Fig. 2.

Label free quantitation of methyl peptides is highly reproducible. A, Schematic of the label free quantitation (LFQ) workflow for methyl peptides. LFQ values were imported to Perseus where peptides with missing values or methionine oxidation were removed. Values were log2 transformed and median normalized. A permutation-based t test with an FDR q-value of 0.05 and S0 value of 0.5 was performed to identify significantly changing methyl peptides. B, SCX and IAP quantify different subsets of the protein methylome. Overlap of (top) quantified MMA peptides comparing SCX and MMA IAP, (middle) quantified DMA peptides comparing SCX and ADMA/SDMA IAPs, and (bottom) quantified mono/di/tri-methyl lysine peptides comparing SCX and PanK IAP. C, Scatter plots of biological replicates demonstrate high reproducibility. The log₁₀ LFQ values between biological replicates were plotted for each methyl-peptide enrichment. Each dot is colored by the local density of points. The number of peptides and the Pearson correlation coefficient for each comparison is shown.