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.

Figure 1.

Flow chart of ISPIDER Central general architecture. The integration of the different results from independent queries over member repositories is achieved via spidyXML. This in turn may be processed by internal ISPIDER viewers or external clients. Objects in spidyXML may also be passed to external web services.

Figure 2.

The ISPIDER Interactive tabular view. Example results are shown for a protein accession-based query over multiple repositories.

Figure 3.

The ISPIDER Interactive matrix view. An example is shown displaying peptide identifications cross-referenced against their parent proteins from a variety of experiments taken from repositories.

Figure 4.

Dasty2 client displaying the ISPIDER search results. Results from an ISPIDER query may be linked out to the Dasty2 client, which shows peptide identifications in line with other annotations.