Linked Life Data

18558733

Source:http://linkedlifedata.com/resource/pubmed/id/18558733

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
8
pubmed:dateCreated
2008-8-4
pubmed:abstractText
Confident peptide identification is one of the most important components in mass-spectrometry-based proteomics. We propose a method to properly combine the results from different database search methods to enhance the accuracy of peptide identifications. The database search methods included in our analysis are SEQUEST (v27 rev12), ProbID (v1.0), InsPecT (v20060505), Mascot (v2.1), X! Tandem (v2007.07.01.2), OMSSA (v2.0) and RAId_DbS. Using two data sets, one collected in profile mode and one collected in centroid mode, we tested the search performance of all 21 combinations of two search methods as well as all 35 possible combinations of three search methods. The results obtained from our study suggest that properly combining search methods does improve retrieval accuracy. In addition to performance results, we also describe the theoretical framework which in principle allows one to combine many independent scoring methods including de novo sequencing and spectral library searches. The correlations among different methods are also investigated in terms of common true positives, common false positives, and a global analysis. We find that the average correlation strength, between any pairwise combination of the seven methods studied, is usually smaller than the associated standard error. This indicates only weak correlation may be present among different methods and validates our approach in combining the search results. The usefulness of our approach is further confirmed by showing that the average cumulative number of false positive peptides agrees reasonably well with the combined E-value. The data related to this study are freely available upon request.
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/18558733-10612281, http://linkedlifedata.com/resource/pubmed/commentcorrection/18558733-12143966, http://linkedlifedata.com/resource/pubmed/commentcorrection/18558733-12403597, http://linkedlifedata.com/resource/pubmed/commentcorrection/18558733-12422357, http://linkedlifedata.com/resource/pubmed/commentcorrection/18558733-14976030, http://linkedlifedata.com/resource/pubmed/commentcorrection/18558733-15473683, http://linkedlifedata.com/resource/pubmed/commentcorrection/18558733-16047398, http://linkedlifedata.com/resource/pubmed/commentcorrection/18558733-17068079, http://linkedlifedata.com/resource/pubmed/commentcorrection/18558733-17961253, http://linkedlifedata.com/resource/pubmed/commentcorrection/18558733-17983478, http://linkedlifedata.com/resource/pubmed/commentcorrection/18558733-9520501
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Aug
pubmed:issn
1535-3893
pubmed:author
pubmed:issnType
Print
pubmed:volume
7
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
3102-13
pubmed:dateRevised
2009-11-18
pubmed:meshHeading
pubmed:year
2008
pubmed:articleTitle
Enhancing peptide identification confidence by combining search methods.
pubmed:affiliation
National Center for Biotechnology Information, Library of Medicine, NIH, Bethesda, MD 20894, USA.
pubmed:publicationType
Journal Article, Research Support, N.I.H., Intramural