title: ISPIDER Central: an integrated database web-server for proteomics.
abstract: 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.
authors.affiliation: Faculty of Life Sciences, University of Manchester, M13 9PT, UK.
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Siepen
authors.forename: Khalid
authors.initials: K
authors.lastname: Belhajjame
authors.forename: Julian N
authors.initials: JN
authors.lastname: Selley
authors.forename: Suzanne M
authors.initials: SM
authors.lastname: Embury
authors.forename: Norman W
authors.initials: NW
authors.lastname: Paton
authors.forename: Carole A
authors.initials: CA
authors.lastname: Goble
authors.forename: Stephen G
authors.initials: SG
authors.lastname: Oliver
authors.forename: Robert
authors.initials: R
authors.lastname: Stevens
authors.forename: Lucas
authors.initials: L
authors.lastname: Zamboulis
authors.forename: Nigel
authors.initials: N
authors.lastname: Martin
authors.forename: Alexandra
authors.initials: A
authors.lastname: Poulovassillis
authors.forename: Philip
authors.initials: P
authors.lastname: Jones
authors.forename: Richard
authors.initials: R
authors.lastname: Côté
authors.forename: Henning
authors.initials: H
authors.lastname: Hermjakob
authors.forename: Melissa M
authors.initials: MM
authors.lastname: Pentony
authors.forename: David T
authors.initials: DT
authors.lastname: Jones
authors.forename: Christine A
authors.initials: CA
authors.lastname: Orengo
authors.forename: Simon J
authors.initials: SJ
authors.lastname: Hubbard
mesh_terms: D003196:Computer Graphics; D030562:Databases, Protein; D020407:Internet; D013058:Mass Spectrometry; D040901:Proteomics; D012984:Software; D018511:Systems Integration