http://link.springer.com/article/10.1007%2FBF01055047 . Sir I found this article about in vitro assay on particles isolated from mitochondria. Toxicity of different chemicals is measured. 

Hello Mohammad,

please have a look at the articles in the attachment. I am sure that they will help you with your question.

Regards, Christian

Article Blue native PAGE

Article Assessment of mitochondrial respiratory chain enzymatic acti...

Thank you Chris. Indeed they are useful.

 Thank you Dr. Salman

I find this app note very  interesting when it comes to workflow for screening effect of chemicals on the functions of mitochondria: https://www.caymanchem.com/requestables/800126.pdf

Thank you a lot Dr. Mihail. This is more relevant and technically helpful information. Which instruments will be required with specifications for a lab to carry out similar work?

It is better to look for the effect on the marker enzymes of mitochondria such as succinate dehydrogenase or succinate -  cytochrome reductase. For in vivo,  treat the rats or mice for about 48 hours and isolate the mitochondria from the liver and assay the above mentioned enzymes. Similarly, in vitro could be done on untreated animals. You should run different doses or concentrations of the chemical substance to determine the IC50 values. 

Thank you Dr. Mehmood for very helpful suggestions.