PXD074575-1

PXD074575 is an original dataset announced via ProteomeXchange.

Title	Expanding glycopeptide identification with Match-Between-Glycans (MBG) in FragPipe
Description	Glycosylation is one of the most important, but also most complex, post-translational modifications of proteins. Mass spectrometry-based glycoproteomics analysis offers a powerful approach to explore the fundamental roles of glycosylation, but achieving sufficient fragmentation for glycopeptide assignment remains challenging, especially for low-abundant glycopeptides and large, complex glycans. We introduce match-between-glycans (MBG), a lightweight, modular MS1-based method integrated into the FragPipe computational platform that expands glycopeptide identification by leveraging learned retention time (RT) and ion mobility (IM) shifts between glycan compositions. MBG can also identify glycans not included in the glycan database, such as those containing adducts or modifications, without expanding the search space. This submission includes original human plasma PASEF data (6 technical replicates, timsTOF HT) and re-analysis results from four publicly available datasets: fission yeast (PXD005565), mouse liver (PXD005553), mouse brain (PXD005411), and CPTAC glioblastoma (GBM, from the Proteomic Data Commons at https://pdc.cancer.gov/). MBG expanded glycopeptide identifications across all datasets, including 14.6% more in human plasma, and enabled detection of glycopeptide adducts (NH4+, Fe3+, Na+) and mannose-6-phosphate glycans.
HostingRepository	PRIDE
AnnounceDate	2026-09-01
AnnouncementXML	Submission_2026-09-01_13:24:26.159.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jiechen Shen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090; scientific name: Candida albicans (Yeast); NCBI TaxID: NEWT:5476;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF HT

Revision	Datetime	Status	ChangeLog Entry
0	2026-02-17 20:47:28	ID requested
⏵ 1	2026-09-01 13:24:26	announced

Dataset with its publication pending

submitter keyword: Human plasma

glycoproteomics

N-glycopeptides

PASEF

timsTOF

MSFragger-Glyco

FragPipe

ion mobility

Alexey Nesvizhskii
contact affiliation	Department of Pathology, University of Michigan Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan
contact email	nesvi@med.umich.edu
lab head
Jiechen Shen
contact affiliation	University of Michigan
contact email	jishen@umich.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/2026/09/PXD074575

PRIDE project URI

• PRIDE
  1. PXD074575
     1. Label: PRIDE project
     2. Name: Expanding glycopeptide identification with Match-Between-Glycans (MBG) in FragPipe