Identification of rare alternative splicing events in MS/MS data reveals a significant fraction of alternative translation initiation sites.

ABSTRACT: Integration of transcriptome data is a crucial step for the identification of rare protein variants in mass-spectrometry (MS) data with important consequences for all branches of biotechnology research. Here, we used Splooce, a database of splicing variants recently developed by us, to search MS data derived from a variety of human tumor cell lines. More than 800 new protein variants were identified whose corresponding MS spectra were specific to protein entries from Splooce. Although the types of splicing variants (exon skipping, alternative splice sites and intron retention) were found at the same frequency as in the transcriptome, we observed a large variety of modifications at the protein level induced by alternative splicing events. Surprisingly, we found that 40% of all protein modif

SUBMITTER: Kroll JE 

PROVIDER: S-EPMC4232841 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature