Duet its compatibility with proteas actitiy at high cocentration, sodium deoxycholate (SDC) can be used to effectively improve the solubilizaion and enzymlsis of emmbrance proteins and has received increasing attention in the field of membrane proteore analysis in recent years. SDC can be removed from digests by meas of acidification followed by centrifugation ie. acid precipitation, AP) or extraction with ethyl acetate ie phase trasfer, PT so as not to interfere with the downstream analyses like IC-MS/MS. In this study, the two strategies were systematically evalutated, compard and optimized. The results of the study demonstrated that both of the AP adn PT strategies led to a certain amount of tryptic peptides being lost, and in PT strategy even more pepties were lost during SDC removal process. Howere, the lost pepetieds could be mostly recovered by washing the pellet and solid content produced durig AP and PT, respectively. By reco-veromg the lost peptides, the identification efficiency of proteins, especially transmembrane and low abundance ones, was significanl improved Comparatively, after optimization by recovering the lost peptides, AP strategy was superior to PT stratgey because the former not only could achieve the comparable identification efficiency with the latter but also was more economical, safer andd easier to operate than the latter.