title: Plasma proteome coverage is increased by unique peptide recovery from sodium deoxycholate precipitate.
abstract: The ionic detergent sodium deoxycholate (SDC) is compatible with in-solution tryptic digestion and LC-MS/MS-based shotgun proteomics by virtue of being easy to separate from the peptide products via precipitation in acidic buffers. However, it remains unclear whether unique human peptides co-precipitate with SDC during acid treatment of complex biological samples. In this study, we demonstrate for the first time that a large quantity of unique peptides in human blood plasma can be co-precipitated with SDC using an optimized sample preparation method prior to shotgun proteomic analysis. We show that the plasma peptides co-precipitated with SDC can be successfully recovered using a sequential re-solubilization and precipitation procedure, and that this approach is particularly efficient at the extraction of long peptides. Recovery of peptides from the SDC pellet dramatically increased overall proteome coverage (>60 %), thereby improving the identification of low-abundance proteins and enhancing the identification of protein components of membrane-bound organelles. In addition, when we analyzed the physiochemical properties of the co-precipitated peptides, we observed that SDC-based sample preparation improved the identification of mildly hydrophilic/hydrophobic proteins that would otherwise be lost upon discarding the pellet. These data demonstrate that the optimized SDC protocol is superior to sodium dodecyl sulfate (SDS)/urea treatment for identifying plasma biomarkers by shotgun proteomics.
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
authors.forename: Aida
authors.initials: A
authors.lastname: Serra
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
authors.forename: Hongbin
authors.initials: H
authors.lastname: Zhu
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
authors.forename: Xavier
authors.initials: X
authors.lastname: Gallart-Palau
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
authors.forename: Jung Eun
authors.initials: JE
authors.lastname: Park
authors.affiliation: Department of Cardiology, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore.
authors.forename: Hee Haw
authors.initials: HH
authors.lastname: Ho
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
authors.forename: James P
authors.initials: JP
authors.lastname: Tam
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore. SKSZE@NTU.EDU.SG.
authors.forename: Siu Kwan
authors.identifier: http://orcid.org/0000-0002-5652-1687
authors.initials: SK
authors.lastname: Sze
mesh_terms: D001798:Blood Proteins / Q000737:chemistry*; D011232:Chemical Precipitation; D003840:Deoxycholic Acid / Q000737:chemistry*; D003902:Detergents / Q000737:chemistry*; D006801:Humans; D010455:Peptides / Q000032:analysis*; D020543:Proteome / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D012967:Sodium Dodecyl Sulfate / Q000737:chemistry; D053719:Tandem Mass Spectrometry / Q000379:methods; D014357:Trypsin / Q000737:chemistry
chemical_list: D001798:Blood Proteins; D003902:Detergents; D010455:Peptides; D020543:Proteome; D003840:Deoxycholic Acid; D012967:Sodium Dodecyl Sulfate; D014357:Trypsin
keywords: Mass spectrometry; Plasma proteome; Shotgun proteomics; Sodium deoxycholate; Trypsin digestion