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Enhanced SDC-assisted digestion coupled with lipid chromatography-tandem mass spectrometry for shotgun analysis of membrane proteome

Lin, Yong, Wang, Kunbo, Liu, Zhonghua, Lin, Haiyan, Yu, Lijun·2015·Journal of Chromatography B
DOI 10.1016/j.jchromb.2015.08.019
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Abstract

Despite the biological importance of membrane proteins, their analysis has lagged behind that of soluble proteins and still presents a great challenge mainly because of their highly hydrophobic nature and low abundance. Sodium deoxycholate (SDC)-assisted digestion strategy has been introduced in our previous papers, which cleverly circumvents many of the challenges in shotgun membrane proteomics. However, it is associated with significant sample loss due to the slightly weaker extraction/solubilization ability of 1% SDC. In this study, an enhanced SDC-assisted digestion method (ESDC method) was developed that incorporates the almost strongest ability of SDC with a high concentration (5%) to lyse membrane and extract/solubilize hydrophobic membrane proteins, and then dilution to 1% for more efficient digestion. The comparative study using rat liver membrane-enriched sample showed that, compared with previous SDC-assisted method and the "universal" filter-aided sample preparation (FASP) method, the ESDC method not only increased the identified number of total proteins, membrane proteins, hydrophobic proteins, integral membrane proteins (IMPs) and IMPs with more than 5 transmembrane domains (TMDs) by an average of 10.8%, 13.2%, 17.8%, 17.9% and 52.9%, respectively, but also enhanced the identified number of total peptides and hydrophobic peptides by averagely 12.5% and 14.2%. These results demonstrated that the ESDC method provides a substantial improvement in the recovery and i…

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Metadata

Authors
Lin, Y., Wang, K., Liu, Z., Lin, H., & Yu, L.
Venue
Journal of Chromatography B
Publisher
Elsevier BV
Published
2015-10
Volume
1002
Pages
144-151
ISSN
1570-0232
DOI
10.1016/j.jchromb.2015.08.019
Cited by
14
References
1
Language
en
Licence
www.elsevier.com/tdm/userlicense/1.0/ (tdm)

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Lin, Y., Wang, K., Liu, Z., Lin, H., & Yu, L. (2015). Enhanced SDC-assisted digestion coupled with lipid chromatography-tandem mass spectrometry for shotgun analysis of membrane proteome. Journal of Chromatography B. https://doi.org/10.1016/j.jchromb.2015.08.019