Mass spectrometry assay for DIA

SH Sai Han
XL Xiaoli Liu
SJ Shuang Ju
WM Wendi Mu
GA Gulijinaiti Abulikemu
QZ Qianwei Zhen
JY Jiaqi Yang
JZ Jingjing Zhang
YL Yi Li
HL Hongli Liu
QC Qian Chen
BC Baoxia Cui
SW Shuxia Wu
YZ Youzhong Zhang
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The peptides from each sample were analysed by LC‒MS/MS operating in the DIA mode by Shanghai Applied Protein Technology Co., Ltd. Each DIA cycle contained one full MS–SIM scan, and 30 DIA scans covered a mass range of 350–1800 m/z with the following settings: SIM full scan resolution, 120,000 at 200 m/z; AGC, 3e6; maximum IT, 50 ms; profile mode, DIA scan parameters were set as follows: resolution, 15,000; AGC target, 3e6; max IT, auto; and normalized collision energy, 30 eV. The run time was 120 min with a linear gradient of buffer B (84% acetonitrile and 0.1% formic acid) at a flow rate of 250 nl/min. QC samples (pooled sample from an equal aliquot of each sample in the experiment) were injected in DIA mode at the beginning of the MS study and after every 6 injections throughout the experiment, which was used to monitor the MS performance.

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