Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
BMC Bioinformatics. 2010 Mar 5;11:118. doi: 10.1186/1471-2105-11-118.
High-resolution tandem mass spectra can now be readily acquired with hybrid instruments, such as LTQ-Orbitrap and LTQ-FT, in high-throughput shotgun proteomics workflows. The improved spectral quality enables more accurate de novo sequencing for identification of post-translational modifications and amino acid polymorphisms.
In this study, a new de novo sequencing algorithm, called Vonode, has been developed specifically for analysis of such high-resolution tandem mass spectra. To fully exploit the high mass accuracy of these spectra, a unique scoring system is proposed to evaluate sequence tags based primarily on mass accuracy information of fragment ions. Consensus sequence tags were inferred for 11,422 spectra with an average peptide length of 5.5 residues from a total of 40,297 input spectra acquired in a 24-hour proteomics measurement of Rhodopseudomonas palustris. The accuracy of inferred consensus sequence tags was 84%. According to our comparison, the performance of Vonode was shown to be superior to the PepNovo v2.0 algorithm, in terms of the number of de novo sequenced spectra and the sequencing accuracy.
Here, we improved de novo sequencing performance by developing a new algorithm specifically for high-resolution tandem mass spectral data. The Vonode algorithm is freely available for download at http://compbio.ornl.gov/Vonode.
现在，混合仪器（如 LTQ-Orbitrap 和 LTQ-FT）可轻松获取高分辨率串联质谱，用于高通量 shotgun 蛋白质组学工作流程。更高的光谱质量使得更准确的从头测序成为可能，从而鉴定翻译后修饰和氨基酸多态性。
在这项研究中，专门开发了一种名为 Vonode 的新从头测序算法，用于分析此类高分辨率串联质谱。为了充分利用这些光谱的高精度质量，提出了一种独特的评分系统，主要基于片段离子的质量精度信息来评估序列标签。从 Rhodopseudomonas palustris 24 小时蛋白质组学测量中获取的 40,297 个输入光谱中，推断出了 11,422 个平均肽长度为 5.5 个残基的光谱的共识序列标签。推断出的共识序列标签的准确性为 84%。根据我们的比较，Vonode 算法在从头测序光谱数量和测序准确性方面的性能优于 PepNovo v2.0 算法。
在这里，我们通过开发专门针对高分辨率串联质谱数据的新算法来提高从头测序性能。Vonode 算法可在 http://compbio.ornl.gov/Vonode 免费下载。
