The Metabolomics Toolbox (MetTB): Analysis of Extracellular Metabolomic Data in the Context of the Metabolic Model

Extracellular metabolomic data provides a direct read-out of the intracellular metabolism and can be used to predict metabolic phenotypes. In our previous work, we demonstrated the generation of contextualized subnetworks from metabolic models constrained with semi-quantitative extracellular metabolomic data and their potential for predicting cellular metabolism ¹.

Our methods have been compiled to form the Metabolomics toolbox (MetTB), which is an extension to the COBRA toolbox ². MetTB contains more than 20 matlab functions supporting (1) the generation of condition-specific metabolic models from both quantitative and semi-quantitative extracellular metabolomic data, (2) the prediction of intracellular metabolic phenotypes and the outcome of systems perturbation, and allows (3) multi-omics integrative analysis in the context of the metabolic model. Along with the MetTB we provide a protocol that describes in detail the consecutive steps to the analysis of extracellular metabolomic data in the network context. We provide “recipes” that list, which input data is required to integrate quantitative and semi-quantitative metabolomic data into the network context, enabling scientists to take the requirements into account already in the planning phase of their experiments. Moreover, we provide tutorials directed to scientists with limited computational experience, which will enable them to interpret their own data in the model context, and guide through the reproduction of the results as presented in the primary work.

Taken together, the MetTB together with the accompanying tutorials and the protocol will make the interpretation of metabolomic data in the model context accessible to a large scientific community.

References:

1   Aurich, M.K. et al. Prediction of intracellular metabolic states from extracellular metabolomic data. Metabolomics 11, 603-619 (2015).

2   Schellenberger, J. et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 6, 1290-1307 (2011).