Nucleic Acids Research Advance Access published online on April 25, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn196
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Web Server |
ISPIDER Central: an integrated database web-server for proteomics
1Faculty of Life Sciences, University of Manchester, M13 9PT, 2School of Computer Science, Faculty of Engineering and Physical Sciences, University of Manchester, 3Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, 4School of Computer Science and Information Systems, Birkbeck College, University of London, 5Department of Biochemistry and Molecular Biology, University College London, Gower street, London, 6EMBL Outstation European Bioinfomatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge and 7Department of Computer Science, University College London, Gower street, London, UK
*To whom correspondence should be addressed. Tel: +44 161 3068930; Fax: +44 161 2755082; Email: simon.hubbard{at}manchester.ac.uk
Received January 31, 2008. Revised March 14, 2008. Accepted April 3, 2008.
Despite the growing volumes of proteomic data, integration of the underlying results remains problematic owing to differences in formats, data captured, protein accessions and services available from the individual repositories. To address this, we present the ISPIDER Central Proteomic Database search (http://www.ispider.manchester.ac.uk/cgi-bin/ProteomicSearch.pl), an integration service offering novel search capabilities over leading, mature, proteomic repositories including PRoteomics IDEntifications database (PRIDE), PepSeeker, PeptideAtlas and the Global Proteome Machine. It enables users to search for proteins and peptides that have been characterised in mass spectrometry-based proteomics experiments from different groups, stored in different databases, and view the collated results with specialist viewers/clients. In order to overcome limitations imposed by the great variability in protein accessions used by individual laboratories, the European Bioinformatics Institute's Protein Identifier Cross-Reference (PICR) service is used to resolve accessions from different sequence repositories. Custom-built clients allow users to view peptide/protein identifications in different contexts from multiple experiments and repositories, as well as integration with the Dasty2 client supporting any annotations available from Distributed Annotation System servers. Further information on the protein hits may also be added via external web services able to take a protein as input. This web server offers the first truly integrated access to proteomics repositories and provides a unique service to biologists interested in mass spectrometry-based proteomics.