I just saw a mention of different salts of MDMA in an earlier post in this thread, here's a thought:
1. Different salts have different solubility parameters.
2. Slow, or incomplete absorbtion of the salt could lead to lower blood concentrations.
3. The average chromatography test will usually react pills with aqueous base and then extract organics with e.g. chloroform. This would mean that the MDMA would indeed be detected as MDMA and would appear as potent a pill as any other.
The problem here is:
1. I would think that most common salts of MDMA would have significant water solubility and you'd have to go out of your way to do. Effectively every single MDMA recipe I know of makes the hydrochloride salt. I think the phosphate salt might have been a thing? I do know that you usually have to go out of your way with wacky aromatic salts (napthalenesulfonate, benzenesulfonate, etc) or polymers to make compositions that don't dissolve as rapidly in water.
2. Analysis could be modified to also check the identity of the counterion in the salt, maybe through LC-MS or some proper ion chromatography/electrophoresis (of which I have little practical experience).
3. Lower blood levels of MDMA present would be a dead giveaway.
4. Different salts of MDMA would have different crystal shapes.
5. I have a feeling dissolving the pills in e.g. cola beforehand could effectively convert the MDMA to a "known good" salt (I believe the phsophate & citrate should both be highly bioavailiable)
6. Your small intestine in concert with bile salts as emulsifiers should convert the salt to a freebase in a PTC reaction of sorts anyway?
Vecktor's idea of triturating the compound with antisolvent and running anlysis on the liquid is known as "Swish TLC" when one uses TLC as analysis and is a cool pharmacy chemistry trick. Fractional equilibrium dissolution I think it's called. Maybe use a few diff solvents in paralell washes for ideal maximum screening power, If you can't find you mystery impurity on GCMS with that it's not there
Also worth considering, GC-GC-MS. GC's can be set up to use two different seperation media to give an additional means of seperating compounds that may co-elute with others (if you are too lazy to pick a proper column in the first place, IMO).