Wu Zhan, Lajoie Gilles, Ma Bin
Department of Computer Science, University of Western Ontario, London, Ontario N6A 5B8, Canada.
Comput Syst Bioinformatics Conf. 2008;7:63-71.
Along with the wide application of mass spectrometry in proteomics, more and more mass spectrometry data are becoming publicly available. Several public mass spectrometry data repositories have been built on the Internet. However, most of these repositories are devoid of effective searching methods. In this paper we describe a new mass spectrometry data library, and a novel method to efficiently index and search in the library for spectra that are similar to a query spectrum. A public online server have been set up and demonstrated outstanding speed and scalability of our methods. Together with the mass spectrometry library, our searching method can improve the protein identification confidence by comparing a spectrum with the ones that are already characterized in the database. The searching method can also be used alone to cluster the similar spectra in a mass spectrometry dataset together, in order to to improve the speed and accuracy of the protein identification or quantification.
随着质谱技术在蛋白质组学中的广泛应用，越来越多的质谱数据开始公开可用。互联网上已经建立了几个公共质谱数据库。然而，这些数据库大多缺乏有效的搜索方法。在本文中，我们描述了一个新的质谱数据库，以及一种在该数据库中高效索引和搜索与查询光谱相似的光谱的新方法。我们已经建立了一个公共在线服务器，证明了我们方法具有出色的速度和可扩展性。结合质谱数据库，我们的搜索方法可以通过将一个光谱与数据库中已鉴定的光谱进行比较来提高蛋白质鉴定的可信度。该搜索方法也可以单独用于将质谱数据集中的相似光谱聚类在一起，以提高蛋白质鉴定或定量的速度和准确性。
