||The primary active chemical in peyote is mescaline. Mescaline is a specific molecule composed of a unique configuration of atoms (C11H17NO3). See Mescaline Chemistry for a picture of the mescaline molecule.|
Mescaline can be created synthetically in the lab starting with other synthetic chemicals. Or it can be created by plants such as peyote. Both processes result in the same molecule...mescaline. Thus the potency of the resulting mescaline is the same in both cases.
Mescaline can be extracted from peyote in a variety of ways. Depending on the method used, the results can vary. A high-quality extraction would result in pure mescaline nearly indistinguishable from synthetically produced material. A rough extraction can result in a combination of mescaline and other chemicals/alkaloids found in peyote. Because of these additional alkaloids, the experiential effects from a rough extraction can be noticeably different than those from pure mescaline (whether synthetic or naturally produced).
Hope this helps.