Supplementary Figure 2: Peptide fractionation and SILAC analysis scheme for MEFs and ESCs.

a) Schematic representation of the experimental design used for total proteome and acetylome identification by LC-MS. Cells were labeled with heavy lysine (K8) and arginine (R10) and reciprocal labeling setup (“label swap”) was implemented (Methods). Tryptic peptides were fractionated on a C18 (solid phase extraction) column and underwent two rounds of anti-acetyl (Lys) immunoprecipitation procedures using two different antibody resins. Samples were measured by nano LC-MS/MS (Methods). Additionally, IP input samples were measured. b) Correlation matrix scatter plots with Pearson-r correlation values for acetyl (Lys) sites in replicates from MEFs and ESCs control and Mof KO. Raw ratios were log2 transformed and ratio distributions were adjusted by quartile normalization. c) Histograms representing ratio distributions across replicates in anti-acetyl(Lys) IP samples in MEFs and ESCs. Raw ratio values were log2 transformed (white) and subsequently adjusted by quartile normalization (blue). d) Numerical UpSet diagram representing the overlap between identified acetyl(K)sites within all replicates in MEFs (left panel) and ESCs (right panel). From the total number of 6534 unique acetyl(K)sites in MEFs, 4048 were found in at least 3 replicates. For ESCs, 1964 acetyl(K)sites were found in at least 3 replicates out of 3020 unique acetyl(K)sites. For b, c and d n=6 independent biological replicates.