title: Evaluation of the combinative application of SDS and sodium deoxycholate to the LC-MS-based shotgun analysis of membrane proteomes.
abstract: SDS and sodium deoxycholate (SDC) as two representative detergents have been widely used in LC-MS/MS-based shotgun analysis of membrane proteomes. However, some inherent disadvantages limit their applications such as interference with MS analysis or their weak ability to disrupt membranes. To address this, the combinative application of SDS and SDC was developed and evaluated in our study, which comprehensively used the strong ability of SDS to lyse membranes and solubilize hydrophobic membrane proteins, and the high efficiencies of an optimized acetone precipitation method and SDC in sample clean-up, protein recovery, and redissolution and digestion of precipitated proteins. The comparative study using a rat-liver-membrane-enriched sample showed that, compared with other three commonly used methods including the filter-aided sample preparation strategy, the combinative method not only increased the identified number of total proteins, membrane proteins, and integral membrane proteins by an average of 19.8, 23.9, and 24.8%, respectively, but also led to the identification of the highest number of matching peptides. All these results demonstrate that the method yielded better recovery and reliability in the identification of the proteins especially highly hydrophobic integral membrane proteins than the other three methods, and thereby has more potential in shotgun membrane proteomics.
authors.affiliation: National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, P. R. China; Key Laboratory of Tea Science of Ministry of Education, College of Horticulture and Landscape, Hunan Agricultural University, Changsha, P. R. China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Lin
authors.forename: Kunbo
authors.initials: K
authors.lastname: Wang
authors.forename: Yujun
authors.initials: Y
authors.lastname: Yan
authors.forename: Haiyan
authors.initials: H
authors.lastname: Lin
authors.forename: Bin
authors.initials: B
authors.lastname: Peng
authors.forename: Zhonghua
authors.initials: Z
authors.lastname: Liu
mesh_terms: D000818:Animals; D002462:Cell Membrane / Q000737:chemistry; D002853:Chromatography, Liquid; D003840:Deoxycholic Acid / Q000737:chemistry*; D008099:Liver / Q000737:chemistry / Q000166:cytology; D008565:Membrane Proteins / Q000032:analysis*; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D051381:Rats; D012967:Sodium Dodecyl Sulfate / Q000737:chemistry*; D053719:Tandem Mass Spectrometry
chemical_list: D008565:Membrane Proteins; D020543:Proteome; D003840:Deoxycholic Acid; D012967:Sodium Dodecyl Sulfate
keywords: Combinative methods; Membrane proteomes; Shotgun analysis; Sodium deoxycholate; Sodium dodecyl sulfate