A fast Peptide Match service for UniProt Knowledgebase

doi:10.1093/bioinformatics/btt484

. 2013 Nov 1;29(21):2808-9.

doi: 10.1093/bioinformatics/btt484. Epub 2013 Aug 19.

A fast Peptide Match service for UniProt Knowledgebase

Chuming Chen¹, Zhiwen Li, Hongzhan Huang, Baris E Suzek, Cathy H Wu; UniProt Consortium

Affiliations

Affiliation

¹ Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneva 4, Switzerland.

PMID: 23958731
PMCID: PMC3799477
DOI: 10.1093/bioinformatics/btt484

A fast Peptide Match service for UniProt Knowledgebase

Chuming Chen et al. Bioinformatics. 2013.

. 2013 Nov 1;29(21):2808-9.

doi: 10.1093/bioinformatics/btt484. Epub 2013 Aug 19.

Authors

Chuming Chen¹, Zhiwen Li, Hongzhan Huang, Baris E Suzek, Cathy H Wu; UniProt Consortium

Affiliation

¹ Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneva 4, Switzerland.

PMID: 23958731
PMCID: PMC3799477
DOI: 10.1093/bioinformatics/btt484

Abstract

Summary: We have developed a new web application for peptide matching using Apache Lucene-based search engine. The Peptide Match service is designed to quickly retrieve all occurrences of a given query peptide from UniProt Knowledgebase (UniProtKB) with isoforms. The matched proteins are shown in summary tables with rich annotations, including matched sequence region(s) and links to corresponding proteins in a number of proteomic/peptide spectral databases. The results are grouped by taxonomy and can be browsed by organism, taxonomic group or taxonomy tree. The service supports queries where isobaric leucine and isoleucine are treated equivalent, and an option for searching UniRef100 representative sequences, as well as dynamic queries to major proteomic databases. In addition to the web interface, we also provide RESTful web services. The underlying data are updated every 4 weeks in accordance with the UniProt releases.

Availability: http://proteininformationresource.org/peptide.shtml.

Contact: chenc@udel.edu.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

**Fig. 1.**
The search interfaces and functionalities of the Peptide Match server. (A) search interfaces; (B) matched result summary; (C) dynamic proteomic databases search results; (D) taxonomic views

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References

1. Askenazi M, et al. The complete peptide dictionary-a meta-proteomics resource. Proteomics. 2010;23:4306–4310. - PubMed
1. Craig R, et al. Open source system for analyzing, validating, and storing protein identification data. J. Proteome Res. 2004;3:1234–1242. - PubMed
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1. Koskinen JP, Holm L. SANS: high-throughput retrieval of protein sequences allowing 50% mismatches. Bioinformatics. 2012;28:i438–i443. - PMC - PubMed

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[1] Askenazi M, et al. The complete peptide dictionary-a meta-proteomics resource. Proteomics. 2010;23:4306–4310. - PubMed

[2] Askenazi M, et al. The complete peptide dictionary-a meta-proteomics resource. Proteomics. 2010;23:4306–4310. - PubMed

[3] Craig R, et al. Open source system for analyzing, validating, and storing protein identification data. J. Proteome Res. 2004;3:1234–1242. - PubMed

[4] Craig R, et al. Open source system for analyzing, validating, and storing protein identification data. J. Proteome Res. 2004;3:1234–1242. - PubMed

[5] Desiere F, et al. The PeptideAtlas project. Nucleic Acids Res. 2006;34:D655–D658. - PMC - PubMed

[6] Desiere F, et al. The PeptideAtlas project. Nucleic Acids Res. 2006;34:D655–D658. - PMC - PubMed

[7] Huang H, et al. A comprehensive protein-centric ID mapping service for molecular data integration. Bioinformatics. 2011;27:1190–1191. - PMC - PubMed

[8] Huang H, et al. A comprehensive protein-centric ID mapping service for molecular data integration. Bioinformatics. 2011;27:1190–1191. - PMC - PubMed

[9] Koskinen JP, Holm L. SANS: high-throughput retrieval of protein sequences allowing 50% mismatches. Bioinformatics. 2012;28:i438–i443. - PMC - PubMed

[10] Koskinen JP, Holm L. SANS: high-throughput retrieval of protein sequences allowing 50% mismatches. Bioinformatics. 2012;28:i438–i443. - PMC - PubMed

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A fast Peptide Match service for UniProt Knowledgebase

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A fast Peptide Match service for UniProt Knowledgebase

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