Native MS dataset for: Substrate directed transpososomes control copy-out-paste-in transposition

Native mass spectrometry dataset used in: Substrate directed transpososomes control copy-out-paste-in transposition. K. Janacova, A. Brzezina, A. Kadek, V. Obsilova, D. Kosek Journal XX (2026) Description: Native mass spectrometry (MS) analysis of the oligomeric state and protein-DNA complex formation of the transposon complexes Tnp-STCC as well as Tnp-STCI. Sample processing: To confirm the complex formation and its stoichiometry, we performed native MS analysis on a Waters Synapt G2Si instrument. Protein complex fraction from size exclusion chromatography was transferred into 100 mM ammonium acetate pH 7.5, which acts as an MS-compatible buffer surrogate, by two cycles of spin gel filtration (Micro Bio-Spin P-6 Gel columns, 6-kDa cut off; BioRad). The samples were then electrosprayed at 1.2 kV capillary voltage from in-house prepared borosilicate glass spraying tips (10.1038/nprot.2007.73) (Kwik-Fil 1B120F-4, World Precision Instruments) pulled with a P-1000 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 over the mass range 500 – 20.000 m/z with the trap collision energy stepwise acquired at 10 V (for stoichiometry) as well as 40 V and 80 V (for mass determination). Argon flow as collision gas was maintained at 8 ml/min, sampling cone voltage 80 V, source offset 0 V, and source temperature 80 °C. Quadrupole was operated in broad transmission mode up to 8000 m/z. Initial instrument parameter snapshot is saved in the .raw data, parameter changes during acquisition (with relevant scan ranges) are described in the "raw-file-description.txt" text file. Data processing: Acquired data were externally mass recalibrated on caesium iodide clusters, summed over 60 scans, and smoothed using two passes of Savitzky-Golay filtering (500 scan window) (10.1021/ac60214a047) in MassLynx 4.1 (Waters). Subsequently, mass deconvolution of the spectra was performed manually and in UniDec v6.0.4 (10.1021/acs.analchem.5b00140).