Ultraflextreme instrument

Mass spectra were acquired on an Ultraflextreme instrument (Bruker, Billerica, MA). Before MS analysis, all samples were desalted using Pierce C-18 Spin Columns (Thermo Fisher Scientific, Waltham, MA) and dried in a speed-vac. Desiccated samples were resuspended in 30% aqueous ACN and mixed 1:1 with matrix solution. The matrix solution was composed of either 10 mg/mL 4-chloro-α-cyanocinnamic acid or 10 mg/mL α-cyano-4-hydroxycinnamic acid in 50% aqueous ACN and 2.5% formic acid. The instrument was calibrated using a homemade bovine serum albumin digest (in the appropriate corresponding matrix) in reflector positive detection mode in the 500–5000 mass/charge (m/z) range.
The extent of methylation by Set7 was assessed by comparing the relative intensities of the unmodified peptide mass to the methylated peptide mass (+15 Da per methyl group for ¹³C-SAM). Methylated peptides from final time points were subjected to fragmentation by MS/MS in LIFT mode. Expected peptide fragment masses were calculated using the MS-product mode in the Protein Prospector web tool (see Table S2). The theoretical peaks were assigned by hand to the experimental fragments corresponding to methylated H3 peptide. The MS/MS peaks and corresponding peptide fragments are shown in Figs. S1D and S2, B, D and F. All mass spectra were plotted, visualized, and analyzed using in-house Python scripts.