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Bioinformatics Advance Access published online on April 7, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti439
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received November 12, 2004
Revised March 29, 2005
Accepted April 6, 2005

Applications note

pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry

Dequan Li 1*, Yan Fu 1, Ruixiang Sun 2, Charles X. Ling 3, Yonggang Wei 2, Hu Zhou 4, Rong Zeng 4, Qiang Yang 5, Simin He 2, and Wen Gao 1

1 Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China; Graduate School of Chinese Academy of Sciences, Beijing 100039, China
2 Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China
3 Department of Computer Science, The University of Western Ontario, Canada
4 Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
5 Department of Computer Science, Hong Kong University of Science and Technology, Hong Kong, China

* To whom correspondence should be addressed.
Dequan Li, E-mail: dqli{at}jdl.ac.cn


  Abstract

Summary: Research in proteomics requires powerful database-searching software to automatically identify protein sequences in a complex protein mixture via tandem mass spectrometry. In this paper, we describe a novel database-searching software system called pFind (peptide/protein Finder), which employs an effective peptide-scoring algorithm that we previously reported. The pFind server is implemented with the C++ STL, .Net and XML technologies. As a result, high speed and good usability of the software are achieved.

Availability: The pFind web server can be freely accessed through the web site http://pfind.jdl.ac.cn. In this web site, the compiled binary of the local version is also available.


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