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Protein planets were a type of food planet utilised by the Nestene Consciousness.
During the Nestenes' war with the Time Lords, most of the worlds in the Illia Galaxy were enslaved and became protein planets or Auton factory worlds, all of which were lost when Rassilon used the Moment. (PROSE: Pandoric's Box)
Later the Plastic Conjunction was a group of seventeen protein planets that farmed smoke and oil for the Nestenes, (PROSE: Revenge of the Nestene) but this food stock was destroyed in the Last Great Time War with all the protien planets rotting.
Following this, the Nestenes planned another invasion of Earth in 2005, as the planet had lots of smoke and oil with plenty of toxins and dioxins in the air, which as the Ninth Doctor explained was "Perfect. Just what the Nestene Consciousness needs." (TV: Rose)