Yes. Protein skimmers remove nutrients from the aquarium water.

Aquarium Protein Skimmer by Dreadnaught426 is licensed under the  license.
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Many marine aquarium hobbyists like to make their own equipment, even protein skimmers. For some, the DIY approach saves money, appeals to the desire to build gear, and helps develop better understanding of saltwater aquariums. The endeavor requires careful planning and execution, particularly for a protein skimmer.
A protein skimmer increases the efficiency of large aquarium filtration systems.
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Catalina Aquarium's super efficient Vortex Protein Skimmers for 10 to 400 gallon aquariums. These protein skimmers have been tested and are highly recommended by Tony Griffitts of .

If you have ammonia in your aquarium water it cannot be removed by protein skimming.
Photo provided by FlickrProtein skimmers physically remove the nitrogen-rich, foamy organics from the aquarium.
Photo provided by FlickrIn sump protein skimmer brands popular among marine and reef aquarium hobbyists include , ,  and .
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I have run many marine fish only and reef aquariums with and without protein skimmers for many years. To this day I can not say that there is a noticeable benefit running a protein skimmer. I ran a protein skimmer for many years on a fish only system and then I took it off the system. The system was ran for years without a protein skimmer and there was no noticeable affect on fish health. I have also set up many reef systems without protein skimmers, and had excellent results with small polypstony (SPS) corals growing very well, and several species of marine fish spawning. Some reef system setups had undetectable nitrate levels after being set up for years.A protein skimmer, also sometimes referred to as a foam fractionator, is a piece of aquarium equipment that is primarily used in saltwater aquariums in order to remove dissolved organic compounds (DOC) and other harmful substances that if not removed can breakdown in the aquarium or filter adding to the biological load on an aquarium. Protein skimmers remove these hydrophilic substances completely from the water using air bubbles that are collected in a collection cup. As air and water are mixed in the skimmer chamber the bubbles rise and take with them the dissolved organics that are attracted to the bubble surface. When the bubbles with the proteins, amino acids and other nasty stuff bubble up the tube into the collection cup they are completely removed from the aquarium.The theory behind running a protein skimmer on a marine aquarium sounds good, but in reality its impact on well established marine aquarium appears to be minimal. Real independent research needs to be done to validate the value of running a protein skimmer on a marine system. With all the examples of marine aquariums that are doing exceptionally well without protein skimmers, I am finding it harder and harder to justify the expense for all marine aquariums.There are some saltwater aquarium hobbyists that don’t use protein skimmers and their tanks do just fine, but using a protein skimmer really helps with easier maintenance of the tank.