MetaNetter 2: a Cytoscape plugin for ab initio network analysis and metabolite feature classification

Burgess, K.E.V., Borutzki, Y., Rankin, N. , Daly, R. and Jourdan, S. (2017) MetaNetter 2: a Cytoscape plugin for ab initio network analysis and metabolite feature classification. Journal of Chromatography B, 1071, pp. 68-74. (doi:10.1016/j.jchromb.2017.08.015) (PMID:29030098) (PMCID:PMC5726607)

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Abstract

Metabolomics frequently relies on the use of high resolution mass spectrometry data. Classification and filtering of this data remain a challenging task due to the plethora of complex mass spectral artefacts, chemical noise, adducts and fragmentation that occur during ionisation and analysis. Additionally, the relationships between detected compounds can provide a wealth of information about the nature of the samples and the biochemistry that gave rise to them. We present a biochemical networking tool: MetaNetter 2 that is based on the original MetaNetter, a Cytoscape plugin that creates ab initio networks. The new version supports two major improvements: the generation of adduct networks and the creation of tables that map adduct or transformation patterns across multiple samples, providing a readout of compound relationships. We have applied this tool to the analysis of adduct patterns in the same sample separated under two different chromatographies, allowing inferences to be made about the effect of different buffer conditions on adduct detection, and the application of the chemical transformation analysis to both a single fragmentation analysis and an all-ions fragmentation dataset. Finally, we present an analysis of a dataset derived from anaerobic and aerobic growth of the organism Staphylococcus aureus demonstrating the utility of the tool for biological analysis.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Jourdan, Miss Sylvie and Burgess, Dr Karl and Borutzki, Ms Yasmin and Daly, Dr Ronan and Rankin, Dr Naomi
Authors: Burgess, K.E.V., Borutzki, Y., Rankin, N., Daly, R., and Jourdan, S.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
College of Medical Veterinary and Life Sciences > School of Medicine, Dentistry & Nursing
Journal Name:Journal of Chromatography B
Publisher:Elsevier
ISSN:1387-2273
Published Online:23 September 2017
Copyright Holders:Copyright © 2017 The Authors
First Published:First published in Journal of Chromatography B 1071: 68-74
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
623593Institutional Strategic Support Fund (ISSF)Anna DominiczakWellcome Trust (WELLCOTR)105614/Z/14/ZRI CARDIOVASCULAR & MEDICAL SCIENCES
593571Manipulation of cancer cells by nanotopography: strategies to control migration, proliferation and apoptosis (ISSF Catalyst Fund)Penelope TsimbouriWellcome Trust (WELLCOTR)097821/Z/11/ZRI MOLECULAR CELL & SYSTEMS BIOLOGY