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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Genome-based peptide fingerprint scanning
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Genome-based peptide fingerprint scanning

机译：基于基因组的肽指纹扫描

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We have implemented a method that identifies the genomic origins of sample proteins by scanning their peptide-mass fingerprint against the theoretical translation and proteolytic digest of an entire genome. Unlike previously reported techniques, this method requires no predefined ORF or protein annotations. Fixed-size windows along the genome sequence are scored by an equation accounting for the number of matching peptides, the number of missed enzymatic cleavages in each peptide, the number of in-frame stop codons within a window, the adjacency between peptides, and duplicate peptide matches. Statistical significance of matching regions is assessed by comparing their scores to scores from windows matching randomly generated mass data. Tests with samples from Saccharomyces cerevisiae mitochondria and Escherichia coli have demonstrated the ability to produce statistically significant identifications, agreeing with two commonly used programs, PEPTIDENT and MASCOT, in 86% of samples analyzed. This genome fingerprint scanning method has the potential to aid in genome annotation, identify proteins for which annotation is incorrect or missing, and handle cases where sequencing errors have caused framing mistakes in the databases. It might also aid in the identification of proteins in which recoding events such as frameshifting or stop-codon read-through have occurred, elucidating alternative translation mechanisms. The prototype is implemented as a client/server pair, allowing the distribution, among a set of cluster nodes, of a single or multiple genomes for concurrent analysis. [References: 23]
机译：我们已经实施了一种方法，通过相对于整个基因组的理论翻译和蛋白水解消化物扫描其肽质指纹，来鉴定样品蛋白质的基因组起源。与以前报道的技术不同，此方法不需要预定义的ORF或蛋白质注释。沿着基因组序列的固定大小窗口由一个方程式评分，该方程式说明了匹配的肽的数量，每种肽中错过的酶促裂解的数量，窗口内的框内终止密码子的数量，肽之间的邻接以及重复肽匹配。通过将匹配区域的得分与来自与随机生成的质量数据匹配的窗口的得分进行比较，来评估匹配区域的统计显着性。对来自酿酒酵母线粒体和大肠杆菌的样品进行的测试表明，能够对86％的分析样品产生统计学上显着的鉴定结果，与两个常用程序PEPTIDENT和MASCOT相符。这种基因组指纹扫描方法具有帮助基因组注释，识别注释不正确或缺失的蛋白质以及处理测序错误导致数据库中构图错误的情况的潜力。它还可能有助于鉴定其中发生了编码事件（例如移码或终止密码子通读）的蛋白质，从而阐明了其他翻译机制。该原型被实现为客户端/服务器对，从而允许在一组群集节点之间分配单个或多个基因组以进行并发分析。 [参考：23]

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