Figure 1.

This protocol and the MetaboTools provide comprehensive support for the integration of extracellular metabolomic data and for the analysis and phenotypic stratification of metabolic models. The workflow captures the integration of processed and annotated metabolomic data sets, the generation of contextualized submodels, and the computational model analysis to distinguish metabolic phenotypes. Each part of the workflow is discussed in detail in the protocol and supported by the MetaboTools Matlab functions. The tutorials (Supplementary Tutorial I, II) demonstrate two use-cases of the workflow and MetaboTools.