Selivanov Vitaly A, Marin Silvia, Tarragó-Celada Josep, Lane Andrew N, Higashi Richard M, Fan Teresa W-M, de Atauri Pedro, Cascante Marta
Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain.
Institute of Biomedicine of Universitat de Barcelona (IBUB), Barcelona, Spain.
Methods Mol Biol. 2020;2088:271-298. doi: 10.1007/978-1-0716-0159-4_12.
Stable isotope-resolved metabolomics (SIRM), based on the analysis of biological samples from living cells incubated with artificial isotope enriched substrates, enables mapping the rates of biochemical reactions (metabolic fluxes). We developed software supporting a workflow of analysis of SIRM data obtained with mass spectrometry (MS). The evaluation of fluxes starting from raw MS recordings requires at least three steps of computer support: first, extraction of mass spectra of metabolites of interest, then correction of the spectra for natural isotope abundance, and finally, evaluation of fluxes by simulation of the corrected spectra using a corresponding mathematical model. A kinetic model based on ordinary differential equations (ODEs) for isotopomers of metabolites of the corresponding biochemical network supports the final part of the analysis, which provides a dynamic flux map.
稳定同位素分辨代谢组学（SIRM）基于对用人工富集同位素底物孵育的活细胞生物样品的分析，能够绘制生化反应速率（代谢通量）图谱。我们开发了支持对通过质谱（MS）获得的SIRM数据进行分析工作流程的软件。从原始MS记录开始评估通量至少需要三步计算机支持：首先，提取感兴趣代谢物的质谱，然后校正质谱的天然同位素丰度，最后，使用相应的数学模型通过模拟校正后的质谱来评估通量。基于相应生化网络代谢物同位素异构体的常微分方程（ODE）的动力学模型支持分析的最后一部分，该部分提供动态通量图。
