Interactomics

For the bulk identification of protein interaction partners, we commonly apply co-immunoprecipitation/co-affinity purification together with quantitative mass spectrometry (Figure 1). For this, the protein of interest is precipitated from cells together with its interacting proteins, which are subsequently identified by mass spectrometry. Because such precipitates will also contain contaminants (e.g. unspecific binders to affinity beads, IgG beads, antibody,...), a control sample not containing the bait is needed. In the end, true interactors can be distuinguished from contaminants by looking at their respective abundances in both samples. While contaminants are equally present in both samples, specific interactors are enriched in the bait sample. For determining the proteins abundances different quantification strategies are available, both label-free (spectral count, MaxQuant-LFQ) and label-based (SILAC, DML) (see Quantitative Proteomics).