Novor: real-time peptide de novo sequencing software.
Novor: real-time peptide de novo sequencing software.
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Novor：实时肽从头测序软件。
DOI：
10.1007/s13361-015-1204-0
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发表时间：
2015-11
影响因子：
3.2
通讯作者：
Ma B
中科院分区：
文献类型：
--
作者：
Ma B
从头测序软件已广泛用于蛋白质组学中，从串联质谱数据中对新肽进行测序。这项研究提出了一种新的软件工具，Novor，大大提高了今天的肽从头测序分析的速度和准确性。为了提高准确性，Novor的评分功能基于两个大型决策树，这两个决策树是通过机器学习从肽光谱库中构建的，该肽光谱库具有超过300，000个光谱。关于肽片段化的重要知识自动从库中提取并并入评分函数中。决策树模型还可以实现高效的分数计算，并有助于提高速度。为了进一步提高速度，一个两阶段的算法方法，即动态规划和细化，使用。软件程序也进行了精心优化。在测试数据集上，Novor测序的正确残基比最先进的从头测序工具PEAKS多7%-37%，同时速度快一个数量级。Novor可以在笔记本电脑上每秒对300多个MS/MS光谱进行从头测序。该速度超过了当今质谱仪的采集速度，因此，在质谱仪采集光谱数据的同时，开辟了在真实的时间中从头序列的新的可能性。本文的在线版本（doi：10.1007/s13361-015-1204-0）包含补充材料，可供授权用户使用。
De novo sequencing software has been widely used in proteomics to sequence new peptides from tandem mass spectrometry data. This study presents a new software tool, Novor, to greatly improve both the speed and accuracy of today’s peptide de novo sequencing analyses. To improve the accuracy, Novor’s scoring functions are based on two large decision trees built from a peptide spectral library with more than 300,000 spectra with machine learning. Important knowledge about peptide fragmentation is extracted automatically from the library and incorporated into the scoring functions. The decision tree model also enables efficient score calculation and contributes to the speed improvement. To further improve the speed, a two-stage algorithmic approach, namely dynamic programming and refinement, is used. The software program was also carefully optimized. On the testing datasets, Novor sequenced 7%–37% more correct residues than the state-of-the-art de novo sequencing tool, PEAKS, while being an order of magnitude faster. Novor can de novo sequence more than 300 MS/MS spectra per second on a laptop computer. The speed surpasses the acquisition speed of today’s mass spectrometer and, therefore, opens a new possibility to de novo sequence in real time while the spectrometer is acquiring the spectral data. ᅟ The online version of this article (doi:10.1007/s13361-015-1204-0) contains supplementary material, which is available to authorized users.