Database Support for Top-Down Proteomics

Kim, Yong-Bin

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

Description

Title

Database Support for Top-Down Proteomics

Author(s)

Kim, Yong-Bin

Issue Date

2010-07-13

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

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

Copyright and License Information

Copyright 2010 Yong-Bin Kim

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