title: Improvement of a sample preparation method assisted by sodium deoxycholate for mass-spectrometry-based shotgun membrane proteomics.
abstract: In current shotgun-proteomics-based biological discovery, the identification of membrane proteins is a challenge. This is especially true for integral membrane proteins due to their highly hydrophobic nature and low abundance. Thus, much effort has been directed at sample preparation strategies such as use of detergents, chaotropes, and organic solvents. We previously described a sample preparation method for shotgun membrane proteomics, the sodium deoxycholate assisted method, which cleverly circumvents many of the challenges associated with traditional sample preparation methods. However, the method is associated with significant sample loss due to the slightly weaker extraction/solubilization ability of sodium deoxycholate when it is used at relatively low concentrations such as 1%. Hence, we present an enhanced sodium deoxycholate sample preparation strategy that first uses a high concentration of sodium deoxycholate (5%) to lyse membranes and extract/solubilize hydrophobic membrane proteins, and then dilutes the detergent to 1% for a more efficient digestion. We then applied the improved method to shotgun analysis of proteins from rat liver membrane enriched fraction. Compared with other representative sample preparation strategies including our previous sodium deoxycholate assisted method, the enhanced sodium deoxycholate method exhibited superior sensitivity, coverage, and reliability for the identification of membrane proteins particularly those with high hydrophobicity and/or multiple transmembrane domains.
authors.affiliation: National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients, College of Horticulture and Landscape, 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: Haiyan
authors.initials: H
authors.lastname: Lin
authors.forename: Zhonghua
authors.initials: Z
authors.lastname: Liu
authors.forename: Kunbo
authors.initials: K
authors.lastname: Wang
authors.forename: Yujun
authors.initials: Y
authors.lastname: Yan
mesh_terms: D000818:Animals; D019295:Computational Biology; D003840:Deoxycholic Acid / Q000737:chemistry*; D008099:Liver / Q000378:metabolism; D008390:Markov Chains; D013058:Mass Spectrometry / Q000379:methods*; D008565:Membrane Proteins / Q000032:analysis; D008567:Membranes, Artificial; D010455:Peptides / Q000737:chemistry; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D051381:Rats; D015203:Reproducibility of Results; D012967:Sodium Dodecyl Sulfate / Q000737:chemistry
chemical_list: D008565:Membrane Proteins; D008567:Membranes, Artificial; D010455:Peptides; D020543:Proteome; D003840:Deoxycholic Acid; D012967:Sodium Dodecyl Sulfate
keywords: Mass spectrometry; Membrane proteomics; Sample preparation; Shotgun analysis; Sodium deoxycholate