Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications

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• 作者：Hao YangHao Chi ; Wen-Jing Zhou ; Wen-Feng Zeng ; Kun He ; Chao Liu ; Rui-Xiang Sun ; Si-Min He
• 刊名：Journal of Proteome Research
• 出版年：2017
• 出版时间：February 3, 2017
• 年：2017
• 卷：16
• 期：2
• 页码：645-654
• 全文大小：580K
• ISSN：1535-3907

文摘

De novo peptide sequencing has improved remarkably, but sequencing full-length peptides with unexpected modifications is still a challenging problem. Here we present an open de novo sequencing tool, Open-pNovo, for de novo sequencing of peptides with arbitrary types of modifications. Although the search space increases by ∼300 times, Open-pNovo is close to or even ∼10-times faster than the other three proposed algorithms. Furthermore, considering top-1 candidates on three MS/MS data sets, Open-pNovo can recall over 90% of the results obtained by any one traditional algorithm and report 5–87% more peptides, including 14–250% more modified peptides. On a high-quality simulated data set, ∼85% peptides with arbitrary modifications can be recalled by Open-pNovo, while hardly any results can be recalled by others. In summary, Open-pNovo is an excellent tool for open de novo sequencing and has great potential for discovering unexpected modifications in the real biological applications.