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首页> 外文期刊>Computational Biology and Bioinformatics, IEEE/ACM Transactions on >Determination of Glycan Structure from Tandem Mass Spectra
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Determination of Glycan Structure from Tandem Mass Spectra

机译：串联质谱法测定聚糖结构

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摘要

Glycans are molecules made from simple sugars that form complex tree structures. Glycans constitute one of the most important protein modifications and identification of glycans remains a pressing problem in biology. Unfortunately, the structure of glycans is hard to predict from the genome sequence of an organism. In this paper, we consider the problem of deriving the topology of a glycan solely from tandem mass spectrometry (MS) data. We study, how to generate glycan tree candidates that sufficiently match the sample mass spectrum, avoiding the combinatorial explosion of glycan structures. Unfortunately, the resulting problem is known to be computationally hard. We present an efficient exact algorithm for this problem based on fixed-parameter algorithmics that can process a spectrum in a matter of seconds. We also report some preliminary results of our method on experimental data, combining it with a preliminary candidate evaluation scheme. We show that our approach is fast in applications, and that we can reach very well de novo identification results. Finally, we show how to count the number of glycan topologies for a fixed size or a fixed mass. We generalize this result to count the number of (labeled) trees with bounded out degree, improving on results obtained using Pólya''s enumeration theorem.
机译：聚糖是由简单的糖制成的分子，形成复杂的树状结构。聚糖构成最重要的蛋白质修饰之一，聚糖的鉴定仍然是生物学中的紧迫问题。不幸的是，很难从生物的基因组序列中预测聚糖的结构。在本文中，我们仅考虑从串联质谱（MS）数据推导聚糖拓扑的问题。我们研究了如何生成与样品质谱图充分匹配的聚糖树候选物，从而避免了聚糖结构的组合爆炸。不幸的是，已知的结果是计算上很困难。我们提出了一种基于固定参数算法的有效精确算法，该算法可以在几秒钟内处理频谱。我们还报告了我们的方法在实验数据上的一些初步结果，并将其与初步的候选评估方案相结合。我们证明了我们的方法在应用中是快速的，并且可以达到很好的从头识别结果。最后，我们展示了如何计算固定大小或固定质量的聚糖拓扑数。我们对该结果进行泛化，以计算出有界度的（标记的）树的数量，改进了使用Pólya枚举定理获得的结果。

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