PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns - PubMed (original) (raw)

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

Thomas McLaughlin et al. Nucleic Acids Res. 2006.

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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Figures

Figure 1

Figure 1

PepSeeker database scheme, showing the relationship between tables.

Figure 2

Figure 2

Screen-shot of the PepSeeker front-end, showing an example of the navigation from a simple ion search to a list of the matching peptides through to a graphical representation of the spectra and associated ion information. An example PepSeeker query is shown searching for all peptides within the database containing the sequence PPPP. The first window is the query entry, the second window is the output and the third window displays the spectrum and table associated to the peptide SQGPPPPGKPQGPPPQGGSK.

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