MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools

Ernst, M. et al. (2019) MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools. Metabolites, 9(7), 144. (doi:10.3390/metabo9070144) (PMID:31315242)

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Abstract

Metabolomics has started to embrace computational approaches for chemical interpretation of large data sets. Yet, metabolite annotation remains a key challenge. Recently, molecular networking and MS2LDA emerged as molecular mining tools that find molecular families and substructures in mass spectrometry fragmentation data. Moreover, in silico annotation tools obtain and rank candidate molecules for fragmentation spectra. Ideally, all structural information obtained and inferred from these computational tools could be combined to increase the resulting chemical insight one can obtain from a data set. However, integration is currently hampered as each tool has its own output format and efficient matching of data across these tools is lacking. Here, we introduce MolNetEnhancer, a workflow that combines the outputs from molecular networking, MS2LDA, in silico annotation tools (such as Network Annotation Propagation or DEREPLICATOR), and the automated chemical classification through ClassyFire to provide a more comprehensive chemical overview of metabolomics data whilst at the same time illuminating structural details for each fragmentation spectrum. We present examples from four plant and bacterial case studies and show how MolNetEnhancer enables the chemical annotation, visualization, and discovery of the subtle substructural diversity within molecular families. We conclude that MolNetEnhancer is a useful tool that greatly assists the metabolomics researcher in deciphering the metabolome through combination of multiple independent in silico pipelines.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Rogers, Dr Simon and Wandy, Dr Joe and Van Der Hooft, Mr Justin
Authors: Ernst, M., Kang, K. B., Caraballo-Rodríguez, A. M., Nothias, L.-F., Wandy, J., Chen, C., Wang, M., Rogers, S., Medema, M. H., Dorrestein, P. C., and van der Hooft, J. J.J.
College/School:College of Medical Veterinary and Life Sciences
College of Science and Engineering > School of Computing Science
Journal Name:Metabolites
Publisher:MDPI
ISSN:2218-1989
ISSN (Online):2218-1989
Copyright Holders:Copyright © 2019 by the authors
First Published:First published in Metabolites 9(7):144
Publisher Policy:Reproduced under a Creative Commons license

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