Hello, To my knowledge, Protonix contains Pantoprazole as active ingredient, used to treat acid reflux basically. If combined with Amitryptiline, it might help treat acid reflux related anxiety too. If you are taking this combination, then, this explains why the anxiety symptoms seem to be going away. Please do give more details regarding the medication you are currently taking. Take care. Hope I have answered your question. Let me know if I can assist you further. Regards, Dr. Albana Sejdini, General & Family Physician