It will be OK if you immunoprecipitate for the expressed Flag.

Good luck!

Dear Yulia

are you secreting the protein in the media?

in this case, i think that of you would like ti purify the protein in mg scale with out alter the folding could be better replace the FLAG tag with a c terminal 6 or 10x his tag abd perform an imac purification which works very well for purification from cell culture surnatatnts.

Generally i'm doing it from expi293 which are a powerfull derivate of hek293 able to growth in suspension similar to bacteria up to very high cell density.

you can easly generate the new clobe where replace the FLAG tag with the his just performing a single pcr followed by dpni digestion and trasformation in MACH1 e.coli cells using the PIPE Cloning approach.

You can find details about it on my blog: https://proteocool.blogspot.com/p/cloning.html?m=1

good luck

Manuele