We found the UB-Ghost extraction method provides a cleaner extract of surface proteins, link to paper : http://www.sciencedirect.com/science/article/pii/S0167701215000056
I would say, it depends on what you are looking for. You can try ultrasonication, then washing and centrifugation in combination with other methods of protein isolation as mentioned by Hung
addtionally to Pawel's "what" question. Is the extract to be used for quantitative or qualitative analysis? The "what" answer will also define whether you need to use something like a french press and then spin out the wall fragments or just use surface stripping techniques
Cell Wall Protein Extraction
Culture the probiotic isolate in MRS broth. Harvest the cells by centrifugation and wash thrice with 0.85% saline and resuspend in double distilled water (A600 ~ 2) and centrifuge it. Extract the cell wall proteins from the final cell pellet with 0.5 ml solution of Extract buffer (0.01 M Tris-HCl, 0.04 M EDTA, 0.01M NaCl, 2.0 % SDS, and pH 8.0) at 100°C for 5 min. After treatment centrifuge samples at 11,600 g for 10 min and the cell wall proteins will come in the supernatant.
Estimate the protein concentration by Folins Method. Analyze the cell wall proteins by Tris-Glycine SDS-PAGE with 5 % stacking and 12 % separating gel.
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