Database support for top-down proteomics

Kim, Yong-Bin

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

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

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

Copyright and License Information

Copyright 2010 Yong-Bin Kim

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