From FrugalReef

Protein Skimming, also called foam fractionating, is a technique where thousands of tiny air bubbles are blown into a column of water. Organic molecules stick to the surface of the bubbles as they rise through the water, and a foam collects on the surface. Pressure from new bubbles forming below eventually forces the column of foam to rise and spill over into some kind of collection cup. The water evaporates out, leaving the organic proteins behind to be removed.

[edit] See Also

http://saltaquarium.about.com/cs/proteinskimmers/a/aa052200.htm