There are many ways to assess mitochondrial/bioenergetic capacity.
Of course the most direct and wildly accepted is to measure mitochondrial
respiration through a Clark-type electrode.
Alternatively, cellular oxygen consumption can be measured through an oxygen
sensitive probe (used to be called A65N, but now commercialized as
MitoXpress via Luxcell). This method only requires a fluorescent plate
reader in addtion to mitoXpress, which should be available to most
biomedical labs/departments.
My personal preference for measuring cellular metabolic activity is to use
the Seahorse Metabolic analyzer. It measures oxygen consumption (indicator
of mitochondrial respiration) and extracellular acidification rate (
indicator of aerobic glycolysis). It is so easy and relatively medium
throughput.
Then, there are auxiliary assays to confirm your findings:
Hexokianse activity assay
Pyruvate dehydrogenase activity assay
Lactate dehydrogenase activity assay
Complex I- V activity assay.
Feel free to contact me, if you have futher questions.