The advantages of the affinity chromatography is that it is highly sensitive and even detect weak interactions  in proteins,  also it tests all the sample proteins equally for interaction with the coupled protein in the column. However sometimes false positive results also arises in the column which is due to highly specific interaction among proteins, even through they do not get interacted in the cellular system. Thus protein interaction studies cannot be fully dependent on affinity chromatography and hence requires some other methods in order to cross check and verify results obtained . The Affinity chromatography can also be associated with SDS-PAGE technique and Mass Spectroscopy in order to generate a high throughput data.

Figure 1: Diagrammatic representation of protein-protein interaction studies by affinity chromatography