Glycoprotein-Notebook: A Pan-Cancer Glycoproteomic Database and Toolkit for Analysis of Protein Glycosylation Changes Associated With Cancer Phenotypes.

Protein glycosylation plays a pivotal role in various biological processes, and the analysis of intact glycopeptides (IGPs) has emerged as a powerful approach for characterizing alterations in protein glycosylation associated with diseases. Despite the critical insights gained from IGP analysis, dedicated databases and specialized tools for comprehensive glycoproteomics remain scarce. In response to this deficiency, we developed "Glycoprotein-Notebook," an online resource that consolidates the mass spectrometry evidence for IGPs identified from pan-cancer types studied in the Clinical Proteomic Tumor Analysis Consortium projects and provides analytical tools for in-depth glycopeptide characterization. Using pancreatic ductal adenocarcinoma as a case study, we validated and showcased the toolkit's analytical capabilities. Our results underscore the promise of IGPs as cancer-specific diagnostic and therapeutic targets. Accordingly, Glycoprotein-Notebook emerges as a valuable resource for cancer researchers exploring the intricate relationship between protein glycosylation and cancer phenotypes.