Protein skimmers have been around for many years. If you’ve been to an ocean beach and seen foam at the edge of the water, you’ve seen protein foam. FYI protein skimming only happens in saltwater because saltwater is denser. Freshwater is 1.0000 while saltwater varies around 1.0235. This density allows extremely tiny bubbles to form and stay that way. Another thing that happens when air molecules rub against plastic, a static charge is applied to the bubbles.
Protein molecules are large, oily and hydrophobic or “fear water”. They attach to the surface of the microbubbles. Sticky bubbles combine to form foam that makes its way up into the collection cup where it breaks down into a dark, smelling liquid, aka skimmate. Think of your skimmer as a sewage treatment plant for your aquarium. Besides proteins, include a variety of fats, fatty acids, carbohydrates, metals such as copper and trace elements such as iodine. Particulates, phytoplankton bacteria and detritus are also removed. Iodine or iodide can be added as replacement element but DO NOT OVERDOSE. Corals cannot handle extra iodide.
To properly adjust your skimmer
Get a good water flow through your skimmer with the air completely off. The water level should be half way up the lower, wider cone under the collection cup. Then open your air adjusting valve until a white cloud begins inside and looks like milk. Tiny bubbles are better than larger bubbles. Remember that dirty/oily skimmers work much better than clean ones so don’t do more than rinse your skimmer when it gets super dirty. Skimmers only work when there is something in the tank to skim.
Many collections have a drain nipple to attach a drain hose. Either permanently plug the hole and manually empty the cup or attach a hose with valve in the line to drain the cup periodically. DO NOT allow the hose to run freely. Under certain conditions skimmers can start foaming wildly and fill a collection cup in seconds. With the valve closed the foam stays in the skimmer. With the hose open, a one gallon collection container will overflow on the floor in seconds and not stop.