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Detection of Alternative Splice Variants at the Proteome Level in Aspergillus flavus

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Date
2010
Authors
Chang, Kung-Yen
Georgianna, D Ryan
Heber, Steffen
Payne, Gary A
Muddiman, David C
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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.
Type
Other article
Subject
mass spectrometry
proteomics
alternative splicing
database
aspergillus flavus
cystathionine beta-synthase
tandem mass-spectrometry
identification
gene
sequence
genome
proteins
peptides
polymorphisms
biochemical research methods
Permalink
https://hdl.handle.net/10161/4113
Published Version (Please cite this version)
10.1021/pr900602d
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.
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