Have a look at the following technical bulletin:

https://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Bulletin/pe0230bul.pdf 

I am wondering whether the 'gossypol' will have an effect on the extraction of cotton proteins and late their analysis.

Hello,

If you wish to extract total soluble proteins use a slightly alkaline buffer (Tris-HCl or Hepes 50 mM pH 7.5-8) to counterbalance the pH drop due to vacuoles leakage; 10% glycerol for better conservation of proteins on freezing; a cocktail of protease inhibitors and 1% PVP to eliminate phenolic compounds. You can also add NaCl 100-150 mM