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首页> 外文会议>IEEE International Conference on Bioinformatics and Biomedicine >A spectrum graph-based protein sequence filtering algorithm for proteoform identification by top-down mass spectrometry
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A spectrum graph-based protein sequence filtering algorithm for proteoform identification by top-down mass spectrometry

机译：基于谱图的蛋白质序列过滤算法，用于自上而下的质谱鉴定

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摘要

Database search is the main approach for identifying proteoforms using top-down tandem mass spectra. However, it is extremely slow to align a query spectrum against all protein sequences in a large database when the target proteoform that produced the spectrum contains post-translational modifications and/or mutations. As a result, efficient and sensitive protein sequence filtering algorithms are essential for speeding up database search. In this paper, we propose a novel filtering algorithm, which generates spectrum graphs from subspectra of the query spectrum and searches them against the protein database to find good candidates. Compared with the sequence tag and gaped tag approaches, the proposed method circumvents the step of tag extraction, thus simplifying data processing. Experimental results on real data showed that the proposed method achieved both high speed and high sensitivity in protein sequence filtration.
机译：数据库搜索是使用自上而下的串联质谱识别蛋白形式的主要方法。但是，当产生光谱的目标蛋白形式包含翻译后修饰和/或突变时，将查询光谱与大型数据库中的所有蛋白质序列进行比对非常慢。因此，高效而敏感的蛋白质序列过滤算法对于加快数据库搜索至关重要。在本文中，我们提出了一种新颖的过滤算法，该算法可以从查询光谱的子光谱中生成光谱图，然后根据蛋白质数据库对其进行搜索以找到合适的候选者。与序列标签和缺口标签方法相比，该方法避开了标签提取的步骤，从而简化了数据处理。真实数据的实验结果表明，该方法在蛋白质序列过滤中既实现了高速又具有很高的灵敏度。

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