Protein skimming (or foam fractionating) is accomplished by generating a mass of air bubbles in a water column, which collect proteins on their surface, then rise to the surface of the water. The protein is then "skimmed" off into a collection cup. The more bubbles created and the longer they stay in the skimmer water column, the more proteins can attach to the bubbles.
Different methods are incorporated to generate bubbles and keep them in the water column longer. Air bubbles want to rise to the surface of the water. If they are generated at the bottom of the skimmer, they will rise to the surface and burst, leaving the proteins. This is called "co-current" (with the water current generated by the rising bubbles) skimming.
Counter-current (opposite the current) skimmers redirect the water in a skimmer downward or sideways to keep the bubbles suspended in the water column longer.
Air is introduced into the skimmer either mechanically ("needle wheel" or venturi), or with an air pump and diffuser (air stone). Smaller bubbles have a tendency to rise less quickly, so they can gather more proteins before they finally get to the surface. To take advantage of this piece of physics, some skimmers use needle wheels or pin wheels, which chop large bubbles into smaller, finer bubbles.
Some protein skimmers, such as the Red Sea C-Skim 1200 use one pump to power the pin or needle wheel and another to move water from the tank or sump, through the skimmer, then back to either the tank or sump.