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The GlycoPaSER Prototype as a Real-Time N-Glycopeptide Identification Tool Based on the PaSER Parallel Computing Platform

Real-time database searching allows for simpler and automated proteomics workflows as it eliminates technical bottlenecks in high-throughput experiments. Most importantly, it enables results-dependent acquisition (RDA), where search results can be used to guide data acquisition during acquisition. T...

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Autores principales: Armony, Gad, Brehmer, Sven, Srikumar, Tharan, Pfennig, Lennard, Zijlstra, Fokje, Trede, Dennis, Kruppa, Gary, Lefeber, Dirk J., van Gool, Alain J., Wessels, Hans J. C. T.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10178020/
https://www.ncbi.nlm.nih.gov/pubmed/37175577
http://dx.doi.org/10.3390/ijms24097869
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author Armony, Gad
Brehmer, Sven
Srikumar, Tharan
Pfennig, Lennard
Zijlstra, Fokje
Trede, Dennis
Kruppa, Gary
Lefeber, Dirk J.
van Gool, Alain J.
Wessels, Hans J. C. T.
author_facet Armony, Gad
Brehmer, Sven
Srikumar, Tharan
Pfennig, Lennard
Zijlstra, Fokje
Trede, Dennis
Kruppa, Gary
Lefeber, Dirk J.
van Gool, Alain J.
Wessels, Hans J. C. T.
author_sort Armony, Gad
collection PubMed
description Real-time database searching allows for simpler and automated proteomics workflows as it eliminates technical bottlenecks in high-throughput experiments. Most importantly, it enables results-dependent acquisition (RDA), where search results can be used to guide data acquisition during acquisition. This is especially beneficial for glycoproteomics since the wide range of physicochemical properties of glycopeptides lead to a wide range of optimal acquisition parameters. We established here the GlycoPaSER prototype by extending the Parallel Search Engine in Real-time (PaSER) functionality for real-time glycopeptide identification from fragmentation spectra. Glycopeptide fragmentation spectra were decomposed into peptide and glycan moiety spectra using common N-glycan fragments. Each moiety was subsequently identified by a specialized algorithm running in real-time. GlycoPaSER can keep up with the rate of data acquisition for real-time analysis with similar performance to other glycoproteomics software and produces results that are in line with the literature reference data. The GlycoPaSER prototype presented here provides the first proof-of-concept for real-time glycopeptide identification that unlocks the future development of RDA technology to transcend data acquisition.
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spelling pubmed-101780202023-05-13 The GlycoPaSER Prototype as a Real-Time N-Glycopeptide Identification Tool Based on the PaSER Parallel Computing Platform Armony, Gad Brehmer, Sven Srikumar, Tharan Pfennig, Lennard Zijlstra, Fokje Trede, Dennis Kruppa, Gary Lefeber, Dirk J. van Gool, Alain J. Wessels, Hans J. C. T. Int J Mol Sci Article Real-time database searching allows for simpler and automated proteomics workflows as it eliminates technical bottlenecks in high-throughput experiments. Most importantly, it enables results-dependent acquisition (RDA), where search results can be used to guide data acquisition during acquisition. This is especially beneficial for glycoproteomics since the wide range of physicochemical properties of glycopeptides lead to a wide range of optimal acquisition parameters. We established here the GlycoPaSER prototype by extending the Parallel Search Engine in Real-time (PaSER) functionality for real-time glycopeptide identification from fragmentation spectra. Glycopeptide fragmentation spectra were decomposed into peptide and glycan moiety spectra using common N-glycan fragments. Each moiety was subsequently identified by a specialized algorithm running in real-time. GlycoPaSER can keep up with the rate of data acquisition for real-time analysis with similar performance to other glycoproteomics software and produces results that are in line with the literature reference data. The GlycoPaSER prototype presented here provides the first proof-of-concept for real-time glycopeptide identification that unlocks the future development of RDA technology to transcend data acquisition. MDPI 2023-04-26 /pmc/articles/PMC10178020/ /pubmed/37175577 http://dx.doi.org/10.3390/ijms24097869 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Armony, Gad
Brehmer, Sven
Srikumar, Tharan
Pfennig, Lennard
Zijlstra, Fokje
Trede, Dennis
Kruppa, Gary
Lefeber, Dirk J.
van Gool, Alain J.
Wessels, Hans J. C. T.
The GlycoPaSER Prototype as a Real-Time N-Glycopeptide Identification Tool Based on the PaSER Parallel Computing Platform
title The GlycoPaSER Prototype as a Real-Time N-Glycopeptide Identification Tool Based on the PaSER Parallel Computing Platform
title_full The GlycoPaSER Prototype as a Real-Time N-Glycopeptide Identification Tool Based on the PaSER Parallel Computing Platform
title_fullStr The GlycoPaSER Prototype as a Real-Time N-Glycopeptide Identification Tool Based on the PaSER Parallel Computing Platform
title_full_unstemmed The GlycoPaSER Prototype as a Real-Time N-Glycopeptide Identification Tool Based on the PaSER Parallel Computing Platform
title_short The GlycoPaSER Prototype as a Real-Time N-Glycopeptide Identification Tool Based on the PaSER Parallel Computing Platform
title_sort glycopaser prototype as a real-time n-glycopeptide identification tool based on the paser parallel computing platform
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10178020/
https://www.ncbi.nlm.nih.gov/pubmed/37175577
http://dx.doi.org/10.3390/ijms24097869
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