Proteomic profiling of Hut78 cutaneous T-cell lymphoma cells after SOX4 knockdown

This proteomic dataset was generated from Hut78 human cutaneous T-cell lymphoma cells after SOX4 knockdown (sh-SOX4) versus control (sh-NC). Proteins were extracted using SDT lysis buffer (4% SDS, 100 mM Tris-HCl pH 7.6), sonicated, boiled, and clarified by centrifugation. Protein concentration was determined by BCA assay. 600 μg of protein per sample was reduced with DTT, alkylated with IAA, and digested with trypsin using the FASP method on 30 kD filters. Resulting peptides were desalted with C18 cartridges, dried, and reconstituted in 0.1% formic acid. Peptides were separated on a Vanquish Neo UHPLC system and analyzed by an Orbitrap Astral mass spectrometer in data-independent acquisition (DIA) mode. MS1 scan range: 380–980 m/z at 240,000 resolution; 299 DIA windows with 2 m/z isolation width; HCD collision energy 25 eV. Raw data were processed with Spectronaut (FDR < 1%). Proteins with fold change >1.5 and p < 0.05 were considered differentially expressed.