Vyatkina Kira, Wu Si, Dekker Lennard J M, VanDuijn Martijn M, Liu Xiaowen, Tolić Nikola, Luider Theo M, Paša-Tolić Ljiljana, Pevzner Pavel A
Algorithmic Biology Laboratory, Saint Petersburg Academic University, St Petersburg, Russia Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, St Petersburg, Russia.
Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA.
Bioinformatics. 2016 Sep 15;32(18):2753-9. doi: 10.1093/bioinformatics/btw307. Epub 2016 May 14.
Recent technological advances have made high-resolution mass spectrometers affordable to many laboratories, thus boosting rapid development of top-down mass spectrometry, and implying a need in efficient methods for analyzing this kind of data.
We describe a method for analysis of protein samples from top-down tandem mass spectrometry data, which capitalizes on de novo sequencing of fragments of the proteins present in the sample. Our algorithm takes as input a set of de novo amino acid strings derived from the given mass spectra using the recently proposed Twister approach, and combines them into aggregated strings endowed with offsets. The former typically constitute accurate sequence fragments of sufficiently well-represented proteins from the sample being analyzed, while the latter indicate their location in the protein sequence, and also bear information on post-translational modifications and fragmentation patterns.
Freely available on the web at http://bioinf.spbau.ru/en/twister
vyatkina@spbau.ru or ppevzner@ucsd.edu
Supplementary data are available at Bioinformatics online.
最近的技术进步使许多实验室都能负担得起高分辨率质谱仪，从而推动了自上而下质谱技术的快速发展，这意味着需要有效的方法来分析此类数据。
我们描述了一种用于分析自上而下串联质谱数据中蛋白质样品的方法，该方法利用样品中蛋白质片段的从头测序。我们的算法将使用最近提出的Twister方法从给定质谱中获得的一组从头氨基酸序列作为输入，并将它们组合成带有偏移量的聚合序列。前者通常构成来自被分析样品中代表性充分的蛋白质的准确序列片段，而后者则表明它们在蛋白质序列中的位置，并且还承载有关翻译后修饰和片段化模式的信息。
可在网页http://bioinf.spbau.ru/en/twister上免费获取
vyatkina@spbau.ru或ppevzner@ucsd.edu
补充数据可在《生物信息学》在线版获取。
