Identification of alternative splice variants in Aspergillus flavus through comparison of multiple tandem MS search algorithms.

ABSTRACT:

Background

Database searching is the most frequently used approach for automated peptide assignment and protein inference of tandem mass spectra. The results, however, depend on the sequences in target databases and on search algorithms. Recently by using an alternative splicing database, we identified more proteins than with the annotated proteins in Aspergillus flavus. In this study, we aimed at finding a greater number of eligible splice variants based on newly available transcript sequences and the latest genome annotation. The improved database was then used to compare four search algorithms: Mascot, OMSSA, X! Tandem, and InsPecT.

Results

The updated alternative splicing database predicted 15833 putative protein variants, 61% more than the previous results. There was tr

SUBMITTER: Chang KY 

PROVIDER: S-EPMC3146456 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature