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Ionic liquid 1-butyl-3-methyl imidazolium tetrafluoroborate for shotgun membrane proteomics

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Abstract

The solubility and digestion efficiency are two crucial factors that might affect the identification of integral membrane proteins (IMPs). In this work, 1% (v/v) ionic liquid (IL), 1-butyl-3-methyl imidazolium tetrafluoroborate (BMIM BF4), added in NH4HCO3 buffer (pH 8.3), was applied as a sample preparation buffer for IMPs analysis. Compared to the commonly used sodium dodecyl sulfate and methanol methods, the number of identified IMPs from rat brain by microcolumn reversed phase liquid chromatography (μRPLC)-electrospray ionization tandem mass spectrometry (ESI-MS/MS) was improved by over three times, which might be due to the fact that BMIM BF4 offered high solubilizing ability for IMPs and good compatibility for tryptic digestion. Furthermore, compared to Rapigest and urea methods, with BMIM BF4 method, the number of identified IMPs from rat brain could be improved 25% and 80%, respectively, which might be contributed to the good solubilizing ability and high thermal stability of such IL. With the sample treated by BMIM BF4 method, by 2D-nanoSCX-RPLC-ESI-MS/MS, 1,450 non-redundant proteins and 7,978 unique peptides were identified from rat brain, and 418 proteins contained at least one predicted transmembrane domain, with false discovery rates of less than 1% for peptide identification, and at least two identified unique peptides per protein. All these results demonstrate that the BMIM BF4 method is of high potential for the large-scale identification of IMPs.

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Acknowledgements

The authors are grateful for the financial support from National Basic Research Program of China (2007CB914100), National Natural Science Foundation (20935004), and Knowledge Innovation Program of Chinese Academy of Sciences (KJCX2YW.H09).

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Authors and Affiliations

  1. National Chromatographic R. & A. Center, Key Laboratory of Separation Science on Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China

    Liangliang Sun, Dingyin Tao, Bin Han, Junfeng Ma, Guijie Zhu, Zhen Liang, Yichu Shan, Lihua Zhang & Yukui Zhang

  2. Graduate School of Chinese Academy of Sciences, Beijing, 100039, China

    Liangliang Sun & Dingyin Tao

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  1. Liangliang Sun
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  2. Dingyin Tao
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  8. Lihua Zhang
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Correspondence to Lihua Zhang.

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Published in the special issue Analytical and Bioanalytical Science in China with Guest Editors Lihua Zhang, Qiankun Zhuang, and Yukui Zhang.

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Sun, L., Tao, D., Han, B. et al. Ionic liquid 1-butyl-3-methyl imidazolium tetrafluoroborate for shotgun membrane proteomics. Anal Bioanal Chem 399, 3387–3397 (2011). https://doi.org/10.1007/s00216-010-4381-5

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  • DOI: https://doi.org/10.1007/s00216-010-4381-5

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