You can pass your sample through an endotoxin removal column.

Dear Xinxin

Due to the negatively charged phosphoryl and carboxl groups in endotoxins, anion exchange chromatography was  the  common depyrogenation method for proteins

https://www.ncbi.nlm.nih.gov/pubmed/18996203

However the success rate of this approach depends from the pI of your protein (because if it as low pI can bind the coloumn with the LPS and the separation is not efficient) and from the stability of your protein in the pH condition required for optimal binding of the endotoxin to the coloumn.

An interesting alternative in lab scale, that i would like to suggest to you are the Endotrap coloumn (http://www.hyglos.de/en/products-services/products/endotoxin-removal/endotrapr-hd.html) that are based on affinity.

There are several kind of this coloumn that allow to you to operate with common buffers used for protein storage and purification and in my experience work very well. 

good luck

Manuele

Thanks a lot.

Hello Xinxin,

Endotoxin can be removed with three possible mechanisms:

1. Affinity based : Affi-Prep Polymyxin resin from Bio-rad

http://www.bio-rad.com/en-in/product/affi-prep-polymyxin-resin?ID=5c53a1f3-b0da-4799-8a54-7e94f090e0f9

2. Charge based : MacroPrep High Q ( When your Protein have basic pI and operating at neutral pH) , You can try Ceramic Hydroxy Apatite also.

Selecting right resin for endotoxin removal :

http://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_6813.pdf

3. Size based : If your desired protein size less then 5kda then you can try TFF (10kda) in flow-through (permeate mode), Endotoxin have higher size so endotoxin will retain in retenate and your product will come in flow-through.

Please contact me for any more info or support.

Dear Xin xin

in case you are stil interested to the topics you can find a video aboit endotrap

ProteoCool n°14 (EndoTrap: Rapid and efficient EndoToxin removal)

at page3

on my blog:https://proteocool.blogspot.com

ciao

Manuele