Hi,

I am using a NADH dependent regenerative enzyme assay for measuring F1FO ATP synthase enzyme activity in isolated mice brain mitochondria.

While testing different drug peptides on the isolated mitochondria, I am detecting peaks of enzyme activity at different time points. (I detect the OD 340nm for 9 minutes- for mitochondria with no treatment, I detect peak activity at around 6min while for mitochondria with peptide treatment peak is detected at 10min time point).

Although, I understand the regenerative system, I need a biochemist's opinion. Can anyone help me in explaining these results- if I want to compare the drug treatments with no treatment? Should I be comparing the peaks at different time points to check the efficiency of the drug, or it is better to compare the efficiency at the highest peak activity of mitochondria? 

Thanks,

Esha