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

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

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cells, Cultured
  • Embryonic Stem Cells / cytology
  • Embryonic Stem Cells / metabolism*
  • Glycopeptides / analysis*
  • Glycopeptides / chemistry
  • Glycoproteins / analysis*
  • Glycoproteins / chemistry
  • Glycosylation
  • Mice
  • Peptide-N4-(N-acetyl-beta-glucosaminyl) Asparagine Amidase / metabolism*
  • Proteome / analysis*
  • Proteome / chemistry
  • Software*
  • Substrate Specificity

Substances

  • Glycopeptides
  • Glycoproteins
  • Proteome
  • Peptide-N4-(N-acetyl-beta-glucosaminyl) Asparagine Amidase