MS/MS DATA IMPROVES AUTOMATED DETERMINATION OF MOLECULAR FORMULAS BY MASS SPECTROMETRY Markus Meringer †, 1 , Stefan Reinker ‡ , Juan Zhang ‡ , Alban Muller ‡ † German Aerospace Center (DLR), 5 M¨ unchener Straße 20, D–82234 Oberpfaffenhofen–Wessling, Germany ‡ Novartis Institutes for BioMedical Research (NIBR), Postfach, Novartis Campus, CH–4002 Basel, Switzerland 10 March 24, 2010 Keywords: Tandem MS, Orbitrap, Structure Elucidation, Algorithm, Biomarker, Natural Product. Abstract. In theory, the molecular formula of an unknown com- pound can be calculated from its exact molecular mass. However, even with highly accurate modern mass spectrometers with an ac- curacy of 1 ppm or lower, it is generally not possible to determine the molecular formula uniquely from measurements. Intensities of isotopic peaks are typically used as additional information to nar- row down possible formulas associated with a mass spectrum (MS) peak, but this is not sufficient for larger compounds. Here, we introduce a method that takes information from frag- ment peak masses of the MS/MS into account to improve the re- liability of formula determination. Matchvalues that reflect the consistency with MS isotope peaks and MS/MS fragment patterns are computed for candidate molecular formulas. We demonstrate that these matchvalues outperform methods based on isotope peak intensities alone. In test cases with medium sized organic molecules (< 1000 u) the true molecular formula achieves the highest match- values using the MS/MS data. 1. Introduction When elucidating the molecular structure of an unknown compound, 15 one of the first steps is usually the determination of the molecular formula. One of the analytical key methods to determine the molecular formula of an unknown is mass spectrometry. In contrast to electron impact MS, soft ionization techniques tend to keep the molecular ion 1 Corresponding author e–mail markus.meringer@dlr.de, phone +49 8153 281446, fax +49 8153 281446 1