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Updated: Feb 10, 2026

Glycopeptide Capture for Cell Surface Proteomics
Published on: May 9, 2014
Analysis of PNGase F-Resistant N-Glycopeptides Using SugarQb for Proteome Discoverer 2.1 Reveals Cryptic Substrate
Johannes Stadlmann1, David M Hoi2, Jasmin Taubenschmid1
1Institute of Molecular Biotechnology Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030, Vienna, Austria.
Abstract:
SugarQb (www.imba.oeaw.ac.at/sugarqb) is a freely available collection of computational tools for the automated identification of intact glycopeptides from high-resolution HCD MS/MS datasets in the Proteome Discoverer environment. We report the migration of SugarQb to the latest and free version of Proteome Discoverer 2.1, and apply it to the analysis of PNGase F-resistant N-glycopeptides from mouse embryonic stem cells. The analysis of intact glycopeptides highlights unexpected technical limitations to PNGase F-dependent glycoproteomic workflows at the proteome level, and warrants a critical reinterpretation of seminal datasets in the context of N-glycosylation-site prediction.
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