Wash with water or precipitate in ethanol, dialysis.

I am not really sure what you want to do. Do you want to get rid of salt (PBS) from your protein solution?

My crude extract was prepared into PBS and after chromatography, it seems that my eluent contain some salts. What can I do to drive out of these salts without denaturing the structure of protein?

so, you can do dialysis with your buffer without salt or you can concentrate you protein and then dilute it with your buffer without salt.

Some proteins need salt so be careful.

You can use Amicon Centrifugation filters with a molecular cut-off lower than your protein mass. So the protein remain in solution while your salts penetrate the filter and are separated.

Nevertheless you can never be sure that your protein is still in a native state since desalting can lead to a defolding of your protein

But there are proteins which defold in case of desalting and there are which not as well, so it can be tested in small scale for further experiments with your protein.

In order to remove the salts and buffers from protein you'll have to subject this protein + salts solution to gel filtration chromatography... The specific term used for this process is desalting... "chromatographic methods" by braithwaite and smith can provide theoratical and practical aspects regarding this process...

Can I use gel filtration chromatography to drive out the salts from my specimen?

Is there anyone to work with this method previously?

Thanks for your valuable comments and I'm looking forward for your ideas.

Desalting by gel filtration is a very common technique - google "Desalting columns" and select one that fits your needs.

Do gel filtration drive out the salts from my samples, completly?

Do it need one step or many steps with different column?

Please guide me.

Generally speaking one column should be enough even for a peptide unless there is some reason you need the salt in the micromolar range (specific binding of the protein to Na or Cl, for example). A regular PD10 desalting column can remove >99% of the salt with 95% of the protein.

https://www.gelifesciences.com/gehcls_images/GELS/Related%20Content/Files/1314723116657/litdoc52130800BB_20110830191706.pdf

Dear Jeffrey

Thank a lot for sending of this valuable pdf.