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An overview of tools, software, and methods for natural product fragment and mass spectral analysis

Aurélien F. A. Moumbock
  • Corresponding author
  • Albert-Ludwigs-Universität Freiburg, Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Hermann-Herder-Str. 9, 79104 Freiburg, Germany
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/ Fidele Ntie-Kang
  • Corresponding author
  • Department of Chemistry, University of Buea, P. O. Box 63 Buea, Buea, Cameroon
  • Department of Pharmaceutical Chemistry, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck Str. 4, 06120 Halle (Saale), Germany
  • Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Technická 5 166 28 Prague 6, Dejvice, Czech Republic
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/ Sergi H. Akone
  • Faculty of Science, Department of Chemistry, University of Douala, P. O. Box 24157, Douala, Cameroon
  • Institute for Pharmaceutical Biology and Biotechnology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, Geb. 26.23, 40225 Düsseldorf, Germany
  • Other articles by this author:
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/ Jianyu Li
  • Albert-Ludwigs-Universität Freiburg, Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Hermann-Herder-Str. 9, 79104 Freiburg, Germany
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Mingjie Gao
  • Albert-Ludwigs-Universität Freiburg, Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Hermann-Herder-Str. 9, 79104 Freiburg, Germany
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Kiran K. Telukunta
  • Albert-Ludwigs-Universität Freiburg, Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Hermann-Herder-Str. 9, 79104 Freiburg, Germany
  • IT, International Solar Energy Society eV, Wiesentalstr 50, Freiburg, Baden-Württemberg, Germany
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Stefan Günther
  • Albert-Ludwigs-Universität Freiburg, Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Hermann-Herder-Str. 9, 79104 Freiburg, Germany
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Published Online: 2019-06-28 | DOI: https://doi.org/10.1515/psr-2018-0126


One major challenge in natural product (NP) discovery is the determination of the chemical structure of unknown metabolites using automated software tools from either GC–mass spectrometry (MS) or liquid chromatography–MS/MS data only. This chapter reviews the existing spectral libraries and predictive computational tools used in MS-based untargeted metabolomics, which is currently a hot topic in NP structure elucidation. We begin by focusing on spectral databases and the general workflow of MS annotation. We then describe software and tools used in MS, particularly those used to predict fragmentation patterns, mass spectral classifiers, and tools for fragmentation trees analysis. We then round up the chapter by looking at more advanced approaches implemented in tools for competitive fragmentation modeling and quantum chemical approaches.

Keywords: cheminformatics; fragment analysis; drug discovery; natural products; software


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About the article

Aurélien F. A. Moumbock, Fidele Ntie-Kang, and Sergi H. Akone These authors contributed equally and could be considered as joint first authors.

Published Online: 2019-06-28

Citation Information: Physical Sciences Reviews, Volume 4, Issue 9, 20180126, ISSN (Online) 2365-659X, DOI: https://doi.org/10.1515/psr-2018-0126.

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