Xiao Kaijie, Yu Fan, Fang Houqin, Xue Bingbing, Liu Yan, Li Yunhui, Tian Zhixin
School of Chemical Science and Engineering, Tongji University, Shanghai, China; Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, China.
School of Chemical Science and Engineering, Tongji University, Shanghai, China; Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, China.
J Proteomics. 2017 May 8;160:21-27. doi: 10.1016/j.jprot.2017.03.011. Epub 2017 Mar 21.
Neutral loss and internal product ions have been found to be significant in both peptide and protein tandem mass spectra and they have been proposed to be included in database search and for protein identification. In addition to common canonical b/y ions in collision-based dissociation or c/z ions in electron-based dissociation, inclusion of neutral loss and internal product ions would certainly make better use of tandem mass spectra data; however, their ultimate utility for protein identification with false discovery rate control remains unclear. Here we report our proteome-level utility benchmarking of neutral loss and internal product ions with tandem mass spectra of intact E. coli proteome. Utility of internal product ions was further evaluated at the protein level using selected tandem mass spectra of individual E. coli proteins. We found that both neutral loss and internal products ions do not have direct utility for protein identification when they were used for scoring of P Score; but they do have indirect utility for provision of more canonical b/y ions when they are included in the database search and overlapping ions between different ion types are resolved.
Tandem mass spectrometry has evolved to be a state-of-the-art method for characterization of protein primary structures (including amino acid sequence, post-translational modifications (PTMs) as well as their site location), where full study and utilization tandem mass spectra and product ions are indispensable. This primary structure information is essential for higher order structure and eventual function study of proteins.
已发现中性丢失和内部产物离子在肽和蛋白质串联质谱中都很重要，并且有人提议将它们纳入数据库搜索和蛋白质鉴定中。除了基于碰撞解离的常见标准b/y离子或基于电子解离的c/z离子外，纳入中性丢失和内部产物离子肯定会更好地利用串联质谱数据；然而，它们在控制错误发现率的蛋白质鉴定中的最终效用仍不清楚。在此，我们报告了我们对完整大肠杆菌蛋白质组串联质谱中中性丢失和内部产物离子的蛋白质组水平效用基准测试。使用单个大肠杆菌蛋白质的选定串联质谱在蛋白质水平上进一步评估了内部产物离子的效用。我们发现，当中性丢失和内部产物离子用于P分数评分时，它们对蛋白质鉴定没有直接效用；但当它们包含在数据库搜索中并且不同离子类型之间的重叠离子得到解析时，它们对提供更多标准b/y离子具有间接效用。
串联质谱已发展成为一种用于表征蛋白质一级结构（包括氨基酸序列、翻译后修饰（PTM）及其位点定位）的先进方法，其中全面研究和利用串联质谱和产物离子是必不可少的。这种一级结构信息对于蛋白质的高级结构和最终功能研究至关重要。
