University of Illinois Urbana-Champaign

Database support for top-down proteomics

Kim, Yong-Bin

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https://hdl.handle.net/2142/16720

Description

Title
Database support for top-down proteomics
Author(s)
Kim, Yong-Bin
Issue Date
2010-08-20T17:55:52Z
Director of Research (if dissertation) or Advisor (if thesis)
Belford, Geneva
Doctoral Committee Chair(s)
Belford, Geneva G.
Committee Member(s)
  • Kelleher, Neil L.
  • Han, Jiawei
  • Zhai, ChengXiang
Department of Study
Computer Science
Discipline
Computer Science
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
  • Top-down proteomics
  • Database support for proteomics
  • Prosight PTM
  • Prosight Warehouse
  • Biological warehouse integration
  • Data warehouse
Abstract
Top-down proteomics is a revolutionary application for the identification and characterization of protein, known to be one of the most complicated and challenging issues in biology. In top-down proteomics, the quality and speed of the data warehouse is very important, as high accuracy results are returned by a database search. ProSight Warehouse fills the critical role as the data warehouse for ProSight PTM, the first publicly available top-down proteomics software suite. MySQL, a free relational database, was the base of this warehouse. Many annotated and predicted protein forms have been successfully incorporated into the organism-specific database and in the integrated database for human strains. To achieve high quality and efficiency, a database schema (Absolute Mass Search), data annotation methods (Shotgun and Extended Shotgun Annotation), data population strategies (on-the-fly population, bulk-loading method), and a database integration methodology for human protein were developed. With the successful implementation of ProSight Warehouse, ProSight PTM achieved its aspiration, highly accurate protein identification and characterization.
Graduation Semester
2010-08
Permalink
http://hdl.handle.net/2142/16720
Copyright and License Information
Copyright 2010 Yong-Bin Kim

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