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

摘要:

【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(data dependent acquisition，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。

Abstract:

[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.