title: The discovery of novel protein-coding features in mouse genome based on mass spectrometry data.
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.
authors.affiliation: Shanghai Center for Bioinformation Technology, PR China.
authors.forename: Xiao-Bin
authors.initials: XB
authors.lastname: Xing
authors.forename: Qing-Run
authors.initials: QR
authors.lastname: Li
authors.forename: Han
authors.initials: H
authors.lastname: Sun
authors.forename: Xing
authors.initials: X
authors.lastname: Fu
authors.forename: Fei
authors.initials: F
authors.lastname: Zhan
authors.forename: Xiu
authors.initials: X
authors.lastname: Huang
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.forename: Chun-Lei
authors.initials: CL
authors.lastname: Chen
authors.forename: Yu
authors.initials: Y
authors.lastname: Shyr
authors.forename: Rong
authors.initials: R
authors.lastname: Zeng
authors.forename: Yi-Xue
authors.initials: YX
authors.lastname: Li
authors.forename: Lu
authors.initials: L
authors.lastname: Xie
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D030562:Databases, Protein; D016678:Genome; D051379:Mice / Q000235:genetics*; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010455:Peptides / Q000737:chemistry / Q000235:genetics; D014176:Protein Biosynthesis; D022821:RNA Splice Sites; D016415:Sequence Alignment; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods
chemical_list: D010455:Peptides; D022821:RNA Splice Sites