基于非数据依赖的鞘脂菌蛋白质组学分析方法的建立

Establishment of a data-independent acquisition proteomic analysis method for Sphingobium yanoikuyae

【背景】鞘脂菌是一类可高效降解以菲为代表的多环芳烃有机污染物的菌株,其在环境污染治理及生物技术领域具有广阔的应用前景。【目的】为了优化测试方法,获得更完整的鞘脂菌Sphingobium yanoikuyae SJTF-8在菲胁迫下表达差异的蛋白。【方法】利用数据依赖型及数据非依赖型两种蛋白质组学数据采集方法,比较了鞘脂菌SJTF-8在菲胁迫下蛋白质水平的表达变化。【结果】两种技术方法下共得到580个表达差异蛋白,这些蛋白在细胞代谢、转运和调控等方面发挥一定功能。【结论】数据非依赖性采集(data-independent acquisition,DIA)技术在重复性以及低丰度蛋白的检测上明显好于数据依赖型采集(datadependentacquisition,DDA)技术,因此,DIA在实际可用的表达差异蛋白检出方面具备明显优势,为发现菲胁迫下细胞诱导表达的低丰度调控蛋白提供帮助。

[Background] Sphingobium is a kind of bacteria which can effectively degrade polycyclic aromatic hydrocarbons(PAHs) represented by phenanthrene. This characteristic makes sphingobium have broad application prospects in the field of environmental pollution control and biotechnology. [Objective] The aim of this study is to optimize the quantification method in order to acquire the complete differentially expressed proteins of Sphingobium yanoikuyae SJTF8 under phenanthrene stress. [Methods] Data dependent acquisition(DDA) and data-independent acquisition(DIA) proteomics analysis methods were used in this experiment. [Results] These two methods had commonly quantified 580 differentially expressed proteins, which played important roles in cell metabolism, transport and regulation. [Conclusion] DIA has a significant advantage in the quantification of differentially expressed proteins, which is helpful for the discovery of low abundance regulatory proteins induced by phenanthrene stress.