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

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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.

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References

  1. Zhang Y, Fonslow BR, Shan B, Baek MC, Yates 3rd JR. Protein analysis by shotgun/bottom-up proteomics. Chem Rev. 2013;113(4):2343–94. doi:10.1021/cr3003533.

    Article  CAS  Google Scholar 

  2. Saveliev S, Bratz M, Zubarev R, Szapacs M, Budamgunta H, Urh M. Trypsin/Lys-C protease mix for enhanced protein mass spectrometry analysis. Nat Meth. 2013;10 (11). doi:10.1038/nmeth.f.371.

  3. Leimgruber R. Extraction and solubilization of proteins for proteomic studies. In: Walker J (ed) The proteomics protocols handbook. Humana Press; 2005. pp 1–18. doi:10.1385/1-59259-890-0:001.

  4. Choudhary C, Weinert BT, Nishida Y, Verdin E, Mann M. The growing landscape of lysine acetylation links metabolism and cell signalling. Nat Rev Mol Cell Biol. 2014;15(8):536–50. doi:10.1038/nrm3841.

    Article  CAS  Google Scholar 

  5. Choudhary J, Grant SG. Proteomics in postgenomic neuroscience: the end of the beginning. Nat Neurosci. 2004;7(5):440–5. doi:10.1038/nn1240.

    Article  CAS  Google Scholar 

  6. Fonslow BR, Stein BD, Webb KJ, Xu T, Choi J, Park SK, et al. Digestion and depletion of abundant proteins improves proteomic coverage. Nat Methods. 2013;10(1):54–6. doi:10.1038/nmeth.2250.

    Article  CAS  Google Scholar 

  7. Masuda T, Tomita M, Ishihama Y. Phase transfer surfactant-aided trypsin digestion for membrane proteome analysis. J Proteome Res. 2008;7(2):731–40. doi:10.1021/pr700658q.

    Article  CAS  Google Scholar 

  8. Zhou J, Zhou T, Cao R, Liu Z, Shen J, Chen P, et al. Evaluation of the application of sodium deoxycholate to proteomic analysis of rat hippocampal plasma membrane. J Proteome Res. 2006;5(10):2547–53. doi:10.1021/pr060112a.

    Article  CAS  Google Scholar 

  9. Lasonder E, Ishihama Y, Andersen JS, Vermunt AM, Pain A, Sauerwein RW, et al. Analysis of the plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature. 2002;419(6906):537–42. doi:10.1038/nature01111.

    Article  CAS  Google Scholar 

  10. Leon IR, Schwammle V, Jensen ON, Sprenger RR. Quantitative assessment of in-solution digestion efficiency identifies optimal protocols for unbiased protein analysis. Mol Cell Proteomics. 2013;12(10):2992–3005. doi:10.1074/mcp.M112.025585.

    Article  CAS  Google Scholar 

  11. Proc JL, Kuzyk MA, Hardie DB, Yang J, Smith DS, Jackson AM, et al. A quantitative study of the effects of chaotropic agents, surfactants, and solvents on the digestion efficiency of human plasma proteins by trypsin. J Proteome Res. 2010;9(10):5422–37. doi:10.1021/pr100656u.

    Article  CAS  Google Scholar 

  12. Erde J, Loo RR, Loo JA. Enhanced FASP (eFASP) to increase proteome coverage and sample recovery for quantitative proteomic experiments. J Proteome Res. 2014;13(4):1885–95. doi:10.1021/pr4010019.

    Article  CAS  Google Scholar 

  13. Molloy MP, Herbert BR, Walsh BJ, Tyler MI, Traini M, Sanchez JC, et al. Extraction of membrane proteins by differential solubilization for separation using two-dimensional gel electrophoresis. Electrophoresis. 1998;19(5):837–44. doi:10.1002/elps.1150190539.

    Article  CAS  Google Scholar 

  14. Datta A, Chen CP, Sze SK. Discovery of prognostic biomarker candidates of lacunar infarction by quantitative proteomics of microvesicles enriched plasma. PLoS One. 2014;9(4), e94663. doi:10.1371/journal.pone.0094663.

    Article  Google Scholar 

  15. Pathan M, Keerthikumar S, Ang C-S, Gangoda L, Quek CYJ, Williamson NA, et al. FunRich: an open access standalone functional enrichment and interaction network analysis tool. Proteomics. 2015;15(15):2596–601. doi:10.1002/pmic.201400515.

    Article  Google Scholar 

  16. Vizcaino JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Rios D, et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol. 2014;32(3):223–6. doi:10.1038/nbt.2839.

    Article  CAS  Google Scholar 

  17. Wisniewski JR, Ostasiewicz P, Mann M. High recovery FASP applied to the proteomic analysis of microdissected formalin fixed paraffin embedded cancer tissues retrieves known colon cancer markers. J Proteome Res. 2011;10(7):3040–9. doi:10.1021/pr200019m.

    Article  CAS  Google Scholar 

  18. Yu Y, Leng T, Yun D, Liu N, Yao J, Dai Y, et al. Global analysis of the rat and human platelet proteome—the molecular blueprint for illustrating multi-functional platelets and cross-species function evolution. Proteomics. 2010;10(13):2444–57. doi:10.1002/pmic.200900271.

    Article  CAS  Google Scholar 

  19. Manza LL, Stamer SL, Ham A-JL, Codreanu SG, Liebler DC. Sample preparation and digestion for proteomic analyses using spin filters. Proteomics. 2005;5(7):1742–5. doi:10.1002/pmic.200401063.

    Article  CAS  Google Scholar 

  20. Wisniewski JR, Zougman A, Nagaraj N, Mann M. Universal sample preparation method for proteome analysis. Nat Meth. 2009;6 (5):359–362. doi:http://www.nature.com/nmeth/journal/v6/n5/suppinfo/nmeth.1322_S1.html.

  21. Weber K, Kuter DJ. Reversible denaturation of enzymes by sodium dodecyl sulfate. J Biol Chem. 1971;246(14):4504–9.

    CAS  Google Scholar 

  22. Meng W, Zhang H, Guo T, Pandey C, Zhu Y, Kon OL, et al. One-step procedure for peptide extraction from in-gel digestion sample for mass spectrometric analysis. Anal Chem. 2008;80(24):9797–805. doi:10.1021/ac801344z.

    Article  CAS  Google Scholar 

  23. Lin Y, Liu Y, Li J, Zhao Y, He Q, Han W, et al. Evaluation and optimization of removal of an acid-insoluble surfactant for shotgun analysis of membrane proteome. Electrophoresis. 2010;31(16):2705–13. doi:10.1002/elps.201000161.

    Article  CAS  Google Scholar 

  24. Hao P, Ren Y, Datta A, Tam JP, Sze SK. Evaluation of the effect of trypsin digestion buffers on artificial deamidation. J Proteome Res. 2014;14(2):1308–14. doi:10.1021/pr500903b.

    Article  Google Scholar 

  25. Lin Y, Zhou J, Bi D, Chen P, Wang X, Liang S. Sodium-deoxycholate-assisted tryptic digestion and identification of proteolytically resistant proteins. Anal Biochem. 2008;377(2):259–66. doi:10.1016/j.ab.2008.03.009.

    Article  CAS  Google Scholar 

  26. Lin Y, Lin H, Liu Z, Wang K, Yan Y. Improvement of a sample preparation method assisted by sodium deoxycholate for mass-spectrometry-based shotgun membrane proteomics. J Sep Sci. 2014;37(22):3321–9. doi:10.1002/jssc.201400569.

    Article  CAS  Google Scholar 

  27. Nanjappa V, Thomas JK, Marimuthu A, Muthusamy B, Radhakrishnan A, Sharma R, et al. Plasma Proteome Database as a resource for proteomics research: 2014 update. Nucleic Acids Res. 2014;42(Database issue):D959–65. doi:10.1093/nar/gkt1251.

    Article  CAS  Google Scholar 

  28. Mitchell P. Proteomics retrenches. Nat Biotechnol. 2010;28(7):665–70.

    Article  CAS  Google Scholar 

  29. Ernoult E, Bourreau A, Gamelin E, Guette C. A proteomic approach for plasma biomarker discovery with iTRAQ labelling and OFFGEL fractionation. J Biomed Biotechnol. 2010;2010:8. doi:10.1155/2010/927917.

    Article  Google Scholar 

  30. Smejkal GB, Lazarev A. Separation methods in proteomics. CRC Press, 2005.

  31. Lin Y, Wang K, Yan Y, Lin H, Peng B, Liu Z. Evaluation of the combinative application of SDS and sodium deoxycholate to the LC-MS-based shotgun analysis of membrane proteomes. J Sep Sci. 2013;36(18):3026–34. doi:10.1002/jssc.201300413.

    CAS  Google Scholar 

  32. Ballif BA, Villen J, Beausoleil SA, Schwartz D, Gygi SP. Phosphoproteomic analysis of the developing mouse brain. Mol Cell Proteomics. 2004;3(11):1093–101. doi:10.1074/mcp.M400085-MCP200.

    Article  CAS  Google Scholar 

  33. Thiede B, Lamer S, Mattow J, Siejak F, Dimmler C, Rudel T, et al. Analysis of missed cleavage sites, tryptophan oxidation and N-terminal pyroglutamylation after in-gel tryptic digestion. Rap Comm Mass Spec. 2000;14(6):496–502. doi:10.1002/(sici)1097-0231(20000331)14:6<496::aid-rcm899>3.0.co;2-1.

    Article  CAS  Google Scholar 

  34. Ngoka LC. Sample prep for proteomics of breast cancer: proteomics and gene ontology reveal dramatic differences in protein solubilization preferences of radioimmunoprecipitation assay and urea lysis buffers. Proteome Sci. 2008;6:30. doi:10.1186/1477-5956-6-30.

    Article  Google Scholar 

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Acknowledgments

This work was supported in part by the Singapore Ministry of Education (Tier 2: ARC9/15), NTU-NHG Ageing Research Grant (ARG/14017), and Singapore Ministry of Education (Tier 1: RGT15/13).

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Authors and Affiliations

  1. School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore

    Aida Serra, Hongbin Zhu, Xavier Gallart-Palau, Jung Eun Park, James P. Tam & Siu Kwan Sze

  2. Department of Cardiology, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore

    Hee Haw Ho

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  1. Aida Serra
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  2. Hongbin Zhu
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  3. Xavier Gallart-Palau
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  7. Siu Kwan Sze
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Correspondence to Siu Kwan Sze.

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The study was approved by the Research Ethics Committee of Tan Tock Seng Hospital and Nanyang Technological University, Singapore. Written informed consent was obtained from all study participants (n = 34).

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The authors declare that they have no competing interests.

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Serra, A., Zhu, H., Gallart-Palau, X. et al. Plasma proteome coverage is increased by unique peptide recovery from sodium deoxycholate precipitate. Anal Bioanal Chem 408, 1963–1973 (2016). https://doi.org/10.1007/s00216-016-9312-7

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  • DOI: https://doi.org/10.1007/s00216-016-9312-7

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