ASPMF: a new approach for identifying alternative splicing isoforms using peptide mass fingerprinting.
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.
Lee
Seung-Won
SW
Omics and Integration Research Center, KRIBB, Yuseong-gu, Daejeon, Republic of Korea.
Choi
Jae-Pil
JP
Kim
Hyun-Jin
HJ
Hong
Ji-Man
JM
Hur
Cheol-Goo
CG
D000465:Algorithms; D017398:Alternative Splicing; D030562:Databases, Protein; D006801:Humans; D013058:Mass Spectrometry; D009862:Online Systems; D010449:Peptide Mapping / Q000379:methods*; D020033:Protein Isoforms / Q000737:chemistry* / Q000235:genetics; D012984:Software
D020033:Protein Isoforms