Serum amino acids, in particular phenylalanine, leucine, isoleucine and tryptophan are lower in ME (as well as in FM) because the energy system is dysfunctional. The citric acid cycle is dysfunctional and glycolysis is malfunctioning. In addition carnitine levels are low, PPAR functioning is low and mitochondrial membrane potential is low, both of which are an indicator of poor fat metabolism. This causes energy derivation from proteins, in particular the above amino acids. In simple terms the body, mainly muscle tissue, is deriving more energy than usual from proteins. This, in turn causes low measures of serum amino acids in ME. The high levels of uric acid are due to this excessive reliance on protein derived energy. Where is the evidence that proteases are dysfunctional? Michael Maes was partly onto it when he said "It is hypothesized that the relative deficiency in the BCAAs may play a role in the pathophysiology of fibromyalgia, since the BCAAs supply energy to the muscle and regulate protein synthesis in the muscles.” (http://www.ncbi.nlm.nih.gov/pubmed/17720950) But that was way back in 2000, since then we have found that the aa deficiency problem is metabolic rather than a transcription problem. Michael was trying to postulate that muscle energy deficits were being caused by a lack of protein as a metabolic source. As you would know, proteins are a last resort for energy except in ME.