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. 2008 Dec 16:9:537.
doi: 10.1186/1471-2105-9-537.

A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data

Fan Mo  1 , Xu Hong, Feng Gao, Lin Du, Jun Wang, Gilbert S Omenn, Biaoyang Lin
Affiliations

A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data

Fan Mo et al. BMC Bioinformatics. .

Abstract

Background: Alternative splicing is an important gene regulation mechanism. It is estimated that about 74% of multi-exon human genes have alternative splicing. High throughput tandem (MS/MS) mass spectrometry provides valuable information for rapidly identifying potentially novel alternatively-spliced protein products from experimental datasets. However, the ability to identify alternative splicing events through tandem mass spectrometry depends on the database against which the spectra are searched.

Results: We wrote scripts in perl, Bioperl, mysql and Ensembl API and built a theoretical exon-exon junction protein database to account for all possible combinations of exons for a gene while keeping the frame of translation (i.e., keeping only in-phase exon-exon combinations) from the Ensembl Core Database. Using our liver cancer MS/MS dataset, we identified a total of 488 non-redundant peptides that represent putative exon skipping events.

Conclusion: Our exon-exon junction database provides the scientific community with an efficient means to identify novel alternatively spliced (exon skipping) protein isoforms using mass spectrometry data. This database will be useful in annotating genome structures using rapidly accumulating proteomics data.

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Figures

Figure 1
Figure 1
Top panel, the mass spectrum for the peptide LDEEVKIQR; bottom panel, the mass spectrum for the peptide KAFGENYLFPDGR. Matched b-ions (e.g. b2+, b6+) are indicated by red, and matched y-ions (e.g. y7+) are indicated by blue. The + indicates that an ion is a singly-charged ion.
Figure 2
Figure 2
Illustration of splicing of exons 3 and 7 of the proto-oncogene c-CBL that generates the peptide KAFGENYLFPDGR we identified by MS/MS. Translated amino acid residues (one letter code) were aligned with the combined exon 3 and 7 DNA sequences. The double forward-slash indicates the exon/exon junction. The underlined amino acid residues indicate the peptide corresponding to the mass spectrum we identified.
Figure 3
Figure 3
Flowchart of our pipeline for identifying exon skipping forms using MS/MS data.
See this image and copyright information in PMC

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