Large amount of proteins are accumulated from dead algae, animals and also left over food particles or organic waste. This protein must be remove at once or it will be decomposed by bacteria (nitrogen cycle). Too much load of these proteins will result in an accumulation of harmful intermediate products such as NO3 as nitrification process takes places faster then denitrification. Protein skimmer is design to remove part of the protein and there for placing it after the filter as many Malaysian aquarists do is wrong.

The technical process is one where complex organic molecule compounds, which having opposing hydrophilic and a hydrophobic ends, orientate themselves accordingly between the air and water surface. The hydrophilic end extends towards the water and the hydrophobic end towards the air. These compounds, called surfactants, are strongly attracted to the water surface and they form a 'skin', such as the organic scum you see at the waters surface. This same organic layer can coat an air bubble as it rises within the protein skimmer and are collected as adsorbate in the ‘waste cup’. There are generally 2 types of protein skimmer;

Air Wood Driven Protein Skimmer
Small bubbles in protein skimmer are produce by pumping air using an air pump into a limewood or ceramic material. But regardless of material to be use, it must be change quite often to maintain a proper size and amount of bubbles.
Venturi Skimmer
Venturi skimmer produces air bubbles by pumping hard jet of water through a nozzle into a pipe drawing air in producing a fine mixture of air and water. Powerhead with at least 1000 to 2000 liters per hour have to be use to achieve ideal bubbles. As any other skimmer it needs to be clean regularly.

There are 3 major factors that determine the quality of a protein skimmer.

Bubble Size
If a bubbles size that is too small they will tend to rise not fast enough thus unable to remove protein effectively. On the other hand if a bubble size is too large it will rise too fast and shorten the contact time between water and air. Too large a bubble will also disturb the foam of adsorbate that is collected in the surface thereby causing it to fall down in to the water again.

Air/Water Flow rate
Air bubble exceeding water flow rates will cause many clean bubble to rise up in the ‘waste cup’ without collecting much protein. Water flow that exceed air bubbles then will cause the water to exit the skimmer to fast thus shortening the contact time between air and water.

Contact Time
Water that travel in the same direction as the air bubbles in a protein skimmer is call co-current and water that travel in the opposite direction of the air bubbles is call counter current. A counter current protein skimmer will create more contact time between air and water.