If you have access to a respirometer where you can measure CO2 produced and O2 consumed for calculation of RQ, you could empirically determine when the animals switches from catabolism of dietary substrate (RQ~1 for rodents) and when the animals are undergoing lipolysis (RQ~0.70). The sweet spot for taking your samples is an RQ of ~0.80-0.90.

Dear Prof. C. Loren Buck. Thank you so much for your answer that is very helpful to find the best condition. We do not have a respirometer, and hopefully I can find one in our campus. 

We typically do 6 hours - start fast in the morning and harvest in the afternoon. Fed vs fasting conditions have a big effect on triglycerides, from increasing chylomicron production in the fed state. There is a lesser effect of feeding on cholesterol. With a 6 hour fast your mouse plasma should have most lipoprotein lipid derived from VLDL, IDL, LDL, and mostly HDL, along with no chylomicron lipid. 

What exactly are you planning on looking at (i.e. TG, cholesterol, FFA)? Do you plan to isolate lipoproteins?

Also RQ does not indicate dietary substrate vs lipolysis, it indicates glucose utilization (RQ~1) vs fat utilization (RQ~0.7) because of the O2 consumption and CO2 production associated with glucose vs lipid utilization.

Hello Joshua, I like your thought to fasting the mice for 6 hours. Actually, I already prepared some samples using 6 hours fasting. Our collaborators also want us to do a few hours fasting for plasma lipids profile to decrease effects from diet. I will mainly focus on the lipids species in our WT and KO mice. 

Gut transit time for most mice is considered to be 4-5 hrs. Most protocols that try to limit the effect of dietary lipids without activating the fasting response, such as VLDL secretion, fast the mice for 5hrs. Any longer will risk activating lipolysis.

Hello Ffolliott, thank you so much for your answer. i definitely will consider gut transit time for collecting samples.