University of Illinois Urbana-Champaign

Database Support for Top-Down Proteomics

Kim, Yong-Bin

Content Files
Kim_Yong-Bin.pdf

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https://hdl.handle.net/2142/16577

Description

Title
Database Support for Top-Down Proteomics
Author(s)
Kim, Yong-Bin
Issue Date
2010-07-13
Date of Ingest
2010-07-13T20:33:35Z
Keyword(s)
  • top-down proteomics
  • data warehouse
  • prosight ptm
  • prosight warehouse
  • biological database integration
  • proteomics
Language
en
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.
Type of Resource
text
Permalink
http://hdl.handle.net/2142/16577
Copyright and License Information
Copyright 2010 Yong-Bin Kim

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Dissertations and Theses - Computer Science PRIMARY
Dissertations and Theses from the Siebel School of Computer Science