The protein will be direct infused in mass spectrometry, and it must be diluted in ammonium acetate. So, I have 2 types of analysis:
PTN (26kDa) + glycans - this one I want to clean it (just removing salts/detergents); it's a sample that is already in solution sold by a company and there's too much background, interfering in the identification of peaks
The same PTN (26kDa), but removing glycans - what is the best way to remove the glycans without denaturating the protein?
Perhaps try either size exclusion chromatography or use the pI of the protein for ion exchange (e.g. DEAE cellulose) assuming the glycan has either no charge or an appreciably different pI in your loading buffer. Neither of these methods would necessarily require organic solvents.