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Nucleic Acids Research 2006 34(Database Issue):D649-D654; doi:10.1093/nar/gkj066
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Nucleic Acids Research, 2006, Vol. 34, Database issue D649-D654
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns

Thomas McLaughlin1, Jennifer A. Siepen1, Julian Selley1, Jennifer A. Lynch1,2, King Wai Lau3, Hujun Yin3, Simon J. Gaskell2 and Simon J. Hubbard1,*

1Faculty of Life Sciences, University of Manchester M13 9PT, UK 2School of Electrical and Electronic Engineering, Faculty of Engineering and Physical Sciences, University of Manchester M13 9PT, UK 3School of Chemistry, University of Manchester M13 9PT, UK

*To whom correspondence should be addressed. Tel: +44 161 3068930; Fax: +44 161 2755082; Email: simon.hubbard{at}manchester.ac.uk

Received August 14, 2005. Revised October 8, 2005. Accepted October 8, 2005.

Proteome science relies on bioinformatics tools to characterize proteins via their proteolytic peptides which are identified via characteristic mass spectra generated after their ions undergo fragmentation in the gas phase within the mass spectrometer. The resulting secondary ion mass spectra are compared with protein sequence databases in order to identify the amino acid sequence. Although these search tools (e.g. SEQUEST, Mascot, X!Tandem, Phenyx) are frequently successful, much is still not understood about the amino acid sequence patterns which promote/protect particular fragmentation pathways, and hence lead to the presence/absence of particular ions from different ion series. In order to advance this area, we have developed a database, PepSeeker (http://nwsr.smith.man.ac.uk/pepseeker), which captures this peptide identification and ion information from proteome experiments. The database currently contains >185 000 peptides and associated database search information. Users may query this resource to retrieve peptide, protein and spectral information based on protein or peptide information, including the amino acid sequence itself represented by regular expressions coupled with ion series information. We believe this database will be useful to proteome researchers wishing to understand gas phase peptide ion chemistry in order to improve peptide identification strategies. Questions can be addressed to j.selley{at}manchester.ac.uk.

The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors


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J. A. Siepen, K. Belhajjame, J. N. Selley, S. M. Embury, N. W. Paton, C. A. Goble, S. G. Oliver, R. Stevens, L. Zamboulis, N. Martin, et al.
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[Abstract] [Full Text] [PDF]


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