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

Chang, Kung-Yen

Georgianna, D Ryan

Heber, Steffen

Payne, Gary A

Muddiman, David C

2011-06-21T17:27:12Z

2011-06-21T17:27:12Z

2010

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.

Version of Record

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.

1535-3893

https://hdl.handle.net/10161/4113

en_US

American Chemical Society (ACS)

10.1021/pr900602d

Journal of Proteome Research

mass spectrometry

proteomics

alternative splicing

database

aspergillus flavus

cystathionine beta-synthase

tandem mass-spectrometry

identification

gene

sequence

genome

proteins

peptides

polymorphisms

biochemical research methods

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

Other article

2010-3-0

3

9

1209

1217