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[…] The digests were captured on a trapping column (Waters ACQUITY BEH C18 VanGuard Pre-column 2.1 × 5 mm), and eluted to a Waters BEH C18 UHPLC column (2.1 × 50 mm) for peptide separation on a Waters Nano Acquity HPLC system, using a 12 min 5−50% gradient flowing at 50 μL min−1 of buffer A (0.1% formic acid and 0.05% trifluoroacetic acid in H2O) and buffer B (acetonitrile). The eluted peptides were directed onto a Thermo Orbitrap Elite mass spectrometer with electrospray ionization for detection. Mass spectra were acquired over the m/z range 300−1800 at a resolving power of 60,000 at m/z 400. Peptides were identified using a combination of exact mass and MS/MS aided by Mascot algorithm search (Mascot Daemon V.2.3.2; Mascot Distiller V.2.4.2). Peptide deuterium levels were determined using EXMS and a script developed in-house. Complete peptide coverage was obtained for both uncomplexed and the DNA-bound BAZ1A-PHD protein, and peptides with identical sequence between the two samples (matching peptides) covered all the BAZ1A-PHD protein, except residues 32−42. The relative 2H uptake for peptides from uncomplexed BAZ1A-PHD is reported in Supplementary Fig.  as the ratio between 2H uptake after 4 h labeling and the theoretical maximum 2H uptake (without back-exchange correction), expressed as a percentage. Average relative deuterium uptake difference (ARDD; ref. ) was used to compute the changes in 2H uptake caused by DNA binding. For each HDX time point, the relative 2H uptake fo […]

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