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Comparison of Spectra in Unsequenced Species

机译：未排序物种的光谱比较

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摘要

We introduce a new algorithm for the mass spectromet-ric identification of proteins. Experimental spectra obtained by tandem MS/MS are directly compared to theoretical spectra generated from proteins of evolutionarily closely related organisms. This work is motivated by the need of a method that allows the identification of proteins of unsequenced species against a database containing proteins of related organisms. The idea is that matching spectra of unknown peptides to very similar MS/MS spectra generated from this database of annotated proteins can lead to annotate unknown proteins. This process is similar to ortholog annotation in protein sequence databases. The difficulty with such an approach is that two similar peptides, even with just one modification (i.e. insertion, deletion or substitution of one or several amino acid(s)) between them, usually generate very dissimilar spectra. In this paper, we present a new dynamic programming based algorithm: Packet-SpectralAlignment. Our algorithm is tolerant to modifications and fully exploits two important properties that are usually not considered: the notion of inner symmetry, a relation linking pairs of spectrum peaks, and the notion of packet inside each spectrum to keep related peaks together. Our algorithm, PacketSpectralAlignment is then compared to SpectralAlignment [1] on a dataset of simulated spectra. Our tests show that PacketSpectralAlignment behaves better, in terms of results and execution time.
机译：我们介绍了一种用于蛋白质质谱鉴定的新算法。将通过串联MS / MS获得的实验光谱与从进化上密切相关的生物体的蛋白质产生的理论光谱直接进行比较。这项工作的动机是需要一种方法，该方法允许根据包含相关生物蛋白质的数据库来鉴定未排序物种的蛋白质。这个想法是，将未知肽段的光谱与从该带注释的蛋白质数据库生成的非常相似的MS / MS光谱进行匹配，可以导致对未知蛋白质进行注释。该过程类似于蛋白质序列数据库中的直向同源物注释。这种方法的困难在于，两个相似的肽，即使它们之间只有一个修饰（即一个或多个氨基酸的插入，缺失或取代），通常也会产生非常不同的光谱。在本文中，我们提出了一种基于动态规划的新算法：Packet-SpectralAlignment。我们的算法容忍修改，并充分利用了通常不考虑的两个重要属性：内部对称性概念，将频谱峰对关联的关系以及每个频谱内的数据包概念以将相关峰保持在一起。然后将我们的算法PacketSpectralAlignment与模拟光谱数据集上的SpectralAlignment [1]进行比较。我们的测试表明，PacketSpectralAlignment在结果和执行时间方面表现更好。

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  • 来源
  • 会议地点 Porto Alegre(BR);Porto Alegre(BR)
  • 作者

    Freddy Cliquet; Guillaume Fertin; Irena Rusu; Dominique Tessier;

  • 作者单位

    LINA, UMR CNRS 6241 Universite de Nantes, 2 rue de la Houssiniere, 44322, Nantes, Cedex 03, France UR1268 BIA, INRA, Rue de la Geraudiere, BP 71627, 44316 Nantes, France;

    LINA, UMR CNRS 6241 Universite de Nantes, 2 rue de la Houssiniere, 44322, Nantes, Cedex 03, France;

    LINA, UMR CNRS 6241 Universite de Nantes, 2 rue de la Houssiniere, 44322, Nantes, Cedex 03, France;

    UR1268 BIA, INRA, Rue de la Geraudiere, BP 71627, 44316 Nantes, France;

  • 会议组织
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类 生物工程学（生物技术）;
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