Updated project metadata. In this project, CSF samples from healthy volunteers and patients diagnosed with congenital disorders of glycosylation (CDG) were analyzed with MS-based glycoproteomics to characterize the glycoproteome in the two cohorts. In order to identify highly truncated glycopeptides and glycopeptides that show the complete loss of glycosylation, we chose to not perform a glycopeptide enrichment. Using the high identification rate of the timsTOF Pro including PASEF fragmentation, we were able to detect over 800 unique glycopeptides. We show that changes in protein N-glycosylation of CDG patients can be different on brain-derived proteins compared to blood derived proteins.