Exon Skipping Events Identification and Analysis by Mass Spectrometry Data

Exon skipping events often occur during the transcription process of organisms. Analyzing protein or peptide sequences translated from transcripts is an effective way to detect exon-skipping events. In this study, RNA-Seq reads derived from two human breast cancer subtypes are mapped to the reference genome sequence in order to detect exon-skipping patterns, which have been reported to be related to a phenomenon called exon-mediated activation of transcription starts. The peptide sequences, whether they contain the skipped exons or not, are divided into different datasets. The amino acid sequences of exon-skipped peptides are confirmed by searching the mass spectra against the peptide sequence datasets. The efficiency of an exon included in peptides is evaluated by computing the ratio using the number of peptides including or excluding exons. The ability of identifying exon skipping patterns based on mass spectra is evaluated by comparing with the percentage of splice in, which is calculated based on RNA-Seq reads. Experimental results demonstrate that exon-skipping patterns can be sensitively detected only based on mass spectra.