They dont target proteins specifically but instead filter out the organic waste products in the water. This is a protein-based waste.
Why There Is White Foamy Bubbles Covering My Fish Tank Like A Blanket My Aquarium Club
Protein will come from decomposition of dead plants fish animals or surplus food etc.

Protein foam in fish tank. Protein skimmers clean your saltwater tank by collecting and removing these microscopic pollutants and suspending them in a layer of fine foam or bubbles. The first reason is that the build-up of debris in your filter can cause protein build-up. Biofilm and Protein Buildup.
If you notice foam on the water surface with a smelly odor its likely protein foam. Well this might be less obvious. The other main purpose of using protein skimmer is to increase aeration in your aquarium with the removal of organic matter.
Then the air bubbles stick together and form together at the surface and produce an odor. If the foam is the result of protein build-up it may not directly harm your fish but it could be a sign of other problems in the tank. All this might explain why.
The other reason is decomposing fish waste and decaying fish food causing protein build-up. It is important to know that this type of foam is not at all harmful to your fish. You will usually see that these bubbles disappear again fairly quickly.
This causes the bubbles that would normally dissipate to stick together in a foul smelling foam. There are foams and oils that form in an aquarium which are caused by proteins. It is wise to visualize and count your fish daily to ensure none are missing.
In the simplest terms protein skimmer also known as a foam fractionator is a device used in saltwater aquariums in the removal of organic wastes which include fish excrement undigested food and proteins. It will not kill your fish. If this happens your tank is telling you that it.
This leaves your water clearer cleaner and safer for your fish and corals. A disintegrating fish corpse is a rich source of protein and frequently the root cause of protein foam. Protein foam or oily biofilms are created when waste proteins fish waste decaying debris deceased aquatic life or natural oils from food attach to small air bubbles.
Another thing that causes foam on the waters surface is a build-up of protein. Saltwater aquarists can use a protein skimmer to extract proteins and oils from the water column. If there is excess protein in your fish tank that can become a reason for foam appearing in it.
Additionally should there be air bubbles in my fish tank. Protein accumulation can cause foam in your aquarium. Decaying plants can also produce protein wastes so trim dead leaves off.
This occurs when waste that is protein-based coats small air bubbles. It is important to remove surplus protein before it converts to ammmonia then nitrite etc. Protein foam is an indicator that your tank needs to be cleaned.
How does this work exactly. In the process the skimmer pulls out all the oils and soaps as it dispenses its foam. Protein accumulation can cause bubbles Another cause of white foamy bubbles covering your fish tank could be the result of protein-based waste.
Draining takes about two or three hours depending on the chemical quantity in your tank and the productivity of your protein skimmer before the skimmer is back to normal. Protein can form because of two major reasons. Protein build-up generally occurs in tanks where there is a high quantity of organic debris this may happen in cases of overfeeding failure to perform routine water changes or if a fish dies and is left to decompose in the tank.
Fish waste their meaty food residues small dead fish which go unnoticed or any other decomposing matter containing proteins can eventually link itself to the air bubbles and coat them with a smelly surface. A dirty filter and debris in the aquarium can cause this problem. Too much protein in the water of a fish tank can coat the bubbles preventing them from popping.
Too much protein in the water of a fish tank can coat the bubbles preventing them from popping. Protein foam is an indicator that your tank needs to be cleaned. When fish leave excrement some of the waste material is left and can coat small air bubbles.
Here is another perfectly valid reason which can force you to clean your tank immediately.
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