title: Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling.
abstract: BACKGROUND
  The knowledge of metabolic pathways and fluxes is important to understand the adaptation of organisms to their biotic and abiotic environment. The specific distribution of stable isotope labelled precursors into metabolic products can be taken as fingerprints of the metabolic events and dynamics through the metabolic networks. An open-source software is required that easily and rapidly calculates from mass spectra of labelled metabolites, derivatives and their fragments global isotope excess and isotopomer distribution.
  
  
  RESULTS
  The open-source software "Least Square Mass Isotopomer Analyzer" (LS-MIDA) is presented that processes experimental mass spectrometry (MS) data on the basis of metabolite information such as the number of atoms in the compound, mass to charge ratio (m/e or m/z) values of the compounds and fragments under study, and the experimental relative MS intensities reflecting the enrichments of isotopomers in 13C- or 15 N-labelled compounds, in comparison to the natural abundances in the unlabelled molecules. The software uses Brauman's least square method of linear regression. As a result, global isotope enrichments of the metabolite or fragment under study and the molar abundances of each isotopomer are obtained and displayed.
  
  
  CONCLUSIONS
  The new software provides an open-source platform that easily and rapidly converts experimental MS patterns of labelled metabolites into isotopomer enrichments that are the basis for subsequent observation-driven analysis of pathways and fluxes, as well as for model-driven metabolic flux calculations.
authors.affiliation: Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
authors.forename: Zeeshan
authors.initials: Z
authors.lastname: Ahmed
authors.forename: Saman
authors.initials: S
authors.lastname: Zeeshan
authors.forename: Claudia
authors.initials: C
authors.lastname: Huber
authors.forename: Michael
authors.initials: M
authors.lastname: Hensel
authors.forename: Dietmar
authors.initials: D
authors.lastname: Schomburg
authors.forename: Richard
authors.initials: R
authors.lastname: Münch
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Eisenreich
authors.forename: Thomas
authors.initials: T
authors.lastname: Dandekar
mesh_terms: D000465:Algorithms; D007554:Isotopes; D016018:Least-Squares Analysis; D013058:Mass Spectrometry / Q000379:methods*; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D012984:Software
chemical_list: D007554:Isotopes