Schematic overview about the workflow of analysis. (A) Assimilation of heavy stable isotopes into the biomass of various species depends on the turnover and the interaction activity of the species. The incorporation of stable13C isotopes from a substrate can be used to pinpoint the metabolically active species within a consortium. The different incorporations are indicated by various amounts of label (gray-color scale). (B) After cell harvesting and protein extraction, samples were tryptically digested and analyzed by MS. The isotopologues shifted to a higher mass range due to their incorporation of heavy labeled carbon into the proteins. A higher level of incorporation indicates a faster growth rate and/or a primary role in the degradation of the labeled substrate within the food web. (C) The incorporation of heavy stable isotopes into peptides/proteins can be estimated using the HDPR. (D) Peptides can be used to obtain phylogenetic information (in case of unique peptides), for structural analysis, and for physiological information about the actual state of the microbial cells. (E) Based on this information, C-fluxes and food web structures can be elucidated and may further help to reconstruct the interaction of microbial communities.