Hi Kim,
Amino acid therapy is promoted by some practitioners to supposedly help balance brain chemicals, (neurotransmitters), and other things of that sort. The only treatment close to that, that I'm aware of, that's used for treating digestive system issues, is the use of amino acids and pre-digested nutritional items, used in enteral feeding, (usually by means to a tube, either directed into the stomach, or implanted into the duodenum, for patients who are unable to eat normally, or in cases where patients are truly allergic to normal food). Some refer to this as an elemental diet.
I'm aware of one individual with MC who tried enteric feeding, and when it didn't resolve the symptoms, her doctors talked her into submitting to an ileostomy, claiming that the ileostomy would resolve her symptoms. We advised her that it wouldn't stop her symptoms, but she decided to go ahead with the surgery anyway. After the surgery, she still had all her symptoms, plus chronic abdominal pain, (that she didn't have before), plus the nuisance of having to deal with an ileostomy. Despite their assurances, doctors don't always have good ideas, and they don't always know what they're doing, unfortunately.
I've heard of amino acid therapy being used in combination with an antihistaminergic drug, and a mast cell stabilizer, to treat ulcerative colitis, (which involved mast cell degranulation issues), as in the following example, but if mast cell degranulation is the problem, then treating that issue will resolve the symptoms, and the amino acid treatment would be irrelevant and unnecessary. Replacing the amino acid therapy with a diet low in histamines, and avoiding foods that are known to trigger mast cell degranulation, would be a much safer and more effective approach.
http://www.ncbi.nlm.nih.gov/pubmed/16944185
That said, maybe your new doctor is a brilliant new innovator, and he's onto something that I'm not aware of, but before I would even consider a treatment of that type, I would want to talk with some of his patients who have had their cases successfully resolved by that treatment program - patients who were successfully treated at least a couple of years ago, not patients who are only a few weeks or a few months into the program, who will probably be enthusiastic about the program, but the jury may still be out.
Here's an article by a doctor, that discusses some of the concerns about treatments of this type:
http://www.lifedynamix.com/articles/Ask ... erapy.html
Tex