Metabolism is controlled by a complex system of transcriptional events and posttranslational modifications stimulated by substrate and metabolite availability. It is becoming clear that neurodegenerative diseases are a symptom of a deficiency in the regulation or execution of metabolic reactions. Mitochondria, as the central organelles in metabolic regulation as well as the chief generators of reactive species, clearly have a role to play in the etiology of neurodegenerative conditions. We are developing antibody-based capture arrays to determine multiple parameters of key mitochondrial proteins. Parameters include enzyme activity, quantity, oxidative modification (including nitrative and oxidative stress), and regulation (phosphorylation and acetylation). At this time the core of this array focuses on the enzymes of oxidative phosphorylation. We continue to expand this array as antibodies for enzyme isolation and modification detection become available. Here we demonstrate the use of this array by analyzing the proteomic differences in oxidative phosphorylation enzymes between human heart and liver tissues, cells grown in media promoting aerobic versus anaerobic metabolism, and the catalytic/proteomic effects of mitochondria exposed to oxidative stress.