LC was performed with digested peptides loaded directly into a 75 μm × 30 cm nanoLC nanocapillary column (CoAnn Technologies, Richland, WA, USA) at 50 °C and then separated using a 100-min gradient (mobile phase A = 0.1% FA in water, B = 0.1% FA in 80% ACN) consisting of 0 min 7% B, 86 min 37% B, 93 min 70% B, and 100 min 70% B at a flow rate of 150 nL/min on an UltiMate 3000 RSLCnano LC system (Thermo Fisher Scientific). MS/MS of the eluted peptides was performed using a quadrupole Orbitrap Exploris 480 hybrid mass spectrometer (Thermo Fisher Scientific) with a normal DIA window. The MS1 scan range was set to a full scan of m/z 495–745 at mass resolution of 60,000, auto gain control (AGC) target of 3 × 106, and maximum injection time of “Auto.” MS2 was performed at m/z 200–1,800, resolution of 45,000, an AGC target of 3 × 106 (maximum injection time of “Auto”), and fixed normalized collision energy of 26%. The isolation width for MS2 was set to 4 Th. For the 500–740 m/z window pattern, an optimized window arrangement was used in Scaffold DIA (Proteome Software, Portland, OR, USA).