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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