蛋白质组串联谱图De novo测序软件的比较与评估  

Comparison and Evaluation of De novo Peptide Sequencing Softwares in Identification of Tandem Mass Spectra

作　　者：成茜 杨筱韵 李婧[1] Cheng Xi;Yang Xiaoyun;Li Jing(School of Life Sciences and Biotechnology,Shanghai Jiao Tong University,Shanghai,200240)

机构地区：[1]上海交通大学生命科学技术学院,上海200240

出　　处：《基因组学与应用生物学》2020年第8期3431-3438,共8页Genomics and Applied Biology

基　　金：上海市自然科学基金(项目编号:17ZR1413900)资助。

摘　　要：基于串联质谱的蛋白质鉴定研究是蛋白质组学领域的重要问题,蛋白质的谱图鉴定主要包括数据库搜索和de novo测序两种策略。不同于数据库搜索鉴定方法,de novo测序的蛋白质鉴定直接从质谱谱图推导得到肽段序列,在鉴定新蛋白、发现翻译后新修饰、鉴定突变氨基酸等领域具有重要应用价值。随着质谱技术与计算方法的不断提升以及大规模蛋白组质谱数据的积累,多个de novo测序软件被提出,但对这些方法全面系统的评估尚未见报道。本研究通过两种不同碎裂方式——碰撞诱导解离(collision-induced dissociation,CID)和高能碰撞解离(high-energy C-trap dissociation,HCD)得到的谱图数据集上比较了3种常用de novo测序软件(Novor,pNovo3和PepNovo+),全面评估了其测序覆盖度、测序准确性、打分系统的特异性及测序速度。研究结果显示,在CID谱图鉴定中,Novor不仅可以对95%及以上的谱图进行全长肽段测序(full-length sequencing),还在测序准确性和内置打分系统特异性上都有明显优势;而在HCD谱图分析中,尽管pNovo3鉴定率较低,但是鉴定准确率跃居最高。在运行速度方面,pNovo3也远远超过其余两种软件。因此,研究者可以按照谱图类型和自身条件和需求选择合适的鉴定软件。Protein identification based on tandem mass spectrometry has always been an important issue in proteomics,usually includes two methods,database searching and de novo sequencing.Different from the strategy of database searching,de novo sequencing can derive peptide sequence directly from mass spectrum and that makes it popular in identification of novel proteins,post-translational modification or amino acid mutation.With the development of mass spectrometry technology and computational methods together with the accumulation of large-scale proteomics data,some softwares for de novo sequencing have emerged.However,a comprehensive and systematic evaluation is still lacking.In this study,we compared sequencing result of three softwares(Novor,pNovo3 and PepNovo+)on two kinds of dataset,which are generated from two different fragmentation methods(CID and HCD).Sequencing coverage,accuracy,scoring system and speed were evaluated.The result showed that Novor is a better choice in CID datasetbecause it can not only fully sequence more than 95%of the spectrums,but also has the highest accuracy.In addition,its built-in scoring system is able to separate the correct and incorrect identification well.In HCD dataset,although the pNovo3 achieved a lower identification ratio,its accuracy is the highest compared with the other two.Among the 3 softwares,pNovo3 can sequence spectrums with the highest speed.Researchers can choose the sequencing software according to the spectrum type and their own conditions and needs.

关 键 词：串联质谱技术 蛋白质鉴定 de novo测序 软件评估 

分 类 号：Q51[生物学—生物化学] TP311.53[自动化与计算机技术—计算机软件与理论]