Centrifugation using right rotor diameter and centrifuge tube you should be able to separate them. Other method would be use of size exclusion column. Hope this helps

Hi Joon, there are easier methods:

http://www.biosyn.com/tew/protein-precipitation-methods-for-proteomics.aspx

My suggestion is to pass the sample through a suitable HPLC or UPLC size exclusion column to fractionate the peptides by size.

 Thanks for all answers!!

Is it possible to checking 'trypsin digestion' using C18 column ; RP-HPLC ?

OR should i use only size exclusion column?

RP-HPLC is a very good way to separate peptides from a trypsin digest, but the separation is based on hydrophobicity, not size.