Database support for top-down proteomics

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.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Computer Science

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2010

Author dc:creator

• Kim, Yong-Bin

Contributors dc:contributor

• Belford, Geneva
• Belford, Geneva G.
• Kelleher, Neil L.
• Han, Jiawei
• Zhai, ChengXiang

• Top-down proteomics
• Database support for proteomics
• Prosight PTM
• Prosight Warehouse
• Biological warehouse integration
• Data warehouse

Statement dc:rights

• Copyright 2010 Yong-Bin Kim

Language dc:language

en

Handle dc:identifier

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

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/16720