Interdisciplinary Bio Central
 
Etc. (Bioinformatics/Computational biology/Molecular modeling)

Proteomics Data Analysis using Representative Database
Kyung-Hoon Kwon1, Gun Wook Park1, Jin Young Kim2, Young Mok Park1 and Jong Shin Yoo3,*
1Systems Biology Core Facility, Korea Basic Science Institute, Eoeun-dong, Yusung-gu, Daejeon 305-333, Republic of Korea
2Proteomics Team, Korea Basic Science Institute, Eoeun-dong, Yusung-gu, Daejeon 305-333, Republic of Korea
3Division of Instrument Development , Korea Basic Science Institute, Eoeun-dong, Yusung-gu, Daejeon 305-333, Republic of Korea
*Corresponding author
  Published : May 31, 2007
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Synopsis

In the proteomics research using mass spectrometry, the protein database search gives the protein information from the peptide sequences that show the best match with the tandem mass spectra. The protein sequence database has been a powerful knowledgebase for this protein identification. However, as we accumulate the protein sequence information in the database, the database size gets to be huge. Now it becomes hard to consider all the protein sequences in the database search because it consumes much computing time. For the high-throughput analysis of the proteome, usually we have used the non-redundant refined database such as IPI human database of European Bioinformatics Institute. While the non-redundant database can supply the search result in high speed, it misses the variation of the protein sequences. In this study, we have concerned the proteomics data in the point of protein similarities and used the network analysis tool to build a new analysis method. This method will be able to save the computing time for the database search and keep the sequence variation to catch the modified peptides.

Keyword: Proteomics Data Analysis, Representative Database
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