Strategies to label proteins, such as protein-stable isotope probing (SIP), and click chemistry approaches, such as bioorthogonal non-canonical amino acid tagging (BONCAT), are additional tools to identify and quantify the impact of microbial effectors on the metabolic activities and nutrient fluxes of microbiomes. Newly synthesized proteins in actively growing cells are detectable by incorporating labels, which cause a mass shift in the peptide spectra. Protein-SIP uses the incorporation of 2 H, 13 C, 15 N, or 18 O from respectively labeled substrates ,