Native MS dataset for: "De-novo heterozygous variants in EHMT2 genocopy Kleefstra syndrome via a loss of G9a methyltransferase activity"

Native mass spectrometry dataset used in: De-novo heterozygous variants in EHMT2 genocopy Kleefstra syndrome via a loss of G9a methyltransferase activity. A. Hnizda, B. Martinez-Delgado et al. XXX (YYYY) Description: Native mass spectrometry (MS) analysis of the oligomeric state as well as histone H3 peptide / SAM cofactor binding to patient-derived GLP and G9a protein variants. Sample processing: Recombinant G9a and GLP variants were first transferred into 150 mM ammonium acetate pH 7.5 containing 0.5 mM DTT by one or two cycles of spin gel filtration (Micro Bio-Spin P-6 Gel columns, 6-kDa cut off; Bio-Rad). Next, the protein samples were diluted to 5 μM concentration, optionally mixed with SAM or histone H3 peptide in an equimolar ratio, and incubated for 10 min at 4 °C. The samples were electrosprayed into a Synapt G2Si instrument (Waters) at 0.9-1.2 kV from an in-house prepared borosilicate glass spraying tips (10.1038/nprot.2007.73) (Kwik-Fil 1B120F-4, World Precision Instruments) pulled with P-97 platinum-wire Flaming/Brown Micropipette puller (Sutter Instrument) and coated with 40 nm thick layer of gold using an ACE600 sputter coater (Leica). Data acquisition was performed in positive ionization sensitivity mode. For assessing the dimerization and substrate binding of the G9a and GLP variants, the trap collision energy was optimized to maximize sensitivity while keeping ion activation minimal at 10 V and 40 V, respectively. The argon flow as collision gas was maintained at 6 ml/min, sampling cone voltage set to 80 V, source offset to 0 V, and source temperature to 80 °C. Quadrupole was operated in broad transmission mode up to 4000 m/z. Data processing: Acquired data were externally mass recalibrated on caesium iodide clusters, summed over 50 scans, and smoothed using two passes of Savitzky-Golay filtering (window 50 scans) (10.1021/ac60214a047) in MassLynx 4.1 (Waters). Subsequently, mass deconvolution of the spectra was performed in UniDec v6.0.4 (10.1021/acs.analchem.5b00140). Additionally, spectra were background-subtracted in UniDec v6.0.4 and used to quantify the monomer-dimer distribution of the analysed proteins in their apo-form. The averaged spectra were exported for ZENODO deposition as plain in plain intensity vs m/z .txt files and also uploaded as part of the .raw file format of the whole analysis (including initial metadata) with scan descriptions and parameter changes described in a stand-alone .txt descriptor file.