Plasma proteome coverage is increased by unique peptide recovery from sodium deoxycholate precipitate

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Plasma proteome coverage is increased by unique peptide recovery from sodium deoxycholate precipitate

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作者：Aida Serra ; Hongbin Zhu ; Xavier Gallart-Palau…
关键词：Plasma proteome ; Mass spectrometry ; Shotgun proteomics ; Sodium deoxycholate ; Trypsin digestion
刊名：Analytical and Bioanalytical Chemistry
出版年：2016
出版时间：March 2016
年：2016
卷：408
期：7
页码：1963-1973
全文大小：752 KB
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作者单位：Aida Serra (1)
Hongbin Zhu (1)
Xavier Gallart-Palau (1)
Jung Eun Park (1)
Hee Haw Ho (2)
James P. Tam (1)
Siu Kwan Sze (1)

1. School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
2. Department of Cardiology, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore
刊物类别：Chemistry and Materials Science
刊物主题：Chemistry
Analytical Chemistry
Food Science
Inorganic Chemistry
Physical Chemistry
Monitoring, Environmental Analysis and Environmental Ecotoxicology
出版者：Springer Berlin / Heidelberg
ISSN：1618-2650

文摘

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.