Figure 3.

Reproducibility of relative peptide abundance measurements obtained on the LTQ Velos Pro and the Orbitrap Velos Pro. (A, B) Each point represents a particular modified form of either (A) an H3 peptide or (B) an H4 peptide, while the color of the point indicates the identity of the peptide. The black line indicates perfect correlation between relative peptide abundance values on the two instruments. The dashed line is a linear regression for all data points on the plot (Pearson, (A) R² = 0.878, (B) R² = 0.839; Spearman, (A) R² = 0.853, (B) R² = 0.883). The modified peptides shown in the figure include the following: (A) 3–8, unmodified, K4me1; 9–17, unmodified, K9me1, K9me1K14ac, K9me3K14ac, K9me2, K9me3, K9 or K14ac, K9me2K14ac; 18–26, unmodified, K18ac or K23ac; 27–40, unmodified, K36me1, K36me2, K27me1, K27me2, K27me3, K27me2K36me1, K27me1K36me2, K27me1K36me3, K27me1K36me1; (B) 4–17, unmodified, monoacetylated, and diacetylated; 20–23, unmodified, K20me1, K20me2. (C) Normalization of endogenous relative peptide abundances to synthetic peptide standards. Each point represents a particular modified form of the H3 9–17 peptide, listed in panel B. The blue points represent the data before normalization as shown in panel B, and the red points represent the data after normalization to the synthetic peptide standards. The solid black line represents perfect correlation. The dashed blue line is a linear regression fit of the data before normalization (R² = 0.579), and the red dotted line is a linear regression fit of the data after normalization (R² = 0.979).