[tmz]

The water a protein skimmer pushes to the cup will pass along some small amounts of dissolved nutrients like a very small water change will as Jon noted.

The rising flow action in the skimmer will also push along bits of this and that algae detritus bacteria etc.

However, the foam fractionation function( the actual "skimming") relies on the attraction of organic molecules to water and their repulsion from it. Amphipathic molecules like proteins and others with bi-polarity are pulled toward the water on one side and repelled by it on the other. These ampipathic molecules are most susceptible to removal via skimming as they get cling to the air and water surface there at the same time and get trapped between the bubbles.