Like Johnny said this comes from indigestion, not protein specifically. In fact, this indigestion means you are a walking breeding ground for bacteria, and this places a strain on your immune system thereby shortening your lifespan.
Shitty news eh?
The way to work around this is not to eat foods that require alkali to digest when you are mixing in foods that require acidic digestion. This however would make eating a further chore, especially when you are doing 4-6,000 calories a day. However, the better your digestion it is yet one more contributing factor to a long healthy lifespan.