Proteomic data of samples from lipid droplets of ASFV-infected cells

Peptide separations were carried out on an Easy-nLC 1000 nano system (Thermo Scientific). For the analysis, triplicates were loaded into a precolumn Acclaim PepMap 100 (Thermo Scientific) and eluted in a RSLC PepMap C18, 50 cm long, 75 µm inner diameter and 2 µm particle size (Thermo Scientific). The mobile phase flow rate was 300 nL/min using 0.1% formic acid in water (solvent A) and 0.1% formic acid and 100% acetonitrile (solvent B). The gradient profile was set as follows: 5–35% solvent B for 100 min, 35%-45% solvent B 20 min, 45%-100% solvent B 5 min, and 100% solvent B 15 min. Four microliters (about 1 µg) of each sample were injected. MS analysis was performed using a Q-Exactive mass spectrometer (Thermo Scientific). For ionization, 1900 V of liquid junction voltage and 300°C capillary temperature was used. The full scan method employed a m/z 300–1800 mass selection, an Orbitrap resolution of 70,000 (at m/z 200), a target automatic gain control (AGC) value of 3e6, and maximum injection times of 100 ms. After the survey scan, the 15 most intense precursor ions were selected for MS/MS fragmentation. Fragmentation was performed with a normalized collision energy of 27 eV and MS/MS scans were acquired with a starting mass of m/z 200, AGC target was 2e5, resolution of 17500 (at m/z 200), intensity threshold of 8e4, isolation window of 2.0 m/z units and maximum IT was 100 ms. Charge state screening was enabled to reject unassigned, singly charged, and equal or more than seven protonated ions. A dynamic exclusion time of 30s was used to discriminate against previously selected ions.