I was trying to analyse complexes I, II and IV using isolated mitochondria from human skeletal muscle. There were some troubles (they need wery gently approach...), but after all it worked. And we also investigated fatty acid oxidation in primary human myoblasts, so maybe you can try to combine these protocols. Have a nice evening.
take a look at this paper. is about ROS production from ETF:QOR but also has good tips about which substrates to add when you are looking at beta-oxidation. Regarding the isolated mito in the seahorse I guess you are an expert on that :)
Andre Kleinridders , did you try FAO protocol with isolated mito? In this case could share the conditions that you used? thank you. I`m trying to do the same on brown fat mitochondria