Complex Proteomes Analysis Using Label-Free Mass Spectrometry-Based Quantitative Approach Coupled with Biomedical Knowledge

  • Chao Pan
  • Wenxian Peng
  • Huilong Duan
  • Ning Deng
Conference paper
Part of the IFIP Advances in Information and Communication Technology book series (IFIPAICT, volume 432)

Abstract

Label-free quantitative proteomics based on mass spectrometry plays an essential role in large-scale analysis of complex proteomes. Meanwhile, quantitative proteomics is not only a way for data processing, but also an important approach for exploring protein functions and interactions in a large-scale manner. An effective method combining quantitation and qualification should be built. To systematically overcome this challenge, we proposed a new label-free quantitative method using spectral counting in the proposed method, the count of shared peptides was considered as an optimized factor to accurately appraise abundance of Isoforms for complex proteomes. Large-scale functional annotations for complex proteomes were extracted by g:Profiler and were assigned to functional clusters. To test the effect of the methods, three groups of mitochondrial proteins including mouse heart mitochondrial dataset, mouse liver mitochondrial dataset and human heart mitochondrial dataset were selected for analysis. According to the biochemical properties of mitochondrial proteins, all functional annotations were assigned to various signalling pathway or functional clusters. We came to draw a conclusion that the strategy with shared peptides overcame inaccurate and overestimated results for low-abundant isoforms to improve accuracy, and quantitative proteomics coupled with biomedical knowledge can thoroughly comprehend functions and relationships for complex proteomes, and contribute to providing a new method for large-scale comparative or diseased proteomics.

Keywords

Complex Proteomes Label-free Quantitation Mass Spectrometry Biomedical Knowledge 

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References

  1. 1.
    Zhao, Y., Lee, W.N.P., Xiao, G.G.: Quantitative proteomics and biomarker discovery in human cancer. Expert Rev. Proteomics 6(2), 115–118 (2009)CrossRefGoogle Scholar
  2. 2.
    Dong, M.Q., Venable, J.D., Au, N., et al.: Quantitative mass spectrometry identifies insulin signaling targets in C. elegans. Science 317(5838), 660–663 (2007)CrossRefGoogle Scholar
  3. 3.
    Lill, J.: Proteomic tools for quantitation by mass spectrometry. Mass Spectrometry Reviews 22(3), 182–194 (2003)CrossRefGoogle Scholar
  4. 4.
    Schulze, W.X., Usadel, B.: Quantitation in mass-spectrometry-based proteomics. Annual Review of Plant Biology 61, 491–516 (2010)CrossRefGoogle Scholar
  5. 5.
    Zhu, W., Smith, J.W., Huang, C.M.: Mass spectrometry-based label-free quantitative proteomics. Journal of Biomedicine and Biotechnology (2010)Google Scholar
  6. 6.
    Zhang, Y., Wen, Z., Washburn, M.P., et al.: Refinements to label free proteome quantitation: how to deal with peptides shared by multiple proteins. Analytical Chemistry 82(6), 2272–2281 (2010)CrossRefGoogle Scholar
  7. 7.
    Zybailov, B., Mosley, A.L., Sardiu, M.E., et al.: Statistical Analysis of Membrane Proteome Expression Changes in Saccharomyces c erevisiae. Journal of Proteome Research 5(9), 2339–2347 (2006)CrossRefGoogle Scholar
  8. 8.
    Kersey, P.J., Duarte, J., Williams, A., et al.: The International Protein Index: an integrated database for proteomics experiments. Proteomics 4(7), 1985–1988 (2004)CrossRefGoogle Scholar
  9. 9.
    Reimand, J., Kull, M., Peterson, H., et al.: g: Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Research 35(suppl. 2), W193–W200 (2007)Google Scholar
  10. 10.
    Zhang, J., Li, X., Mueller, M., et al.: Systematic characterization of the murine mitochondrial proteome using functionally validated cardiac mitochondria. Proteomics 8(8), 1564–1575 (2008)CrossRefGoogle Scholar
  11. 11.
    Zhang, J., Liem, D.A., Mueller, M., et al.: Altered proteome biology of cardiac mitochondria under stress conditions. The Journal of Proteome Research 7(6), 2204–2214 (2008)CrossRefGoogle Scholar
  12. 12.
    Zhang, J., Lin, A., Powers, J., et al.: Mitochondrial proteome design: From molecular identity to pathophysiological regulation. The Journal of General Physiology 139(6), 395–406 (2012)CrossRefGoogle Scholar
  13. 13.
    Wang, L., Li, D.Q., Fu, Y., et al.: pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry. Rapid Communications in Mass Spectrometry 21(18), 2985–2991 (2007)CrossRefGoogle Scholar
  14. 14.
    Wu, Q., Zhao, Q., Liang, Z., et al.: NSI and NSMT: usages of MS/MS fragment ion intensity for sensitive differential proteome detection and accurate protein fold change calculation in relative label-free proteome quantification. Analyst 137(13), 3146–3153 (2012)CrossRefGoogle Scholar
  15. 15.
    Benjamini, Y., Yekutieli, D.: The control of the false discovery rate in multiple testing under dependency. Annals of Statistics, 1165–1188 (2001)Google Scholar
  16. 16.
    McDonald, T.G., Van Eyk, J.E.: Mitochondrial proteomics. Basic Research in Cardiology 98(4), 219–227 (2003)Google Scholar
  17. 17.
    Weiss, J.N., Korge, P., Honda, H.M., et al.: Role of the mitochondrial permeability transition in myocardial disease. Circulation Research 93(4), 292–301 (2003)CrossRefGoogle Scholar
  18. 18.
    Honda, H.M., Korge, P., Weiss, J.N.: Mitochondria and ischemia/reperfusion injury. Annals of the New York Academy of Sciences 1047(1), 248–258 (2005)CrossRefGoogle Scholar

Copyright information

© IFIP International Federation for Information Processing 2014

Authors and Affiliations

  • Chao Pan
    • 1
  • Wenxian Peng
    • 2
  • Huilong Duan
    • 1
  • Ning Deng
    • 1
  1. 1.College of Biomedical Engineering and Instrument Science, Key Laboratory of Biomedical Engineering of Ministry of Education of ChinaZhejiang UniversityHangzhouChina
  2. 2.Department of RadiologyZhejiang Medical CollegeHangzhouChina

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