Skip to main content
. Author manuscript; available in PMC: 2026 Jul 7.
Published in final edited form as: J Proteome Res. 2025 Jul 7;24(8):3808–3817. doi: 10.1021/acs.jproteome.4c01108

Figure 2. Comparison of normalization methods using simulated data.

Figure 2.

(A-B) QQ-plot of root mean of squared error (RMSE) across specimens for each protein, comparing ProMix and PQN (y-axis) to simple averaging of replicates (x-axis, “Before normalization”). (A) Block effects are absent. (B) Block effects are present. (C-D) Scatter plot comparing replication root mean of squared errors (repRMSE) computed from specimen replicates, using PQN (x-axis) or ProMix-LOO normalization (y-axis). (C) Block effects are absent. (D) Block effects are present.