Comprehensive site- and structure-specific characterization of N-glycosylation in model plant Arabidopsis using mass-spectrometry-based N-glycoproteomics

•Site- and structure-specific identification of N-glycosylation of Arabidopsis at the intact N-glycopeptide level.•With spectrum-level FDR ≤ 1%, 5,687 intact N-glycopeptides coming from 3,713 N-glycosites of 3,140 N-glycoproteins were identified.•With structure-diagnostic fragment ions as experimental evidence, monosaccharide sequence structures of N-glycans on 630 intact N-glycopeptides were unambiguously distinguished from the other sequence isomers with the same monosaccharide compositions.