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Title | ASPMF: A new approach for identifying alternative splicing isoforms using peptide mass fingerprinting |
Authors | Seung-Won Lee; Jae Pil Choi; Hyun Jin Kim; Ji-Man Hong; Cheol-Goo Hur |
Publisher | Elsevier |
Issue Date | 2008 |
Citation | Biochemical and Biophysical Research Communications, vol. 377, no. 1, pp. 253-256 |
Keywords | alternative splicing; mass spectrometry (MS); MS/MS; peptide mass fingerprinting (PMF); protein identification; protein isoform; tandem MS; peptide fragment; algorithm; alternative 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 | |
Appears in Collections | |
Registered Date |
2019-05-02 |
