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MultiProtIdent: Identifying Proteins Using Database Search and Protein−Protein Interactions

Hsien-Da Huang,^† Tzong-Yi Lee,^† Li-Cheng Wu,^‡ Feng-Mao Lin,^‡ Hsueh-Fen Juan,^§ Jorng-Tzong Horng,*^‡ and Ann-Ping Tsou*

Department of Biological Science and Technology and Institute pf Bioinformatics, National Chiao-Tung University, Hsin-Chu 300, Taiwan, Department of Computer Science and Information Engineering, National Central University, Chung-Li 320, Taiwan, Department of Life Science and Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 106, Taiwan, Department of Life Science, National Central University, Chung-Li 320, Taiwan, and Institute of Biotechnology in Medicine, National Yang-Ming University, Taipei 112, Taiwan

J. Proteome Res., 2005, 4 (3), pp 690–697

DOI: 10.1021/pr0498335

Publication Date (Web): April 8, 2005

†

Department of Biological Science and Technology and Institute of Bioinformatics, National Chiao-Tung University.

‡

Department of Computer Science and Information Engineering, National Central University.

Department of Life Science & Institute of Molecular and Cellular Biology, National Taiwan University.

To whom correspondence should be addressed. Jorng-Tzong Horng. E-mail: horng@db.csie.ncu.edu.tw. Phone: +886-3-4227151 Extn. 35307. Fax: +886-3-4222681. Address: Department of Computer Science and Information Engineering, National Central University, Chung-Li City 320, Taiwan. Ann-Ping Tsou. E-mail: aptwou@ym.edu.tw. Phone: +886-2-28267155. Fax: +886-2-28264092. Address: Institute of Biotechnology in Medicine, National Yang-Ming University, Taipei 112, Taiwan.

Department of Life Science, National Central University.

Institute of Biotechnology in Medicine, National Yang-Ming University.

Abstract

Protein identification is important in proteomics. Proteomic analyses based on mass spectra (MS) constitute innovative ways to identify the components of protein complexes. Instruments can obtain the mass spectrum to an accuracy of 0.01 Da or better, but identification errors are inevitable. This study shows a novel tool, MultiProtIdent, which can identify proteins using additional information about protein−protein interactions and protein functional associations. Both single and multiple Peptide Mass Fingerprints (PMFs) are input to MultiProtIdent, which matches the PMFs to a theoretical peptide mass database. The relationships or interactions among proteins are considered to reduce false positives in PMF matching. Experiments to identify protein complexes reveal that MultiProtIdent is highly promising. The website associated with this study is http://dbms104.csie.ncu.edu.tw/.

Keywords: protein identification • peptide mass fingerprint • protein−protein interaction

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