1. Connect the ACQUITY UPLC H-Class Bio to the Synapt
G2Si.
2. Connect the ACQUITY UPLC Protein BEH SEC Column
(200 A ˚ , 1.7 μm, 4.6 mm  150 mm) and equilibrate with
200 mM ammonium acetate at 300 μL/min.
3. Weigh 1.6 mg of alcohol dehydrogenase from Saccharomyces
Cerevisiae (Sigma-Aldrich). Resuspend in 280 μL of 200 mM
ammonium acetate to reach a tetrameric concentration of
40 μM.
Fig. 3 Native MS analysis of the ERRα DBD-BE26PSIR3 complex. (a) Full MS spectrum of protein/DNA
complex. Two charge states distributions in the 2,000–4,000 m/z range are present, first corresponding to the
6+ and 7+ charge states of DNA alone in the 2,000–4,000 m/z range and second to the 9+ and 8+ charge
states of the protein/DNA complex in the 3,000–3,800 m/z range. (b) Zoom in the 3,000–3,600 m/z range
showing the protein/DNA complex 9+ and 8+ charge states revealing the presence of two truncated DNA
species. (c) The associated deconvolution of native mass spectrum with UniDec software highlights a 1:1
stoichiometry for the protein/DNA complex (27,892.5 Da) and confirms the presence of two truncated DNA
species which are also able to interact with the protein (27,740.6 Da and 27,586.3 Da)
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