Detecting and profiling molecular complexes

A method of detecting one or more complexes comprising a first protein and one or more second proteins, the method comprising the steps of:

• providing for each of the one or more complexes a cleaving probe specific for the first protein in each of the one or more complexes, each cleaving probe comprising a cleavage-inducing moiety;
• providing one or more binding compounds specific for the second protein of each of the one or more complexes, such that each binding compound comprises one or more molecular tags each attached thereto by a cleavable linkage, and such that the one or more molecular tags attached to different binding compounds have different separation characteristics so that upon separation molecular tags from different binding compounds form distinct peaks in a separation profile;
• mixing the cleaving probes, the binding compounds, and the one or more complexes such that cleaving probes specifically bind to first proteins of the complexes and binding compounds specifically bind to the second proteins of the complexes and such that cleavable linkages of the binding compounds are within the effective proximity of cleavage-inducing moieties of the cleaving probes so that molecular tags are released;
• and
• separating and identifying the released molecular tags to determine the presence or absence or the amount of the one or more complexes of proteins.