, Switzerland, 11-13 September 2006; Springer: Berlin, Germany, 2006; Volume 4175. , pp. 12–23.
[9]
B？cker, S.; Lipták, Z.; Martin, M.; Pervukhin, A.; Sudek, H. DECOMP—from interpreting Mass Spectrometry peaks to solving the Money Changing Problem. Bioinformatics 2008, 24, 591–593, doi:10.1093/bioinformatics/btm631.
[10]
B？cker, S.; Rasche, F. Towards de novo identification of metabolites by analyzing tandem mass spectra. Bioinformatics 2008, 24, I49–I55, doi:10.1093/bioinformatics/btn270.
[11]
Rasche, F.; Svato？, A.; Maddula, R.K.; B？ttcher, C.; B？cker, S. Computing fragmentation trees from tandem mass spectrometry data. Anal. Chem. 2011, 83, 1243–1251, doi:10.1021/ac101825k.
[12]
Rasche, F.; Scheubert, K.; Hufsky, F.; Zichner, T.; Kai, M.; Svato？, A.; B？cker, S. Identifying the unknowns by aligning fragmentation trees. Anal. Chem. 2012, 84, 3417–3426, doi:10.1021/ac300304u.
[13]
Senior, J. Partitions and their representative graphs. Am. J. Math. 1951, 73, 663–689, doi:10.2307/2372318.
[14]
Kanehisa, M.; Goto, S.; Hattori, M.; Aoki-Kinoshita, K.F.; Itoh, M.; Kawashima, S.; Katayama, T.; Araki, M.; Hirakawa, M. From genomics to chemical genomics: New developments in KEGG. Nucleic Acids Res. 2006, 34, D354–D357, doi:10.1093/nar/gkj102.
[15]
Rauf, I.; Rasche, F.; Nicolas, F.; B？cker, S. Finding Maximum Colorful Subtrees in Practice. In Proceedings of Research in Computational Molecular Biology (RECOMB 2012), Barcelona, Spain, 21-24 April 2012; Springer: Berlin, Germany, 2012; Volume 7262. , pp. 213–223.
[16]
SIRIUS2. Available online: http://bio.informatik.uni-jena.de/sirius2/ (accessed on 7 June 2013).
[17]
Stravs, M.A.; Schymanski, E.L.; Singer, H.P.; Hollender, J. Automatic recalibration and processing of tandem mass spectra using formula annotation. J. Mass Spectrom. 2013, 48, 89–99, doi:10.1002/jms.3131.
[18]
Hufsky, F.; Rempt, M.; Rasche, F.; Pohnert, G.; B？cker, S. De novo analysis of electron impact mass spectra using fragmentation trees. Anal. Chim. Acta 2012, 739, 67–76, doi:10.1016/j.aca.2012.06.021.
