PXD025407-1

PXD025407 is an original dataset announced via ProteomeXchange.

Title	A systematic evaluation of fragmentation methods for unlabeled and isobaric mass tag-labeled O-glycopeptides
Description	Dissecting site-specific functions of O-glycosylation requires simultaneous identification and quantification of differentially ex-pressed O-glycopeptides by mass spectrometry. However, different dissociation methods have not been systematically compared in their performance in terms of identification, glycosite localization and quantification with isobaric labeling. Here, we conducted this comparison with higher-energy collision dissociation (HCD), electron-transfer/collision-induced dissociation (ETciD) and electron transfer/higher-energy collisional dissociation (EThcD), concluding that ETciD with optimal supplemental activation re-sulted in most identifications and unambiguous site localizations. We later described a pseudo EThcD strategy that in silico com-bines ETciD spectrum with HCD spectrum acquired sequentially for the same precursor, which combines the identification ad-vantage of ETciD with the superior reporter ion quality of HCD. We demonstrated its improvements in identifications and quantification of isobaric mass tag-labeled O-glycopeptides and showcased the discovery of the specific glycosylation sites of GalNAc tansferase 11 (GalNAc-T11) in HepG2 cells.
HostingRepository	PRIDE
AnnounceDate	2021-11-25
AnnouncementXML	Submission_2021-11-25_06:42:22.070.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sergey Vakhrushev
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Hex-HexNAc
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-04-14 21:36:01	ID requested
⏵ 1	2021-11-25 06:42:22	announced

Dataset with its publication pending

submitter keyword: Glycoproteomics, LC-MS/MS, ETD, HCD

Sergey Vakhrushev
contact affiliation	Copenhagen Center for Glycomics, University of Copenhagen
contact email	seva@sund.ku.dk
lab head
Sergey Vakhrushev
contact affiliation	Department of Cellular and Molecular Medicine
contact email	seva@sund.ku.dk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD025407
     1. Label: PRIDE project
     2. Name: A systematic evaluation of fragmentation methods for unlabeled and isobaric mass tag-labeled O-glycopeptides