Linked Life Data

16381951

Source:http://linkedlifedata.com/resource/pubmed/id/16381951

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
Database issue
pubmed:dateCreated
2005-12-29
pubmed:abstractText
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.
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/16381951-10612281, http://linkedlifedata.com/resource/pubmed/commentcorrection/16381951-11231557, http://linkedlifedata.com/resource/pubmed/commentcorrection/16381951-12720328, http://linkedlifedata.com/resource/pubmed/commentcorrection/16381951-12923771, http://linkedlifedata.com/resource/pubmed/commentcorrection/16381951-14755292, http://linkedlifedata.com/resource/pubmed/commentcorrection/16381951-14976030, http://linkedlifedata.com/resource/pubmed/commentcorrection/16381951-14987077, http://linkedlifedata.com/resource/pubmed/commentcorrection/16381951-15085804, http://linkedlifedata.com/resource/pubmed/commentcorrection/16381951-15377392, http://linkedlifedata.com/resource/pubmed/commentcorrection/16381951-15595733, http://linkedlifedata.com/resource/pubmed/commentcorrection/16381951-15642101, http://linkedlifedata.com/resource/pubmed/commentcorrection/16381951-15966824, http://linkedlifedata.com/resource/pubmed/commentcorrection/16381951-16041671
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jan
pubmed:issn
1362-4962
pubmed:author
pubmed:issnType
Electronic
pubmed:day
1
pubmed:volume
34
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
D649-54
pubmed:dateRevised
2009-11-18
pubmed:meshHeading
pubmed:year
2006
pubmed:articleTitle
PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns.
pubmed:affiliation
Faculty of Life Sciences, University of Manchester, M13 9PT, UK.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't