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2030-01-01
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SEARCH ENGINE PROCESSOR: FILTERING AND ORGANIZING PEPTIDE SPECTRUM MATCHES
Carvalho, Paulo C. et al. | Date Issued: 2012
Author
Carvalho, Paulo C.
Fischer, Juliana S. G.
Xu, Tao
Cociorva, Daniel
Balbuena, Tiago S.
Valente, Richard H.
Perales, Jonas
Yates, John R.
Barbosa, Valmir C.
Affilliation
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. Rio de Janeiro, RJ. Brasil / Fundação Oswaldo Cruz. Instituto Carlos Chagas. Paraná, Brasil
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. Rio de Janeiro, RJ. Brasil / Fundação Oswaldo Cruz. Instituto Carlos Chagas. Paraná, Brasil
The Scripps Research Institute. Department of Chemical Physiology. La Jolla, CA, USA.
The Scripps Research Institute. Department of Chemical Physiology. La Jolla, CA, USA.
University of Missouri. Department of Biochemistry. Columbia, MO, USA.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. Rio de Janeiro, RJ. Brasil.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. Rio de Janeiro, RJ. Brasil.
The Scripps Research Institute. Department of Chemical Physiology. La Jolla, CA, USA.
Universidade Federal do Rio de Janeiro. COPPE. Programa de Engenharia de Sistemas e Ciência da Computação. Rio de Janeiro, RJ, Brasil.l
Abstract
The search engine processor (SEPro) is a tool for filtering, organizing, sharing, and displaying peptide spectrum matches. It employs a novel three-tier Bayesian approach that uses layers of spectrum, peptide, and protein logic to lead the data to converge to a single list of reliable protein identifications. SEPro is integrated into the PatternLab for proteomics environment, where an arsenal of tools for analyzing shotgun proteomic data is provided. By using the semi-labeled decoy approach for benchmarking, we show that SEPro significantly outperforms a commercially available competitor.
Keywords in Portuguese
Bioinformática
Filtragem
Qualidade
Compartilhamento
Avaliação comparativa
 
Keywords
Bioinformatics
Filtering
Quality
Semi-labeled decoy approach
Sharing
Shotgun proteomics
 
Publisher
Wiley
Citation
CARVALHO, Paulo C. et al. Search engine processor: Filtering and organizing peptide spectrum matches. Proteomics, v.12, p.944-949, 2012.
DOI
10.1002/pmic.201100529
ISSN
1615-9853