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dc.contributor.author Georgianna, D. Ryan en_US
dc.date.accessioned 2011-06-21T17:27:12Z
dc.date.available 2011-06-21T17:27:12Z
dc.date.issued 2010 en_US
dc.identifier.citation Chang,Kung-Yen;Georgianna,D. Ryan;Heber,Steffen;Payne,Gary A.;Muddiman,David C.. 2010. Detection of Alternative Splice Variants at the Proteome Level in Aspergillus flavus. Journal of Proteome Research 9(3): 1209-1217. en_US
dc.identifier.issn 1535-3893 en_US
dc.identifier.uri http://hdl.handle.net/10161/4113
dc.description.abstract Identification of proteins from proteolytic peptides or intact proteins plays an essential role in proteomics. Researchers use search engines to match the acquired peptide sequences to the target proteins. However, search engines depend on protein databases to provide candidates for consideration. Alternative splicing (AS), the mechanism where the exon of pre-mRNAs can be spliced and rearranged to generate distinct mRNA and therefore protein variants, enable higher eukaryotic organisms, with only a limited number of genes, to have the requisite complexity and diversity at the proteome level. Multiple alternative isoforms from one gene often share common segments of sequences. However, many protein databases only include a limited number of isoforms to keep minimal redundancy. As a result, the database search might not identify a target protein even with high quality tandem MS data and accurate intact precursor ion mass. We computationally predicted an exhaustive list of putative isoforms of Aspergillus flavus proteins from 20 371 expressed sequence tags to investigate whether an alternative splicing protein database can assign a greater proportion of mass spectrometry data. The newly constructed AS database provided 9807 new alternatively spliced variants in addition to 12 832 previously annotated proteins. The searches of the existing tandem MS spectra data set using the AS database identified 29 new proteins encoded by 26 genes. Nine fungal genes appeared to have multiple protein isoforms. In addition to the discovery of splice variants, AS database also showed potential to improve genome annotation. In summary, the introduction of an alternative splicing database helps identify more proteins and unveils more information about a proteome. en_US
dc.language.iso en_US en_US
dc.publisher AMER CHEMICAL SOC en_US
dc.relation.isversionof doi:10.1021/pr900602d en_US
dc.subject mass spectrometry en_US
dc.subject proteomics en_US
dc.subject alternative splicing en_US
dc.subject database en_US
dc.subject aspergillus flavus en_US
dc.subject cystathionine beta-synthase en_US
dc.subject tandem mass-spectrometry en_US
dc.subject identification en_US
dc.subject gene en_US
dc.subject sequence en_US
dc.subject genome en_US
dc.subject proteins en_US
dc.subject peptides en_US
dc.subject polymorphisms en_US
dc.subject biochemical research methods en_US
dc.title Detection of Alternative Splice Variants at the Proteome Level in Aspergillus flavus en_US
dc.title.alternative en_US
dc.description.version Version of Record en_US
duke.date.pubdate 2010-3-0 en_US
duke.description.endpage 1217 en_US
duke.description.issue 3 en_US
duke.description.startpage 1209 en_US
duke.description.volume 9 en_US
dc.relation.journal Journal of Proteome Research en_US

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