ISPIDER Central: an integrated database web-server for proteomics.

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; Simon J. Hubbard

doi:10.1093/nar/gkn196

ISPIDER Central: an integrated database web-server for proteomics.

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, Simon J. Hubbard

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

13 Citations (Scopus)

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.

Original language	English
Pages (from-to)	W485-490
Journal	Nucleic Acids Research
Volume	36
Issue number	Web Server issue
DOIs	https://doi.org/10.1093/nar/gkn196
Publication status	Published - 1 Jul 2008
Externally published	Yes

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Siepen, J. A., Belhajjame, K., Selley, J. N., Embury, S. M., Paton, N. W., Goble, C. A., Oliver, S. G., Stevens, R., Zamboulis, L., Martin, N., Poulovassillis, A., Jones, P., Côté, R., Hermjakob, H., Pentony, M. M., Jones, D. T., Orengo, C. A., & Hubbard, S. J. (2008). ISPIDER Central: an integrated database web-server for proteomics. Nucleic Acids Research, 36(Web Server issue), W485-490. https://doi.org/10.1093/nar/gkn196

@article{18351b175f1540499f843629cb231242,

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.",

author = "Siepen, {Jennifer A.} and Khalid Belhajjame and Selley, {Julian N.} and Embury, {Suzanne M.} and Paton, {Norman W.} and Goble, {Carole A.} and Oliver, {Stephen G.} and Robert Stevens and Lucas Zamboulis and Nigel Martin and Alexandra Poulovassillis and Philip Jones and Richard C{\^o}t{\'e} and Henning Hermjakob and Pentony, {Melissa M.} and Jones, {David T.} and Orengo, {Christine A.} and Hubbard, {Simon J.}",

year = "2008",

month = jul,

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doi = "10.1093/nar/gkn196",

language = "English",

volume = "36",

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Siepen, JA, Belhajjame, K, Selley, JN, Embury, SM, Paton, NW, Goble, CA, Oliver, SG, Stevens, R, Zamboulis, L, Martin, N, Poulovassillis, A, Jones, P, Côté, R, Hermjakob, H, Pentony, MM, Jones, DT, Orengo, CA & Hubbard, SJ 2008, 'ISPIDER Central: an integrated database web-server for proteomics.', Nucleic Acids Research, vol. 36, no. Web Server issue, pp. W485-490. https://doi.org/10.1093/nar/gkn196

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T2 - an integrated database web-server for proteomics.

AU - Siepen, Jennifer A.

AU - Belhajjame, Khalid

AU - Selley, Julian N.

AU - Embury, Suzanne M.

AU - Paton, Norman W.

AU - Goble, Carole A.

AU - Oliver, Stephen G.

AU - Stevens, Robert

AU - Zamboulis, Lucas

AU - Martin, Nigel

AU - Poulovassillis, Alexandra

AU - Jones, Philip

AU - Côté, Richard

AU - Hermjakob, Henning

AU - Pentony, Melissa M.

AU - Jones, David T.

AU - Orengo, Christine A.

AU - Hubbard, Simon J.

PY - 2008/7/1

Y1 - 2008/7/1

N2 - 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.

AB - 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.

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U2 - 10.1093/nar/gkn196

DO - 10.1093/nar/gkn196

M3 - Article

SN - 0305-1048

VL - 36

SP - W485-490

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - Web Server issue

ER -

ISPIDER Central: an integrated database web-server for proteomics.

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