Protein-protein interactions play an essential role in all molecular processes within the cell. Complexome profiling is one of the most recent ‘omics’ tools to get comprehensive insight into protein-protein interactions and protein complexes. Given that it generates a large number of samples, it requires very long measuring times and high costs. This project aims to combine peptide isotopic labelling with complexome profiling to enable pooling of samples before the analysis, reducing measuring times and costs several fold. This implementation may foster a comprehensive use of complexome profiling in basic science and clinical diagnostics, which will advance our understanding of function and dysfunction of macromolecular complexes associated with human metabolic diseases.