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

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.

Key words:Data-independent acquisition, data dependent acquisition, phenanthrene, sphingobium yanoikuyae