Proteomic profiling was performed by nano liquid chromatography–tandem mass spectrometry (nanoLC–MS/MS) operated in data‑independent acquisition (DIA) mode. For retention‑time calibration and quantitative quality control, iRT peptides were spiked into each sample prior to injection at an iRT:sample ratio of 1:20 (v/v). Peptides were separated on a nanoElute nanoLC system (Bruker) equipped with a C18 analytical column (25 cm × 75 μm i.d., 1.6 μm C18, IonOpticks) at a flow rate of 300 nL/min, using mobile phase A (0.1% formic acid in water) and mobile phase B (0.1% formic acid in acetonitrile). The DIA gradient was: 0 min, 2% B; 45 min, 22% B; 50 min, 37% B; 55–60 min, 80% B (followed by re‑equilibration to the initial conditions as defined in the instrument method). MS data were acquired on a timsTOF Pro 2 high‑resolution mass spectrometer (Bruker) in DIA mode. The acquisition parameters were: capillary voltage 1.4 kV; dry temperature 180°C; dry gas 3.0 L/min; mass range m/z 100–1700; ion mobility 0.7–1.3 (as defined in the acquisition method); collision energy 20–59 eV. DIA raw files were processed and quantified using Spectronaut Pulsar (v17.5, Biognosys) with the protein sequence database uniprot-Pinus subgen. Pinus-139271-2023.7.3.fasta, and quantitative reports were exported for downstream analysis.