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. 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 4. Impact of experimental designs on normalization using simulated data.

Figure 4.

QQ-plot of root mean of squared error (RMSE) comparing four experimental designs: Full (two references + replicates), SingleRef (one reference + replicates), NoRep (two references, no replicates), and SingleRef+NoRep (single-reference design without replicates). Full design (x-axis) is used as the benchmark. (A) Block effects are absent. (B) Block effects are present.