mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data

Chokkathukalam, A., Jankevics, A., Creek, D.J., Achcar, F., Barrett, M.P. and Breitling, R. (2013) mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data. Bioinformatics, 29(2), pp. 281-283. (doi:10.1093/bioinformatics/bts674) (PMID:23162054) (PMCID:PMC3546800)

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Abstract

Motivation: Stable isotope-labelling experiments have recently gained increasing popularity in metabolomics studies, providing unique insights into the dynamics of metabolic fluxes, beyond the steady-state information gathered by routine mass spectrometry. However, most liquid chromatography–mass spectrometry data analysis software lacks features that enable automated annotation and relative quantification of labelled metabolite peaks. Here, we describe mzMatch–ISO, a new extension to the metabolomics analysis pipeline mzMatch.R.

Results: Targeted and untargeted isotope profiling using mzMatch–ISO provides a convenient visual summary of the quality and quantity of labelling for every metabolite through four types of diagnostic plots that show (i) the chromatograms of the isotope peaks of each compound in each sample group; (ii) the ratio of mono-isotopic and labelled peaks indicating the fraction of labelling; (iii) the average peak area of mono-isotopic and labelled peaks in each sample group; and (iv) the trend in the relative amount of labelling in a predetermined isotopomer. To aid further statistical analyses, the values used for generating these plots are also provided as a tab-delimited file. We demonstrate the power and versatility of mzMatch–ISO by analysing a 13C-labelled metabolome dataset from trypanosomal parasites.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Achcar, Dr Fiona and Chokkathukalam, Dr Achuthanunni and Breitling, Professor Rainer and Barrett, Professor Michael and Creek, Dr Darren
Authors: Chokkathukalam, A., Jankevics, A., Creek, D.J., Achcar, F., Barrett, M.P., and Breitling, R.
College/School:College of Medical Veterinary and Life Sciences
College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
College of Medical Veterinary and Life Sciences > Institute of Molecular Cell and Systems Biology
Journal Name:Bioinformatics
Publisher:Oxford University Press
ISSN:1367-4803
Published Online:17 November 2012
Copyright Holders:Copyright © 2012 The Authors
First Published:First published in Bioinformatics 29(2):281-283
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
371793The Wellcome Centre for Molecular Parasitology ( Core Support )J BarryWellcome Trust (WELLCOME)073990/Z/03/BIII - BACTERIOLOGY
371796The Wellcome Centre for Molecular Parasitology ( Core Support )Andrew WatersWellcome Trust (WELLCOME)085349/Z/08/ZIII - PARASITOLOGY
371798The Wellcome Centre for Molecular Parasitology ( Core Support )Andrew WatersWellcome Trust (WELLCOME)085349/B/08/ZIII - PARASITOLOGY