title: SpectroGene: A Tool for Proteogenomic Annotations Using Top-Down Spectra.
abstract: In the past decade, proteogenomics has emerged as a valuable technique that contributes to the state-of-the-art in genome annotation; however, previous proteogenomic studies were limited to bottom-up mass spectrometry and did not take advantage of top-down approaches. We show that top-down proteogenomics allows one to address the problems that remained beyond the reach of traditional bottom-up proteogenomics. In particular, we show that top-down proteogenomics leads to the discovery of previously unannotated genes even in extensively studied bacterial genomes and present SpectroGene, a software tool for genome annotation using top-down tandem mass spectra. We further show that top-down proteogenomics searches (against the six-frame translation of a genome) identify nearly all proteoforms found in traditional top-down proteomics searches (against the annotated proteome). SpectroGene is freely available at http://github.com/fenderglass/SpectroGene .
authors.affiliation: Department of Computer Science and Engineering, UCSD , 9500 Gilman Drive, La Jolla, California, United States.
authors.forename: Mikhail
authors.initials: M
authors.lastname: Kolmogorov
authors.affiliation: Department of BioHealth Informatics, IUPUI , 719 Indiana Avenue, Suite 304, Indianapolis, Indiana, United States.
authors.forename: Xiaowen
authors.initials: X
authors.lastname: Liu
authors.affiliation: Department of Computer Science and Engineering, UCSD , 9500 Gilman Drive, La Jolla, California, United States.
authors.forename: Pavel A
authors.initials: PA
authors.lastname: Pevzner
mesh_terms: D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000737:chemistry / Q000235:genetics*; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics*; D019766:Genes, Archaeal; D005798:Genes, Bacterial; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D020543:Proteome / Q000737:chemistry / Q000235:genetics*; D040901:Proteomics / Q000379:methods / Q000592:standards; D020027:Pyrococcus furiosus / Q000235:genetics; D012015:Reference Standards; D012486:Salmonella typhimurium / Q000235:genetics
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D020543:Proteome
keywords: genome annotation; protein identification; proteogenomics; top-down mass spectrometry