Preheat oven to 350 degrees F (175 degrees C). Layer cheese, onions and mushrooms inside pie shell. Whisk together egg whites, yolks, flour and milk. Pour egg mixture on top of cheese and vegetables. Poke the layers gently to allow the egg mixture to distribute evenly throughout the quiche. Sprinkle the thyme, salt and pepper on top of the eggs. Bake in preheated oven for 30 minutes, or until eggs are set and top is golden brown.