GlycoHBF: Mass spectrometry-based glycoproteomics data from 15 types of human body fluids

The study of proteins and N-glycosylation in human body fluids (HBFs) is crucial for understanding both physiological and pathological states, providing valuable insights for disease diagnostics and monitoring. However, systematic and comprehensive research on HBF (glyco)proteomics based on standardized sample processing and mass spectrometry (MS) analysis workflows remains scarce. As a result, it is hard to make parallel comparisons between different HBFs. In this study, we present a (glyco)proteomics dataset (GlycoHBF) featuring 15 types of precious HBFs (plasma (P), urine (U), cerebrospinal fluid (CSF), pleural fluid (PF), ascitic fluid (AF), synovial fluid (SF), pericardial fluid (PCF), peritoneal dialysis effluent (PDE), bile (B), gastric juice (GJ), seminal plasma (SP), saliva (SA), pancreatic juice (PJ), sweat (SW), and tear (T)). We also provide detailed, standardized, and clinically applicable protocols for HBF-specific protein processing in cohort studies. The resulting peptides and enriched intact N-glycopeptides (IGPs) were analyzed via liquid chromatography-tandem mass spectrometry (LC-MS/MS) in data independent acquisition (DIA) mode and combined electron transfer/higher-energy collisional dissociation and stepped collision energy/higher-energy collisional dissociation (EThcD-sceHCD) mode, respectively. Our results demonstrate that hundreds of proteins and IGPs can be quantified in a single LC-MS/MS run, while significant heterogeneity exists in different HBFs. This study establishes a standardized analytical workflow for (glyco)proteomics studies of diverse HBFs and offers a reference framework for identifying potential disease biomarkers in clinical cohort studies.