PXD058153

PXD058153 is an original dataset announced via ProteomeXchange.

Title	Improvements in glycoproteomics through architecture changes to the Orbitrap Tribrid MS platform
Description	Hardware changes introduced on the Orbitrap Ascend MultiOmics Tribrid MS include dual ion routing multipoles (IRMs) that can enable parallelized accumulation, dissociation, and Orbitrap mass analysis of three separate ion populations. The balance between these instrument functions is especially important in glycoproteomics, where complexities of glycopeptide fragmentation necessitate large precursor ion populations and, consequently, long ion accumulation times for quality MS/MS spectra. To compound matters further, dissociation methods like electron transfer dissociation (ETD) that benefit glycopeptide characterization come with overhead times that also slow down scan acquisition. Here we explored how the dual IRM architecture of the Orbitrap Ascend can improve glycopeptide analysis, with a focus on O-glycopeptide characterization using ETD with supplemental collisional activation (EThcD). We found that parallelization of ion accumulation and EThcD fragmentation – uniquely enabled by the Orbitrap Ascend – increased scan acquisition speed without sacrificing spectral quality, subsequently increasing the number of O-glycopeptides identified relative to analyses on the Orbitrap Eclipse (i.e., the previous generation Tribrid MS). Additionally, we systematically evaluated ion-ion reaction times and supplemental activation energies used for EThcD to understand how best to utilize acquisition time in the dual IRM architecture. We observed that shorter-than-expected ion-ion reaction times minimized scan overhead time without sacrificing c/z•-fragment ion generation, and that higher supplemental collision energies can generate combinations of glycan-retaining and glycan-neutral-loss peptide backbone fragments that benefit O-glycopeptide identification. We also saw improvements in N-glycopeptide analysis using collision-based dissociation, especially with methods using faster scan acquisition speeds. Overall, these data show how architectural changes to the Tribrid MS platform benefit glycoproteomic experiments by parallelizing scan functions to minimize overhead time and improve sensitivity.
HostingRepository	PRIDE
AnnounceDate	2025-09-14
AnnouncementXML	Submission_2025-09-14_11:19:51.013.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tim S Veth
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	complex glycosylation
Instrument	Orbitrap Eclipse; Orbitrap Ascend

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-21 17:39:17	ID requested
⏵ 1	2025-09-14 11:19:51	announced

Veth TS, Sutherland E, Markuson KA, Zhang R, Duboff AG, Huang J, Bergen D, Lee AE, Melani RD, Canterbury JD, Zabrouskov V, McAlister GC, Mullen C, Riley NM, Improvements in Glycoproteomics through Architecture Changes to the Orbitrap Tribrid MS Platform. Anal Chem, 97(22):11413-11423(2025) [pubmed]

10.1021/acs.analchem.4c06370;

submitter keyword: N-glycopeptides, fragmentation,Glycoproteomics, tandem mass spectrometry, O-glycopeptides, electron transfer dissociation

Nicholas M. Riley
contact affiliation	Department of Chemistry, University of Washington, Seattle, WA, USA
contact email	nmriley@uw.edu
lab head
Tim S Veth
contact affiliation	University of Washington
contact email	tveth@uw.edu
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/2025/09/PXD058153

PRIDE project URI

• PRIDE
  1. PXD058153
     1. Label: PRIDE project
     2. Name: Improvements in glycoproteomics through architecture changes to the Orbitrap Tribrid MS platform