SDS is strong ionic detergent and Iam pretty sure that it will destroy cell membrane.

As Tomáš said, SDS will definitely destroy the membrane (well, depends on concentration as well). What do you mean by protein loss? Release into solution? Or loss of activity? Because it will probably cause both.

Mao, this paper may be useful.

Article A simple and sensitive antigen retrieval method for free-flo...

Thank you, guys. It is very helpful.

I have done antigen retrerive by 1% SDS at RT. And observed some signal. But it was not very well. There were some red circle on the surface of slice under the confocol microscope.

I will try to use citrate solution.

Hi, I used the sodium citrate solution to do antigen retrieval. 1mM sodium citrate ph 7.4 at 85 degree for 15min and the slice is damaged. 10mM sodium citrate ph 7.4 at 85 degree for 15min and the slice is great.

The slices was frozen sectioned and antigen retrieval for free floating.

The protein loss, I means that SDS can dissolve cell membrane. And some protein may be released in solution.

I have read the paper about CLARITY published in Nature this year. And I think protein loss may happen if I use sds to do antigen retrieval.

I recommend citrate buffer.You can find details by reading (abcam company protocols for IHC : Ag retrieval agents).Choosing Ag retrieval agent is highly related to your Ab and its better to  find all related data in data sheet of your selected Ab.