The dynamic assembly of multi-protein complexes is a central mechanism of many cell signalling pathways. This process is key to maintaining the spatiotemporal specificity required for an accurate, yet adaptive response to rapidly changing cellular conditions. However, there is still a lack of experimental techniques that can facilitate the specific and sensitive deconvolution of multi-molecular signalling complexes. Here we describe a novel technique that overcomes many of these existing limitations and allows the specific isolation and downstream proteomic characterisation of any two interacting proteins, to the exclusion of their individual moieties and competing binding partners (Croucher et al., Science Signaling, In Press). This novel isolation technique is achieved through the combination of a protein-fragment complementation assay and affinity purification with a conformation specific nanobody, which we have termed Bimolecular Complementation Affinity Purification (BiCAP). We demonstrate the utility of this approach through characterisation of the specific interactome of ERBB2 in the form of a homodimer and heterodimers with either EGFR or ERBB3. Through this analysis we have observed dimer-specific interaction patterns for key adaptor proteins and identified a number of novel interacting partners. Functional analysis for one novel interaction has led to the identification of a non-canonical mechanism of ERK activation that is specific to the ERBB2:ERBB3 heterodimer, which acts through FAM59A to induce ERK activation in breast cancer cells.