pFind Studio: a computational solution for mass spectrometry-based proteomics


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 discovery rate (FDR) of peptide identification. However, this is usually done manually by users and all of existing tools lack an automated module to estimate the FDR. 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 FDR before searching. Then the system will calculate a threshold that achieves the FDR 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

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Rapid Communications in Mass Spectrometry, 21,2985-2991,2007. [abstract]

pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry.

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, Wen Gao.

Bioinformatics, 21(13), 3049-3050, 2005. [abstract]

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

De-Quan Li, Yan Fu, Rui-Xiang Sun, Charles X. Ling, Yonggang Wei, Hu Zhou, Rong Zeng, Qiang Yang, Si-Min He and Wen Gao.

Bioinformatics 20, 1948-1954, 2004. [abstract]

Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry.

Yan Fu, Qiang Yang, Rui-Xiang Sun, De-Quan Li, Rong Zeng, Charles X. Ling, Wen Gao.