I've been reading Beating Lyme Disease
http://www.hansacenter.com/beating_lyme_disease.php
The following is all from my memory as I'm at work and don't have the book with me.
He gets into a section where he says he's found a build up of ammonia in almost all of his Lyme patients. He says it's a byproduct of the bacteria. He also states that with diet you have to be careful of a diet that's too alkaline because ammonia is alkaline. He suggests going low carb and low protein and eating eggs and fish for protein sources because they are high in L-Lysine. He says that if you eat red meats and certain foods that it will increase another substance that will make the ammonia worse.
When I was training for my half marathon I found that the ammonia smell was so strong after I exercised that it was sharp. I used to joke that if I passed out I could revive myself.
I take L-Glutamine daily to help combat some of the ammonia. I always take it on an empty stomach, open the capsule, dump it under my tongue and then swish with water.
Next time I see my nutritionist she's going to do muscle testing with a vial of ammonia to help determine where the build up is. I'm guessing it's in my sinuses for sure, not sure where else.
I've learned a lot from this book, however it is an all natural protocol.