Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation
Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation
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DOI：
10.1101/gr.6427907
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发表时间：
2007-09-01
期刊：
影响因子：
7
通讯作者：
Pevzner, Pavel A.
中科院分区：
文献类型：
--
作者：
Gupta, Nitin;Tanner, Stephen;Pevzner, Pavel A.
虽然近年来细菌基因组注释有了显著的改进，但用于细菌蛋白质组注释的技术（包括翻译后化学修饰、信号肽、蛋白水解事件等）仍在继续。仍处于婴儿期与此同时，测序的细菌基因组数量正在急剧上升，远远超过了我们验证预测基因的能力，更不用说注释细菌蛋白质组了。本研究利用串联质谱（MS/MS）技术对一种重要的生物修复微生物希瓦氏菌（Shewanella oneidensis）MR-1的蛋白质组进行了研究。特别是，我们提供了细菌基因组中翻译后修饰的第一个全面的图谱，包括大量的化学修饰，信号肽裂解和N-末端甲硫氨酸残基裂解。我们还检测了多个基因被遗漏或分配不正确的起始位置的基因预测程序，并建议更正，以改善基因注释。这项研究表明，通过MS/MS项目补充每个基因组测序项目将以合理的成本显着改善基因组和蛋白质组注释。
While bacterial genome annotations have significantly improved in recent years, techniques for bacterial proteome annotation (including post-translational chemical modifications, signal peptides, proteolytic events, etc.) are still in their infancy. At the same time, the number of sequenced bacterial genomes is rising sharply, far outpacing our ability to validate the predicted genes, let alone annotate bacterial proteomes. In this study, we use tandem mass spectrometry (MS/MS) to annotate the proteome of Shewanella oneidensis MR-1, an important microbe for bioremediation. In particular, we provide the first comprehensive map of post-translational modifications in a bacterial genome, including a large number of chemical modifications, signal peptide cleavages, and cleavages of N-terminal methionine residues. We also detect multiple genes that were missed or assigned incorrect start positions by gene prediction programs, and suggest corrections to improve the gene annotation. This study demonstrates that complementing every genome sequencing project by an MS/MS project would significantly improve both genome and proteome annotations for a reasonable cost.