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. 2013 Jan 15;29(2):281-3.
doi: 10.1093/bioinformatics/bts674. Epub 2012 Nov 17.

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

Achuthanunni Chokkathukalam  1 , Andris Jankevics, Darren J Creek, Fiona Achcar, Michael P Barrett, Rainer Breitling
Affiliations

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

Achuthanunni Chokkathukalam et al. Bioinformatics. .

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 (13)C-labelled metabolome dataset from trypanosomal parasites.

Availability: mzMatch.R and mzMatch-ISO are available free of charge from http://mzmatch.sourceforge.net and can be used on Linux and Windows platforms running the latest version of R.

Contact: rainer.breitling@manchester.ac.uk.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
A representative example of an unlabelled peak (first peak) and its corresponding 13C-labelled peaks. These peaks elute at the same retention time, but their masses differ by the difference in the mass of heavy and light carbon. Filled circles show the number of labelled carbons that each peak represent
Fig. 2.
Fig. 2.
Representative example of the output PDF file generated by mzMatch–ISO (see text for details)
See this image and copyright information in PMC

References

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