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Proteomics. 2018 Jul;18(13):e1700436. doi: 10.1002/pmic.201700436. Epub 2018 Jun 10.

Analysis of PNGase F-Resistant N-Glycopeptides Using SugarQb for Proteome Discoverer 2.1 Reveals Cryptic Substrate Specificities.

Author information

1
Institute of Molecular Biotechnology Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030, Vienna, Austria.
2
Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, 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.

PMID:
29775240
PMCID:
PMC6055662
DOI:
10.1002/pmic.201700436
[Indexed for MEDLINE]
Free PMC Article

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