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  • Title: ASPMF: a new approach for identifying alternative splicing isoforms using peptide mass fingerprinting.
    Author: Lee SW, Choi JP, Kim HJ, Hong JM, Hur CG.
    Journal: Biochem Biophys Res Commun; 2008 Dec 05; 377(1):253-6. PubMed ID: 18835246.
    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.
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