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Database support for top-down proteomics

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Title: Database support for top-down proteomics
Author(s): Kim, Yong-Bin
Director of Research: Belford, Geneva
Doctoral Committee Chair(s): Belford, Geneva
Doctoral Committee Member(s): Kelleher, Neil L.; Han, Jiawei; Zhai, ChengXiang
Department / Program: Computer Science
Discipline: Computer Science
Degree Granting Institution: University of Illinois at Urbana-Champaign
Degree: Ph.D.
Genre: Dissertation
Subject(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.
Issue Date: 2010-08-20
URI: http://hdl.handle.net/2142/16720
Rights Information: Copyright 2010 Yong-Bin Kim
Date Available in IDEALS: 2010-08-20
Date Deposited: 2010-08
 

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