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Nucleic Acids Research Advance Access published online on November 4, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn804
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

NOPdb: Nucleolar Proteome Database—2008 update

Yasmeen Ahmad1, François-Michel Boisvert1, Peter Gregor2, Andy Cobley2 and Angus I. Lamond1,*

1Wellcome Trust Centre for Gene Regulation & Expression and 2School of Computing, University of Dundee, Dundee DD1 5EH, UK

*To whom correspondence should be addressed. Tel: +44 1382 385473; Fax: +44 1382 345695; Email: angus{at}lifesci.dundee.ac.uk

Received September 12, 2008. Accepted October 10, 2008.

An experimental data handling system has been created as an update to the previous Nucleolar Proteome Database (NOPdb3.0: http://www.lamondlab.com/NOPdb3.0/). This updated system is able to manage large data sets identified by multiple mass spectrometry and has been used to analyse highly purified preparations of human nucleoli from different cell lines. The newly created application includes a dynamic relational database, which is kept up to date by laboratory staff. The data are further annotated with information from specific external sources on the web, including the IPI and Gene Ontology databases. In addition, an Application Programming Interface provides external users with a portal to link into the nucleolar proteome database and hence, gain access to continually updated results. From the initial ~700 human proteins identified in the previous iteration of the NOPdb, we have now identified over 50 000 peptides contained in over 4500 human proteins from purified nucleoli, providing enhanced coverage of the nucleolar proteome.


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