title: Molecular Formula Identification Using Isotope Pattern Analysis and Calculation of Fragmentation Trees.
abstract: We present the results of a fully automated de novo approach for identification of molecular formulas in the CASMI 2013 contest. Only results for Category 1 (molecular formula identification) were submitted. Our approach combines isotope pattern analysis and fragmentation pattern analysis and is completely independent from any (spectral and structural) database. We correctly identified the molecular formula for ten out of twelve challenges, being the best automated method competing in this category.
authors.affiliation: Lehrstuhl für Bioinformatik, Friedrich-Schiller-Universität Jena.
authors.forename: Kai
authors.initials: K
authors.lastname: Dührkop
authors.affiliation: Lehrstuhl für Bioinformatik, Friedrich-Schiller-Universität Jena.
authors.forename: Franziska
authors.initials: F
authors.lastname: Hufsky
authors.affiliation: Lehrstuhl für Bioinformatik, Friedrich-Schiller-Universität Jena.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Böcker
keywords: CASMI 2013; fragmentation patterns; fragmentation trees; isotope patterns; mass spectrometry; molecular formula identification; small molecules
references.citation: Bioinformatics. 2012 Jul 1;28(13):1705-13
references.pmid: 22592377
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D354-7
references.pmid: 16381885
references.citation: J Mass Spectrom. 2013 Mar;48(3):291-8
references.pmid: 23494783
references.citation: J Comput Biol. 2013 Apr;20(4):311-21
references.pmid: 23509858
references.citation: Metabolites. 2013 Jun 13;3(2):506-16
references.pmid: 24958003
references.citation: Anal Chem. 2012 Jan 3;84(1):283-9
references.pmid: 22111785
references.citation: Nat Rev Mol Cell Biol. 2004 Sep;5(9):763-9
references.pmid: 15340383
references.citation: Anal Chem. 2012 Apr 3;84(7):3417-26
references.pmid: 22390817
references.citation: BMC Bioinformatics. 2007 Mar 27;8:105
references.pmid: 17389044
references.citation: Bioinformatics. 2008 Feb 15;24(4):591-3
references.pmid: 18174179
references.citation: Bioinformatics. 2008 Aug 15;24(16):i49-i55
references.pmid: 18689839
references.citation: Nat Rev Mol Cell Biol. 2007 Feb;8(2):167-74
references.pmid: 17213843
references.citation: Bioinformatics. 2012 Sep 15;28(18):2333-41
references.pmid: 22815355
references.citation: Bioinformatics. 2009 Jan 15;25(2):218-24
references.pmid: 19015140
references.citation: Nat Biotechnol. 2008 Feb;26(2):162-4
references.pmid: 18259166
references.citation: Anal Chem. 2011 Feb 15;83(4):1243-51
references.pmid: 21182243