title: mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  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.
  
  
  BACKGROUND
  rainer.breitling@manchester.ac.uk.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: College of Medical Veterinary and Life Sciences, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK.
authors.forename: Achuthanunni
authors.initials: A
authors.lastname: Chokkathukalam
authors.forename: Andris
authors.initials: A
authors.lastname: Jankevics
authors.forename: Darren J
authors.initials: DJ
authors.lastname: Creek
authors.forename: Fiona
authors.initials: F
authors.lastname: Achcar
authors.forename: Michael P
authors.initials: MP
authors.lastname: Barrett
authors.forename: Rainer
authors.initials: R
authors.lastname: Breitling
mesh_terms: D002247:Carbon Isotopes; D002853:Chromatography, Liquid / Q000379:methods; D013058:Mass Spectrometry / Q000379:methods*; D055442:Metabolome; D055432:Metabolomics; D012984:Software; D014346:Trypanosoma brucei brucei / Q000378:metabolism
chemical_list: D002247:Carbon Isotopes