My previous result found that in the stable cell line expressing my protein, basal protein level of the target protein is decreased and the decreasing is more prominent in those cell expressing my protein variant.
I have tried using MG132 to prove that these low protein levels are from ubiquitin proteasome system or not. I know that if the low protein level is from UPS, MG132 should rescue it, and the target protein level should be increased.
What I don't know are
How should I compare each condition?
Should I set the target protein level in control cell (expressing vector control) as 100% in both MG132 untreated and treated condition?
If it was from UPS, should target protein level in cell expressing my protein increase to about 100% in MG132 treated condition?
When I search for results with MG132 treatment, I rarely see anyone set control cell with MG132 treatment as 100%, only those untreated control cell.
I really don't sure how to interpret the results.
Dear Alexandra Stolz
Thank you for your answer. However, I am still curious that what if
4) cells expressing with vector control + MG132: the target protein level increase in comparison to 1)
What would be the ideal result for the conclusion that my POI can decrease target protein level through UPS?
3) = 1) =100% or 3) =4) =100%
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