Preheat oven to 350°F. Spray a 9-inch quiche pan (without removable bottom) or a 7-by-11-inch baking pan with nonstick cooking spray. In a large nonstick skillet, warm the oil over low heat.
Add the peppers and the onion; cook, stirring frequently, until the vegetables have softened - about 5 minutes. Stir in the tomato and cook until almost all the liquid has evaporated, about 5 minutes. Set vegetables aside to cool to room temperature.
Beat together the whole eggs and egg whites. Stir in the milk, Parmesan cheese and black pepper, and mix until well combined. Whisk in the flour. Transfer the vegetables to the prepared pan. Pour the egg mixture over the vegetables and bake until the eggs are just set, about 35 minutes.
Cool the quiche 10 minutes before cutting into 6 wedges. Serve topped with salsa.