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Title 

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

Authors 

Seung-Won LeeJae Pil ChoiHyun Jin KimJi-Man HongCheol-Goo Hur

Publisher 

Elsevier

Issue Date 

2008

Citation 

Biochemical and Biophysical Research Communications, vol. 377, no. 1, pp. 253-256

Keywords 

alternative splicingmass spectrometry (MS)MS/MSpeptide mass fingerprinting (PMF)protein identificationprotein isoformtandem MSpeptide fragmentalgorithmalternative RNA splicing

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.

ISSN 

0006-291X

Link 

http://dx.doi.org/10.1016/j.bbrc.2008.09.115

Appears in Collections

1. Journal Articles > Journal Articles

Registered Date

2019-05-02


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