Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes

A. Rantanen (Corresponding Author), T. Mielikäinen, Juha Rousu, Hannu Maaheimo, Esko Ukkonen

    Research output: Contribution to journalArticleScientificpeer-review

    23 Citations (Scopus)

    Abstract

    Motivation: Flux estimation using isotopomer information of metabolites is currently the most reliable method to obtain quantitative estimates of the activity of metabolic pathways. However, the development of isotopomer measurement techniques for intermediate metabolites is a demanding task. Careful planning of isotopomer measurements is thus needed to maximize the available flux information while minimizing the experimental effort.

    Results: In this paper we study the question of finding the smallest subset of metabolites to measure that ensure the same level of isotopomer information as the measurement of every metabolite in the metabolic network. We study the computational complexity of this optimization problem in the case of the so-called positional enrichment data, give methods for obtaining exact and fast approximate solutions, and evaluate empirically the efficacy of the proposed methods by analyzing a metabolic network that models the central carbon metabolism of Saccharomyces cerevisiae.
    Original languageEnglish
    Pages (from-to)1198-1206
    Number of pages9
    JournalBioinformatics
    Volume22
    Issue number10
    DOIs
    Publication statusPublished - 2006
    MoE publication typeA1 Journal article-refereed

    Keywords

    • metabolites
    • metabolic flux analysis
    • isotopomer distribution
    • metabolic profiling
    • metabolomics

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