The discovery of novel protein-coding features in mouse genome based on mass spectrometry data |
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Authors: | Xing Xiao-Bin Li Qing-Run Sun Han Fu Xing Zhan Fei Huang Xiu Li Jing Chen Chun-Lei Shyr Yu Zeng Rong Li Yi-Xue Xie Lu |
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Institution: | aShanghai Center for Bioinformation Technology, Shanghai 200235, PR China;bKey Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai 200031, PR China;cVICC Cancer Biostatistics Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA;dKey Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, PR China;eDepartment of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, PR China |
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Abstract: | Identifying protein-coding genes in eukaryotic genomes remains a challenge in post-genome era due to the complex gene models. We applied a proteogenomics strategy to detect un-annotated protein-coding regions in mouse genome. High-accuracy tandem mass spectrometry (MS/MS) data from diverse mouse samples were generated by LTQ-Orbitrap mass spectrometer in house. Two searchable diagnostic proteomic datasets were constructed, one with all possible encoding exon junctions, and the other with all putative encoding exons, for the discovery of novel exon splicing events and novel uninterrupted protein-coding regions. Altogether 29,586 unique peptides were identified. Aligning backwards to the mouse genome, the translation of 4471 annotated genes was validated by the known peptides; and 172 genic events were defined in mouse genome by the novel peptides. The approach in the current work can provide substantial evidences for eukaryote genome annotation in encoding genes. |
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Keywords: | Proteogenomics Genome annotation Mouse |
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