Zeno SWATH MS-Based Discovery Proteomics

Discovery proteomics using Zeno SWATH MS (preprint: Wang et al, 2022b (link)) Tryptic digests were analyzed on a 7600 ZenoTOF mass spectrometer system (SCIEX), coupled to an ACQUITY UPLC M‐Class system (Waters). 2 μl of each sample (360 ng sample + 0.02 μl PQ500, Biognosys) were loaded on a HSS T3 column (300 μm × 150 mm, 1.8 μm, Waters) heated to 35°C, then chromatographically separated with a 20‐min gradient using a flow rate of 5 μl/min (Zelezniak et al, 2018 (link)). A Zeno SWATH acquisition scheme with 85 variable‐size windows and 11‐ms accumulation time with 1.4 s cycle time was used (preprint: Wang et al, 2022b (link)) which allows for MS detection for average 7 points per chromatographic peak with the chosen chromatography.