Planta Med 2016; 82(S 01): S1-S381
DOI: 10.1055/s-0036-1596110
Abstracts
Georg Thieme Verlag KG Stuttgart · New York

Integration of molecular networking & in-silico MS/MS fragmentation: a novel dereplication strategy in natural products chemistry

PM Allard
1   School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, Quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland
,
T Péresse
2   Institut de Chimie des Substances Naturelles CNRS UPR 2301, University Paris-Saclay, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
,
J Bisson
3   Center for Natural Product Technologies, Department of Medicinal Chemistry and Pharmacognosy College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
,
K Gindro
4   Mycology and Biotechnology group, Institute for Plant Production Sciences IPS, Agroscope, Route de Duillier 50, P.O. Box 1012, 12 1260 Nyon, Switzerland Geneva 4, Switzerland
,
L Marcourt
1   School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, Quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland
,
VC Pham
5   Institute of Marine Biochemistry of the Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet road, Cau Giay, Hanoi, Vietnam
,
F Roussi
2   Institut de Chimie des Substances Naturelles CNRS UPR 2301, University Paris-Saclay, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
,
M Litaudon
2   Institut de Chimie des Substances Naturelles CNRS UPR 2301, University Paris-Saclay, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
,
JL Wolfender
1   School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, Quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland
› Author Affiliations
Further Information

Publication History

Publication Date:
14 December 2016 (online)

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Bioinformatics methods are perfectly suited to address the complexity and challenges encountered when studying living organisms (plants, bacteria, fungi etc.). Recently, various tools have been developed and are changing the face of natural products chemistry [1]. Molecular networking allows to organize large sets of tandem MS/MS data acquired according to the similarity of the fragmentation data, thus allowing to group detected metabolites in clusters of potentially similar structures [2]. Various in-silico fragmentation methods have also been developed and allow generating theoretical MS/MS spectra or explaining experimental ones [3]. Here, we propose a novel dereplication workflow based on the combination of molecular networking and an in-silico fragmentation database of more than 200000 natural products [4]. This dereplication procedure is generic and allows the user to navigate through the complexity of analysed extracts by visually depicting the dereplicated structures on the network. Furthermore, it was developed by combining free, open-source tools and the full in-silico fragmentation database was made available to all interested researchers, letting open the door for adaptations, transformations and improvements.

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In this presentation the elaboration of the dereplication strategy will be discussed and examples will show how it can be implemented in natural products research workflow.

Keywords: Molecular networking, in-silico fragmentation, natural products databases, dereplication strategy, bioinformatics, open-science.

References:

[1] Hufsky F, Scheubert K, Böcker S. New kids on the block: novel informatics methods for natural product discovery. Nat Prod Rep 2014; 31: 807 – 817

[2] Watrous J, Roach P, Alexandrov T, Heath B. S, Yang J. Y, Kersten R. D, Van der Voort M, Pogliano K, Gross H, Raaijmakers JM, Moore BS, Laskin J, Bandeira N, Dorrestein PC. Mass spectral molecular networking of living microbial colonies. Proc Natl Acad Sci USA 2012; 109: E1743-E1752

[3] Hufsky F, Böcker S. Mining molecular structure databases: Identification of small molecules based on fragmentation mass spectrometry data. Mass Spectrom Rev 2016; DOI: 10.1002/mas.21489

[4] Allard PM, Péresse T, Bisson J, Gindro K, Marcourt L, Pham VC, Roussi F, Litaudon M, Wolfender J-L. Integration of molecular networking and in-silico MS/MS fragmentation for natural products dereplication. Anal Chem 2016; 88: 3317 – 3323