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
<p>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.</p> <p>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.</p>
Item Type: | Articles |
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Status: | Published |
Refereed: | Yes |
Glasgow Author(s) Enlighten ID: | Chokkathukalam, Dr Achuthanunni and Achcar, Dr Fiona and Breitling, Professor Rainer and Creek, Dr Darren and Barrett, Professor Michael |
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 > School of Infection & Immunity College of Medical Veterinary and Life Sciences > School of Molecular Biosciences |
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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