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Title page for ETD etd-03222012-143216

Type of Document Dissertation
Author Ma, Zeqiang
URN etd-03222012-143216
Title Algorithms for shotgun proteomics spectral identification and quality assessment
Degree PhD
Department Biomedical Informatics
Advisory Committee
Advisor Name Title
David L. Tabb Committee Chair
Bing Zhang Committee Member
Daniel C. Liebler Committee Member
Kathleen L. Gould Committee Member
Zhongming Zhao Committee Member
  • mass spectrometry
  • proteomics
  • bioinformatics
  • quality assessment
  • quality control
  • peptide identification
Date of Defense 2012-03-08
Availability unrestricted
Tandem mass spectrometry-based shotgun proteomics has become a widespread technology for analyzing complex protein mixtures. Assessing the full information content of shotgun proteomics experiments has motivated a series of powerful bioinformatics advances. Here I present three bioinformatics tools for shotgun proteomics spectral identification and quality assessment. The IDBoost tool is a post-identification analysis tool that rescues spectral identifications and corrects identification errors by incorporating the relationships inferred through spectral clustering. The ScanRanker tool offers a way to recover unidentified high quality spectra for additional analysis via the assessment of tandem mass spectral quality. The QuaMeter tool focuses on the quality assessment of shotgun proteomics experiments and provides objective criteria for the evaluation of analytical system variability. Each tool was developed to solve one aspect of problems but together they work coordinately to provide an improved shotgun proteomics data analysis pipeline. The source code and binaries of these tools are available from http://fenchurch.mc.vanderbilt.edu/.
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