PXD040716-1

PXD040716 is an original dataset announced via ProteomeXchange.

Title	The GlycoPaSER prototype as a real-time N-glycopeptide identification tool based on the PaSER parallel computing platform
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 literature reference data. The GlycoPaSER prototype presented here provides the first proof-of-concept for real-time glycopeptide identification that unlocks future development of RDA technology to transcend data acquisition.
HostingRepository	PRIDE
AnnounceDate	2023-03-13
AnnouncementXML	Submission_2023-03-13_03:37:44.704.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	GadArmony
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-09 02:55:13	ID requested
⏵ 1	2023-03-13 03:37:45	announced
2	2023-11-14 09:00:37	announced	2023-11-14: Updated project metadata.

submitter keyword: PaSER,glycoproteomics, GlycoPaSER, results dependent acquisition (RDA), real-time search

Hans J.C.T.Wessels
contact affiliation	Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
contact email	Hans.Wessels@radboudumc.nl
lab head
GadArmony
contact affiliation	Utrecht University
contact email	gadi.armony@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/03/PXD040716

PRIDE project URI

• PRIDE
  1. PXD040716
     1. Label: PRIDE project
     2. Name: The GlycoPaSER prototype as a real-time N-glycopeptide identification tool based on the PaSER parallel computing platform