A protein skimmer or foam fractionator is a device used mainly in saltwater aquarium to to remove organic compounds from the water before they break down into nitrogenous waste. Protein skimming is the only form of filtration that physically removes organic compounds before they begin to decompose, lightening the load on the biological filter and improving the water’s redox potential. Although the process of foam fractionation is commonly known for removal of waste from aquarium, it is, in fact, a rapidly developing chemical process used in the large-scale removal of contaminants from wastewater streams and the enrichment of solutions of biomolecules.

Protein skimmers can be classed in two ways depending on whether they operate by co-current flow or counter-current flow. In a co-current flow system, air is introduced at the bottom of the chamber and is in contact with the water as it rises upwards towards the collection chamber. In a counter-current system, air is forced into the system under pressure and moves against the flow of the water for a while before it rises up towards the collection cup. Because the air bubbles may be in contact with the water for a longer period in a counter-current flow system, protein skimmers of this type are considered by some to be more effective at removing organic wastes.

(Source: Extracted from http://en.wikipedia.org/wiki/Protein_skimmer)