PXD034845

PXD034845 is an original dataset announced via ProteomeXchange.

Title	Oxonium Ion-Guided Ion Mobility-Assisted Glycoproteomics on the timsTOF Pro
Description	Spatial separation of ions in the gas-phase, providing information about their size as collisional cross-sections, can readily be achieved through ion mobility. The timsTOF Pro combines a trapped ion mobility device with a quadrupole, collision cell and a time-of-flight analyser to enable the analysis of ions at great speed. Here, we show that the timsTOF Pro is capable of physically separating N-glycopeptides from non-modified peptides and producing high-quality fragmentation spectra, both beneficial for glycoproteomics analyses of complex samples. The glycan moieties enlarge the size of glycopeptides compared to non-modified peptides, yielding a clear cluster in the mobilogram that, next to increased dynamic range from the physical separation of glycopeptides and non-modified peptides, can be used to make an effective selection filter for directing the mass spectrometer to analytes of interest. This new approach was applied to selected glycoproteins, human plasma- and neutrophil-derived glycopeptides. We show that the achieved physical separation, combined with the focussing of the mass spectrometer, allows for improved extraction of information from the samples, even at shorter LC gradients of 15 min. We validated our approach on human neutrophil and plasma samples of known make-up, in which we captured the anticipated glycan heterogeneity (paucimannose, phosphomannose, high mannose, hybrid and complex glycans) from diverse biological samples (plasma and neutrophils) at the expected abundances. As the method is compatible with off-the-shelve data acquisition routines and data analysis software, it can readily be applied by any laboratory with a timsTOF Pro and is reproducible as demonstrated by an inter-laboratory comparison between two laboratories.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:57:18.230.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andris Jankevics
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2022-06-22 14:54:30	ID requested
1	2023-01-17 08:51:38	announced
⏵ 2	2023-11-14 08:57:18	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

ProteomeXchange project tag: EPIC-XS

submitter keyword: TIMS,N-glycopeptides, oxonium ions, plasma, neutrophils, ion mobility

Albert J.R. Heck
contact affiliation	Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
contact email	A.J.R.Heck@uu.nl
lab head
Andris Jankevics
contact affiliation	Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht Netherlands Proteomics Center
contact email	a.jankevics@uu.nl
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/2023/01/PXD034845

PRIDE project URI

• PRIDE
  1. PXD034845
     1. Label: PRIDE project
     2. Name: Oxonium Ion-Guided Ion Mobility-Assisted Glycoproteomics on the timsTOF Pro