SpectroGene: A Tool for Proteogenomic Annotations Using Top-Down Spectra

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• 作者：Mikhail Kolmogorov ; Xiaowen Liu ; Pavel A. Pevzner
• 刊名：Journal of Proteome Research
• 出版年：2016
• 出版时间：January 4, 2016
• 年：2016
• 卷：15
• 期：1
• 页码：144-151
• 全文大小：375K
• ISSN：1535-3907

文摘

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.