Protein deposits have been a problem pretty much since contact lenses became popular. Lipid deposits are something fairly new, and some say that the material that soft contacts are made of ("galyfilcon") are the cause.
Some people also say that Acuvue Advance for Astigmatism is particularly prone to lipid deposits, but others say otherwise.
As far as where lipids and proteins come from, they are a natural component of your tears. And I don't know of any way you can look at your contact lens and tell if the deposits you see there are proteins or lipids. Maybe someone else reading this thread can help with that.