Aggregate Stability Coexists with Peptide-Level Context Dependence in Glaucoma Aqueous Humor Proteomics

Abstract Protein summaries can conceal peptide context. We tested whether aqueous humor vitronectin (VTN) retained an aggregate direction while peptide evidence varied across cohorts and platforms. In PXD027686, VTN was higher in primary chronic angle-closure glaucoma than cataract (1.05 log2; 95% CI, 0.63–1.47). We reprocessed 40 PXD004928 raw files. VTN was higher in primary angle-closure glaucoma (PACG) than cataract (9 versus 7 participants; acquisition-adjusted log2 effect, 0.71; 95% confidence interval [CI], 0.05–1.37; P = 0.0367), with positive point estimates in all 16 participant-deletion fits. Acquisition-stratified aggregates remained positive while peptide point estimates changed direction, but the disease-by-peptide test was not significant: F(2, 10.45) = 1.07 (P = 0.3765). The PACG–primary open-angle glaucoma aggregate was near zero (0.13; 95% CI, −0.27–0.53). Across eligible proteins, aggregate–peptide point-direction mismatch in 20 of 37 PACG–cataract and 27 of 40 PACG–POAG proteins; interval-supported opposition occurred in 1 of 37 and 3 of 40 proteins, and no interaction survived Benjamini–Hochberg correction. Directional aggregate reproducibility therefore coexisted with descriptive peptide discordance; statistically supported interaction was confined to the source-selected targeted panel. Data are deposited in ProteomeXchange under PXD082879.