ABSTRACT
Data independent acquisition ( DIA ) is a novel MS scan mode for quantitative proteomics, acquiring all precursors as well as fragments without any loss of low abundant ions, and breaks the throughput limitation of product ion quantification by high-resolution MS. Here we developed three DIA methods on quadrupole-linear ion trap-Orbitrap ( Q-qIT-OT ) Tribrid MS, classic DIA, as well as novel wide isolation window SIM scan ( WiSIM)-DIA and full scan-DIA ( Full MS-DIA) . Quantitative analysis of 10 low abundant peptides spiked in Hela cell digest was performed by the three methods for linearity, reproducibility and sensitivity evaluation. The results showed that the LOQs reached amol level ( 14-435 amol ) with good linearity and effective MS/MS confirmation. WiSIM-DIA utilizes ultra-high resolution SIM scan for quantification complementary with classic DIA. The isolation window of Full MS-DIA was down to 3 amu, and the data could be directly used for database searching, thus realizing the integration of data dependent acquisition ( DDA) and DIA, and avoiding the limitation of using spectra library.