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Frequent oligonucleotide motifs in genomes of three streptococci

Nucleic Acids Research
Oxford University Press
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gkj066 649..654 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, 2School of Electrical and Electronic Engineering, Faculty of Engineering and Physical Sciences and 3School of Chemistry, University of Manchester, M13 9PT, UK Received August 14, 2005; Revised and Accepted October 8, 2005 ABSTRACT 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 under- stood about the amino acid sequence patterns whichpromote/protect particular fragmentationpath- ways, 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 (, which captures this peptide identification and ion information from proteome experiments. The data- base currently contains.185 000 peptides and asso- ciated database search information. Usersmay query this resource to retrieve peptide, protein and spectral information based on protein or peptide information, including the amino acid sequence itself represen- ted 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 [email protected] INTRODUCTION Proteomics is growin

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