title: Subproteomic tools to increase genome annotation complexity.
abstract: Comprehensive and precise annotations of short protein-coding genes are always a challenging task. Here we propose a new design to facilitate the characterization of previously overlooked short protein-coding genes by integrating a shotgun proteomics method and oligonucleotide array analysis. Using Shigella flexneri as a model, we validate 163 annotated ORFs and 51 hypothetical or putative transcripts at the protein level, and discover four novel short ORFs. This strategy will contribute significantly to comprehensive and accurate genome-wide annotation, and to our understanding of prokaryotic genome structure.
authors.affiliation: State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, P. R. China.
authors.forename: Candong
authors.initials: C
authors.lastname: Wei
authors.forename: Junping
authors.initials: J
authors.lastname: Peng
authors.forename: Zhaohui
authors.initials: Z
authors.lastname: Xiong
authors.forename: Jian
authors.initials: J
authors.lastname: Yang
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.forename: Qi
authors.initials: Q
authors.lastname: Jin
mesh_terms: D001426:Bacterial Proteins / Q000032:analysis / Q000302:isolation & purification; D002853:Chromatography, Liquid; D019295:Computational Biology / Q000379:methods; D016680:Genome, Bacterial; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016366:Open Reading Frames; D040901:Proteomics / Q000379:methods*; D012763:Shigella flexneri / Q000737:chemistry; D012984:Software; D053719:Tandem Mass Spectrometry
chemical_list: D001426:Bacterial Proteins