Comparative evaluation of different MALDI-TOF-MS platforms for plasma IgG N-glycan profiling: impact on analytical...

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a cornerstone technology for high‑throughput immunoglobulin G (IgG) N‑glycan profiling. However, the cross-platform data comparability remains a critical gap. This study systematically evaluated the analytical and clinical consistency of the UltrafleXtreme and the RapifleX® MALDI‑TOF‑MS platforms of Bruker for plasma IgG N‑glycomics. IgG N-glycan profiles from 170 patients with pancreatic cancer and 30 healthy controls were assessed utilizing a standardized workflow. Glycan coverage, intra‑ and inter‑day repeatability, and quantitative agreement (Bland‑Altman analysis) were assessed. The diagnostic performance of individual glycans and combined diagnostic models was evaluated using the receiver operating characteristic (ROC) curve analysis and the area under the curve (AUC). The 33 N-glycans detected by the RapifleX® met the quality screening standards, completely encompassing the 20 N-glycans identified by the UltrafleXtreme, along 13 additional low‑abundance species accounting for 2.34% of total abundance. Analytically, the RapifleX® showed superior intra‑day repeatability (median CV 5.38% vs. 11.92%, p < 0.0001), while inter‑day repeatability was comparable (p = 0.8695). Shared N-glycans exhibited excellent quantitative agreement. A two-glycan model, H4N5F1E1 and H5N4F1E2, yielded comparable AUCs for discriminating cancer and controls (0.869 for the UltrafleXtreme vs. 0.871 for the RapifleX®, DeLong test p = 0.8347). Both platforms generate reliable and quantitatively comparable IgG N‑glycan profiles. While the RapifleX® offers enhanced glycome coverage and superior short-term precision, clinical models yield consistent diagnostic conclusions across both generations of instruments. These findings establish critical methodological evidence for cross-platform data integration and instrument selection in large-scale clinical IgG N-glycomics.