PXD017646-2

PXD017646 is an original dataset announced via ProteomeXchange.

Title	Optimal Dissociation Methods Differ for N- and O-glycopeptides
Description	Site-specific characterization of glycosylation requires intact glycopeptide analysis, and recent efforts have focused on how to best interrogate glycopeptides using tandem mass spectrometry (MS/MS). Beam-type collisional activation, i.e., higher-energy collisional dissociation (HCD), has been a valuable approach, but stepped collision energy HCD (sceHCD) and electron transfer dissociation with HCD supplemental activation (EThcD) have emerged as potentially more suitable alternatives. Both sceHCD and EThcD have been used with success in large-scale glycoproteomic experiments, but they each incur some degree of compromise. Furthermore, N-glycoproteomics has made significant progress in the last few years, and there is growing interest in extending this progress to O-glycoproteomics, which necessitates comparisons of method performance for the two classes of glycopeptides. Here, we systematically explore the advantages and disadvantages of conventional HCD, sceHCD, ETD, and EThcD for intact glycopeptide analysis and comment on their suitability for both N- and O-glycoproteomic applications. For N-glycopeptides, HCD and sceHCD generate similar numbers of identifications, although sceHCD generally provides higher quality spectra. Both significantly outperform EThcD methods, indicating that ETD-based methods are not required for routine N-glycoproteomics. Conversely, ETD-based methods, especially EThcD, are indispensable for site-specific analyses of O-glycopeptides. Our data show that O-glycopeptides cannot be robustly characterized with HCD-centric methods that are sufficient for N-glycopeptides, and glycoproteomic methods aiming to characterize O-glycopeptides must be constructed accordingly.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:09:28.852.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nicholas Riley
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	complex glycosylation
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2020-02-20 01:21:05	ID requested
1	2020-07-19 21:58:12	announced
⏵ 2	2024-10-22 05:09:29	announced	2024-10-22: Updated project metadata.

10.1021/acs.jproteome.0c00218;

Riley NM, Malaker SA, Driessen MD, Bertozzi CR, -Glycopeptides. J Proteome Res, 19(8):3286-3301(2020) [pubmed]

submitter keyword: glycoproteomics, N-glycopeptides, sceHCD, EThcD, O-glycopeptides, ETD

Carolyn Bertozzi
contact affiliation	Department of Chemistry, Stanford University, Stanford, California, USA Howard Hughes Medical Institute, Stanford, California, USA
contact email	bertozzi@stanford.edu
lab head
Nicholas Riley
contact affiliation	Stanford University
contact email	riley.nicholasm@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD017646
     1. Label: PRIDE project
     2. Name: Optimal Dissociation Methods Differ for N- and O-glycopeptides