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Database Commons - PepSeeker

PepSeeker

Citations: 38

z-index 0.00

Short name PepSeeker
Full name A database of proteome peptide identifications for investigating fragmentation patterns
Description PepSeeker captures this peptide identification and ion information from proteome experiments. The database currently contains >185,000 peptides and associated database search information.
URL http://nwsr.smith.man.ac.uk/pepseeker
Year founded 2006
Last update & version 2006-01-01    1.0
Availability Not Available
University/Institution hosted University of Manchester
Address M13 9PT, UK
City Manchester
Province/State
Country/Region United Kingdom
Contact name Simon J. Hubbard
Contact email simon.hubbard@manchester.ac.uk
Data type(s)
Major organism(s)
Keyword(s)
  • ion information
  • peptide identification
  • proteome
Publication(s)
  • PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns. [PMID: 16381951]

    Thomas McLaughlin, Jennifer A Siepen, Julian Selley, Jennifer A Lynch, King Wai Lau, Hujun Yin, Simon J Gaskell, Simon J Hubbard
    Nucleic acids research 2006:34(Database issue)
    38 Citations (Google Scholar as of 2016-01-25)

    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 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@manchester.ac.uk.

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Tags

Expression Protein
Eukaryota Prokaryote
ion information peptide identification proteome

Record metadata

  • Created on: 2015-09-09
  • Curated by:
    • Shixiang Sun [2016-03-25]
    • Shixiang Sun [2015-11-20]
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