Kolmogorov, MikhailLiu, XiaowenPevzner, Pavel A.2019-01-162019-01-162016-01-04Kolmogorov, M., Liu, X., & Pevzner, P. A. (2015). SpectroGene: A Tool for Proteogenomic Annotations Using Top-Down Spectra. Journal of proteome research, 15(1), 144-51.https://hdl.handle.net/1805/18167In 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 .en-USPublisher PolicyGenome annotationProtein identificationProteogenomicsTop-down mass spectrometryArticle