Alves Gelio, Ogurtsov Aleksey Y, Yu Yi-Kuo
National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20894, USA.
J Am Soc Mass Spectrom. 2014 Jan;25(1):57-70. doi: 10.1007/s13361-013-0733-7. Epub 2013 Nov 20.
In this paper, we present Molecular Isotopic Distribution Analysis (MIDAs), a new software tool designed to compute molecular isotopic distributions with adjustable accuracies. MIDAs offers two algorithms, one polynomial-based and one Fourier-transform-based, both of which compute molecular isotopic distributions accurately and efficiently. The polynomial-based algorithm contains few novel aspects, whereas the Fourier-transform-based algorithm consists mainly of improvements to other existing Fourier-transform-based algorithms. We have benchmarked the performance of the two algorithms implemented in MIDAs with that of eight software packages (BRAIN, Emass, Mercury, Mercury5, NeutronCluster, Qmass, JFC, IC) using a consensus set of benchmark molecules. Under the proposed evaluation criteria, MIDAs's algorithms, JFC, and Emass compute with comparable accuracy the coarse-grained (low-resolution) isotopic distributions and are more accurate than the other software packages. For fine-grained isotopic distributions, we compared IC, MIDAs's polynomial algorithm, and MIDAs's Fourier transform algorithm. Among the three, IC and MIDAs's polynomial algorithm compute isotopic distributions that better resemble their corresponding exact fine-grained (high-resolution) isotopic distributions. MIDAs can be accessed freely through a user-friendly web-interface at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/midas/index.html.
在本文中，我们介绍了分子同位素分布分析软件（MIDAs），这是一种旨在计算具有可调节精度的分子同位素分布的新型软件工具。MIDAs提供了两种算法，一种基于多项式，另一种基于傅里叶变换，这两种算法都能准确且高效地计算分子同位素分布。基于多项式的算法几乎没有新的方面，而基于傅里叶变换的算法主要是对其他现有基于傅里叶变换的算法进行了改进。我们使用一组共识基准分子，将MIDAs中实现的两种算法的性能与八个软件包（BRAIN、Emass、Mercury、Mercury5、NeutronCluster、Qmass、JFC、IC）的性能进行了基准测试。在所提出的评估标准下，MIDAs的算法、JFC和Emass在计算粗粒度（低分辨率）同位素分布时具有相当的准确性，并且比其他软件包更准确。对于细粒度同位素分布，我们比较了IC、MIDAs的多项式算法和MIDAs的傅里叶变换算法。在这三者中，IC和MIDAs的多项式算法计算出的同位素分布更类似于其相应的精确细粒度（高分辨率）同位素分布。可以通过用户友好的网页界面（http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/midas/index.html）免费访问MIDAs。
