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

SugarQb (http://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 vers...

Descripción completa

Detalles Bibliográficos
Autores principales: Stadlmann, Johannes, Hoi, David M., Taubenschmid, Jasmin, Mechtler, Karl, Penninger, Josef M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2018
Materias:
Technical Briefs
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6055662/
https://www.ncbi.nlm.nih.gov/pubmed/29775240
http://dx.doi.org/10.1002/pmic.201700436
_version_ 1783341219113336832
author Stadlmann, Johannes
Hoi, David M.
Taubenschmid, Jasmin
Mechtler, Karl
Penninger, Josef M.
author_facet Stadlmann, Johannes
Hoi, David M.
Taubenschmid, Jasmin
Mechtler, Karl
Penninger, Josef M.
author_sort Stadlmann, Johannes
collection PubMed
description SugarQb (http://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.
format Online
Article
Text
id pubmed-6055662
institution National Center for Biotechnology Information
language English
publishDate 2018
publisher John Wiley and Sons Inc.
record_format MEDLINE/PubMed
spelling pubmed-60556622018-07-23 Analysis of PNGase F‐Resistant N‐Glycopeptides Using SugarQb for Proteome Discoverer 2.1 Reveals Cryptic Substrate Specificities Stadlmann, Johannes Hoi, David M. Taubenschmid, Jasmin Mechtler, Karl Penninger, Josef M. Proteomics Technical Briefs SugarQb (http://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. John Wiley and Sons Inc. 2018-06-10 2018-07 /pmc/articles/PMC6055662/ /pubmed/29775240 http://dx.doi.org/10.1002/pmic.201700436 Text en © 2018 The Authors. Proteomics Published by WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Technical Briefs
Stadlmann, Johannes
Hoi, David M.
Taubenschmid, Jasmin
Mechtler, Karl
Penninger, Josef M.
Analysis of PNGase F‐Resistant N‐Glycopeptides Using SugarQb for Proteome Discoverer 2.1 Reveals Cryptic Substrate Specificities
title Analysis of PNGase F‐Resistant N‐Glycopeptides Using SugarQb for Proteome Discoverer 2.1 Reveals Cryptic Substrate Specificities
title_full Analysis of PNGase F‐Resistant N‐Glycopeptides Using SugarQb for Proteome Discoverer 2.1 Reveals Cryptic Substrate Specificities
title_fullStr Analysis of PNGase F‐Resistant N‐Glycopeptides Using SugarQb for Proteome Discoverer 2.1 Reveals Cryptic Substrate Specificities
title_full_unstemmed Analysis of PNGase F‐Resistant N‐Glycopeptides Using SugarQb for Proteome Discoverer 2.1 Reveals Cryptic Substrate Specificities
title_short Analysis of PNGase F‐Resistant N‐Glycopeptides Using SugarQb for Proteome Discoverer 2.1 Reveals Cryptic Substrate Specificities
title_sort analysis of pngase f‐resistant n‐glycopeptides using sugarqb for proteome discoverer 2.1 reveals cryptic substrate specificities
topic Technical Briefs
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6055662/
https://www.ncbi.nlm.nih.gov/pubmed/29775240
http://dx.doi.org/10.1002/pmic.201700436
work_keys_str_mv AT stadlmannjohannes analysisofpngasefresistantnglycopeptidesusingsugarqbforproteomediscoverer21revealscrypticsubstratespecificities
AT hoidavidm analysisofpngasefresistantnglycopeptidesusingsugarqbforproteomediscoverer21revealscrypticsubstratespecificities
AT taubenschmidjasmin analysisofpngasefresistantnglycopeptidesusingsugarqbforproteomediscoverer21revealscrypticsubstratespecificities
AT mechtlerkarl analysisofpngasefresistantnglycopeptidesusingsugarqbforproteomediscoverer21revealscrypticsubstratespecificities
AT penningerjosefm analysisofpngasefresistantnglycopeptidesusingsugarqbforproteomediscoverer21revealscrypticsubstratespecificities

Ejemplares similares