Dynamic alterations of site-specific N-glycoform and plasma proteasome signatures stratify chemotherapy benefit in pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) exhibits profound systemic remodeling during chemotherapy, yet how site-specific intact N-glycosylation in plasma is rewired by treatment remains largely undefined. Here, we perform an integrated plasma multi-omics study combining intact N-glycopeptidomics, deep proteomics, and metabolomics in a longitudinal cohort with paired pre- and post-chemotherapy samples and follow-ups (n = 177). Patients were further stratified according to radiographic treatment response. We identified 17,501 intact N-glycopeptides corresponding to 16,754 glycoforms, together with 6,045 proteins and 1,080 annotated metabolites. Paired analyses revealed extensive chemotherapy-associated changes across all three omics layers. Temporal glycopeptide and protein patterns were consistently enriched for complement, coagulation, extracellular-matrix, proteasome, and immune-related annotations, while oxidative-phosphorylation-related signatures showed relative depletion after treatment. Exploratory comparisons of within-patient changes (Δ = Post - Pre) between patients with partial response (PR) and those with stable or progressive disease highlighted 140 glycoforms, 18 glycosylation sites, and 103 proteins with response-associated patterns. These included coordinated increases in several proteasome-related plasma proteins in the PR group, as well as site- and glycoform-specific changes in complement- and acute-phase-related proteins. Response-associated differences in circulating metabolites further involved pyrimidine-, amino-acid-, and dipeptide-related features. Finally, leakage-controlled nested cross-validation prioritized 11 recurrent N-glycopeptide candidates and yielded modest prognostic discrimination, with a C-index of 0.591 and a 12-month area under the curve of 0.712. Collectively, this study provides a site- and glycoform-resolved view of chemotherapy-associated plasma molecular changes in PDAC and identifies candidate response- and prognosis-related features for future validation.