The folks above pretty much covered your question....below is some additional info I copy/pasted from another site...
In Summary
Protein skimmers can be an effective method in reducing the problems related to waste accumulation in our tanks. The application of skimmers have been associated with reduced waste (reduction of DOCs), reduced algal growth, and increased water quality. Many of the present skimmers on the hobbyist market are too small (height and diameter) and/or underpowered to effectively remove sufficient amounts of organic waste. As a rule of thumb, taller skimmers tend to work better than short, squat ones. The hobbyist needs to ensure bubble production is maximized (smaller bubbles work better than big bubbles), and consequently, the water in the reaction column should be milky white in appearance. The foam produced in the skimmer should be continually moving up towards the collection cup so that is being collected and removed from the system. One final word on skimmate consistency: this topic is often a subject of debate (i.e., thick, mud colored, and dry versus watery and iced-tea colored (image above right)), and I will address skimmate in an upcoming article. But I'll leave the topic for now by saying: you want to collect skimmate (any skimmate), and any skimmate is better than no skimmate at all.
For additional infomation see:
www.proteinskimmers.com
Hope that technical stuff helps!
Bottom line for my reef is my protien skimmer removes some nasty looking stuff that I'm convinced does not belong in the system.