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Mass Spectrometric Method Development and Applications for Comprehensive Proteome Analysis

  • Author / Creator
    Ye, Xiaoxia
  • In the field of proteomics research, it is desirable to detect the entire proteome or all the proteins present in a sample. However, due to the complexity of most samples, this task is challenging. My thesis work is mainly focused on the development of new protein solubilization and fractionation techniques to increase the identification efficiency in shotgun proteomic studies, namely to detect as many proteins as possible at high sample handling throughput. Several techniques have been developed or optimized in this thesis. First, protein level fractionation by using sequential protein precipitation and solubilization was effective in simplifying a complex sample and enhancing the proteome coverage. Second, microwave-assisted sequential protein solubilization (MAPS) was developed to speed up the protein solubilization process, increase protein solubility and protein digestion efficiency. As a result, by using MAPS combined with two dimensional-liquid chromatography (2D-LC) tandem mass spectrometry (MS/MS) analysis, peptide and protein identification efficiency was improved. Third, a faster and better resolution in protein fractionation was achieved by a macro-porous C18 reversed-phase liquid chromatography column (mRP-C18). The mRP-C18 fractionation method was then optimized and applied to the analysis of the phosphoproteome of MDA-MB-231 cells. Finally, sequential phosphopeptide enrichment by metal ion affinity chromatography (IMAC) and metal oxide affinity chromatography (TiO2) combined with strong cation exchange (SCX)-reverse phase liquid chromatography (RPLC) MS/MS method was applied to the analysis of human breast cancer tissues. 297 phosphoproteins were found possibly related to the metastasis of breast tumor and 875 phosphoproteins were found possibly related to the genesis of the breast tumor. The techniques developed or optimized in my thesis work improved sample preparation and fractionation efficiency, and therefore enhanced the overall efficiency of proteome identification. The newly identified phosphoproteins in MDA-MB-231 cells and human breast cancer tissues may generate novel insight into breast cancer biology. These approaches also hold great potential for profiling a wider range of proteomes in a more comprehensive and efficient way.

  • Subjects / Keywords
  • Graduation date
    2012-06
  • Type of Item
    Thesis
  • Degree
    Doctor of Philosophy
  • DOI
    https://doi.org/10.7939/R3TT4G453
  • License
    This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.
  • Language
    English
  • Institution
    University of Alberta
  • Degree level
    Doctoral
  • Department
    • Department of Chemistry
  • Supervisor / co-supervisor and their department(s)
    • Li, Liang (Chemistry Department)
  • Examining committee members and their departments
    • Lucy, Charles (Chemistry)
    • Vederas, John (Chemistry)
    • Yeung, Ken (Chemistry and Biochemistry, University of Western Ontario)
    • Schultz, Michael (Chemistry)
    • Serpe, Michael (Chemistry)