Optimization of data-independent acquisition-MS for deep proteome analysis

Data-independent acquisition (DIA)-MS analysis overtops the existing data-dependent acquisition (DDA)-MS analysis enabling deep proteome coverage and precise relative quantitative analysis in single-shot LC-MS/MS. We constructed a single-shot LC-MS/MS system with an MS measurement time of 90 min for a highly sensitive and deep proteomic analysis by optimizing the parameters of DIA and nanoLC. Furthermore, we applied this system to the proteomic analysis of cerebrums in germ-free and specific pathogen-free mice.