Fig. 2

Sample overview and differentially expressed proteins. A log₂ normalised peptide abundances for each sample, colored by batch (1–8) to visualise potential batch effects and the overall distribution of peptide measurements. B Volcano plots of DEPs with log₂ FC and −log10 p values in stable baseline vs. stable follow-up, C progressor baseline vs. stable baseline, D progressor baseline vs. progressor follow-up, and E progressor follow-up vs. stable follow-up. F PCA of significantly expressed proteins (p < 0.05) in each group. colors: red progressor baseline, green progressor follow-up, purple stable baseline, yellow stable follow-up