Most authorities feel that the compound that causes the odor in urine after consumption of asparagus is methylmercaptan, which is a sulfur-containing derivative of the amino acid, methionine. This is disputed by a few individuals who claim that the odiferous compound is asparagine-amino-succinic-acid monoamide, which is derived from the amino acid, asparagine. In either case, the product is formed as a derivative during the digestion and subsequent breakdown of beneficial amino acids that occur naturally in asparagus.
Ref: Merck Index, 862; Food Chemistry, Belitz and Grosch, pg. 271.