Protein quaternary assembly is central to many cellular processes. Several methods have been developed to detect and measure protein-protein interactions in model organisms. Some methods allow the identification of members of complexes but do not provide information on their spatial relationships. Other methods allow the detection of binary and direct interactions between physically associated proteins but do not provide direct insights into the larger quaternary architecture. In order to dissect the organisation of protein complexes both in terms of composition and spatial relationship among the subunits, it would be optimal to have a method that combines the two approaches described above. Here, we show that Protein-fragment Complementation Assay (PCA) can meet these needs. PCA is based on the association of complementary reporter fragments that reveals protein-protein interactions upon complementation. The reporter fragments are fused to the proteins of interest by a short peptide linker that determines the maximal physical distance at which fragments can complement. We found that we can modulate the length of the linkers to detect novel protein-protein interactions on a proteome-wide scale and more distant protein-protein interactions within large protein complexes. Overall, we show that this modified PCA can act as a molecular ruler for measuring protein-protein interactions and proximity in living cells.