Protein in the water tends to form scum on the surface when aerated. The protein tends to stabilise the surface tension film of the bubbles.
Protein skimmers work by injecting a fine stream of bubbles into a vertical column of tank water. The scum forms on the surface, and as more and more bubbles come up the scum thickens until it is high enough to fall over the edge of the column into a waiting collector. Thus removing the protein.
As to how you would fit that into any particular set up is difficult to say without seeing it.