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

Proteomics
Johannes StadlmannJosef M Penninger

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.

References

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Sep 30, 2017·Nature·Johannes StadlmannJosef M Penninger

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Citations

Mar 18, 2020·Journal of Cellular and Molecular Medicine·Lin WangZhengjun Shang
Jul 30, 2020·Molecular Omics·Simon Ngao MuleGiuseppe Palmisano
Sep 18, 2020·Molecular & Cellular Proteomics : MCP·Nicholas M RileySharon J Pitteri
Jul 3, 2020·Molecular & Cellular Proteomics : MCP·Weiqian CaoPengyuan Yang
Jun 25, 2020·Molecular & Cellular Proteomics : MCP·Daniel G Delafield, Lingjun Li
Feb 9, 2021·Molecular & Cellular Proteomics : MCP·Weiqian CaoPengyuan Yang
Feb 16, 2021·Molecular & Cellular Proteomics : MCP·Nicholas M RileySharon J Pitteri
Aug 10, 2021·Frontiers in Chemistry·Dylan Nicholas TabangLingjun Li
Jun 6, 2020·Journal of Proteome Research·Nicholas M RileyCarolyn R Bertozzi

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Methods Mentioned

BETA
glycosylation

Software Mentioned

Proteome Discoverer Platform
MS Amanda
Proteome Discoverer
HT
MASCOT
SEQUEST
SugarQb

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