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Institute
of Computing Technology,
Chinese
Academy of Sciences,
Beijing, China
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Overview
pFind is a
search engine system for automated peptide and protein identification from
tandem mass spectra.
Although many
available database searching tools have been developed, there are still a
lot of challenges in identification reliability, sensitivity and usability.
For example, the target-decoy database strategy has been widely used for
the estimation of false positive rate (FPR) of peptide identification. However,
this is usually done manually by users and all of existing tools lack an
automated module to estimate the FPR. Another problem is the speed of
searching high-throughput spectra against huge peptide and protein
databases. The improvements in the sensitivity of mass spectrometers and
the rapid expansion of databases have increased the scope and complexity of
searching. Traditional software architecture, i.e., running all tasks in a
stand-alone process and having not any data index, is more and more inadequate.
The newest
version of pFind incorporate several newly developed or improved
algorithms, modules and workflows: The system incorporates the target-decoy
database search strategy for automated FPR estimation. Users only need to
specify a required FPR before searching. Then the system will calculate a
threshold that achieves the FPR and filter search results automatically. We
developed a toolbox to index protein databases for high-throughput
application and designed all modules under a parallel-processing-oriented
architecture for distributing the computational load efficiently among a
lot of computers. These developments greatly improve the overall searching
speed.
Video
and manual
download video(1) video(2)
manual...
Publications
- Le-heng
Wang, De-Quan Li, Yan Fu, Hai-Peng Wang, Jing-Fen Zhang, Zuo-Fei Yuan,
Rui-Xiang Sun, Rong Zeng, Si-Min He and Wen Gao. pFind 2.0: a software
package for peptide and protein identification via tandem mass
spectrometry. Rapid Communications in Mass Spectrometry (RCMS) Vol.21,
No.18, pp2985-2991, 2007. [pdf] [abstract
] [supplementary
information]
- Dequan Li,
Yan Fu, Ruixiang Sun, Charles X. Ling, Yonggang Wei, Hu Zhou, Rong
Zeng, Qiang Yang, Simin He and Wen Gao. pFind: a novel
database-searching software system for automated peptide and protein
identification via tandem mass spectrometry. Bioinformatics, 21(13),
3049-3050, 2005 [pdf][abstract]
- Yan Fu,
Qiang Yang, Ruixiang Sun, Dequan Li, Rong Zeng, Charles X. Ling, Wen
Gao. Exploiting the kernel trick to correlate fragment ions for
peptide identification via tandem mass spectrometry. Bioinformatics
20, 1948-1954, 2004 [pdf] [abstract]
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