ASPMF: A new approach for identifying alternative splicing isoforms using peptide mass fingerprinting

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Title
ASPMF: A new approach for identifying alternative splicing isoforms using peptide mass fingerprinting
Author(s)
Seung-Won Lee; Jae Pil Choi; Hyun Jin Kim; Ji-Man Hong; Cheol-Goo Hur
Bibliographic Citation
Biochemical and Biophysical Research Communications, vol. 377, no. 1, pp. 253-256
Publication Year
2008
Abstract
Alternative splicing is generally accepted as a mechanism that explains the discrepancy between the number of genes and proteins. We used peptide mass fingerprinting with a theoretical database and scoring method to discover and identify alternative splicing isoforms. Our theoretical database was built using published alternative splicing databases such as ECgene, H-DBAS, and TISA. According to our theoretical database of 190,529 isoforms, 37% of human genes have multiple isoforms. The isoforms produced from a gene partially share common peptide fragments because they have common exons, making it difficult to distinguish isoforms. Therefore, we developed a new method that effectively distinguishes a true isoform among multiple isoforms in a gene. In order to evaluate our algorithm, we made test sets for 4226 protein isoforms extracted from our theoretical database randomly. Consequently, 94% of true isoforms were identified by our scoring algorithm.
Keyword
Alternative splicingMass spectrometry (MS)MS/MSProtein identificationProtein isoformTandem MSPeptide mass fingerprinting (PMF)
ISSN
0006-291X
Publisher
Elsevier
DOI
http://dx.doi.org/10.1016/j.bbrc.2008.09.115
Type
Article
Appears in Collections:
1. Journal Articles > Journal Articles
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