Location of Repository

ISPIDER Central: an integrated database web-server for proteomics

By Jennifer A. Siepen, Khalid Belhajjame, Julian N. Selley, Suzanne M. Embury, Norman W. Paton, Carole A. Goble, Stephen G. Oliver, Robert Stevens, Lucas Zamboulis, Nigel Martin, Alexandra Poulovassillis, Philip Jones, Richard Côté, Henning Hermjakob, Melissa M. Pentony, David T. Jones, Christine A. Orengo and Simon J. Hubbard

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

Topics: Articles
Publisher: Oxford University Press
OAI identifier: oai:pubmedcentral.nih.gov:2447780
Provided by: PubMed Central
Download PDF:
Sorry, we are unable to provide the full text but you may find it at the following location(s):
  • http://www.pubmedcentral.nih.g... (external link)
  • http://www.ispider.manchester.... (external link)
  • Suggested articles

    Preview

    Citations

    1. (2004). A common open representation of mass spectrometry data and its application to proteomics research.
    2. (2003). Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS.
    3. (2007). Bioinformatics service reconciliation by heterogeneous schema transformation.
    4. (2007). Biomarker discovery in lung cancer—promises and challenges of clinical proteomics.
    5. (2005). BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis.
    6. (2007). Computational prediction of proteotypic peptides for quantitative proteomics.
    7. (2005). Dasty and UniProt DAS: a perfect pair for protein feature visualization.
    8. (2006). Data access and integration in the ISPIDER proteomics grid.
    9. (2004). Exploring Williams-Beuren syndrome using myGrid.
    10. (2006). GAPP: a fully automated software for the confident identification of human peptides from tandem mass spectra.
    11. (2005). Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.
    12. (2007). Methods, algorithms and tools in computational proteomics: a practical point of view.
    13. (2005). Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides.
    14. (2004). Open source system for analyzing, validating, and storing protein identification data.
    15. (2004). PEDRo: a database for storing, searching and disseminating experimental proteomics data.
    16. (2006). PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns.
    17. (2004). Prediction and functional analysis of native disorder in proteins from the three kingdoms of life.
    18. (2006). PRIDE: a public repository of protein and peptide identifications for the proteomics community.
    19. (2007). ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats.
    20. (2007). Public proteomic MS repositories and pipelines: available tools and biological applications.
    21. (2006). Quantitative proteomics to study mitogen-activated protein kinases.
    22. (2004). TANDEM: matching proteins with tandem mass spectra.
    23. (2002). The bioperl toolkit: Perl modules for the life sciences.
    24. (2001). The distributed annotation system.
    25. (2007). The Google Web Toolkit shines a light on Ajax frameworks.
    26. (2004). The need for a public proteomics repository.
    27. (2007). The protein identifier cross-referencing (PICR) service: reconciling protein identifiers across multiple souce databases.
    28. (2005). The use of proteotypic peptide libraries for protein identification.

    To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.