PXD035775

PXD035775 is an original dataset announced via ProteomeXchange.

Title	Deciphering O-glycoprotease substrate preferences with O-Pair Search
Description	O-glycoproteases are an emerging class of enzymes that selectively digest glycoproteins at positions decorated with specific O-linked glycans. O-glycoprotease substrates range from any O-glycoprotein (albeit with specific O-glycan modifications) to only glycoproteins harboring specific O-glycosylated sequence motifs, such as those found in mucin domains. Their utility for multiple glycoproteomic applications is driving the search to both discover new O-glycoproteases and to understand how structural features of characterized O-glycoproteases influence their substrate specificities. One challenge of characterizing O-glycoprotease specificity restraints is the need to characterize O-glycopeptides with site-specific analysis of O-glycosites. Here, we demonstrate how O-Pair Search, a recently developed O-glycopeptide-centric identification platform that enables rapid searches and confident O-glycosite localization, can be used to determine substrate specificities of various O-glycoproteases de novo from LC-MS/MS data of O-glycopeptides. Using secreted protease of C1 esterase inhibitor (StcE) from enterohemorrhagic Escherichia coli and O-endoprotease OgpA from Akkermansia mucinophila, we explore numerous settings that effect O-glycopeptide identification and show how non-specific and semi-tryptic searches of O-glycopeptide data can produce candidate cleavage motifs that can be used to define new protease cleavage settings that lower search times and improve O-glycopeptide identifications. We use this platform generate the first consensus motif for the recently characterized immunomodulating metalloprotease (IMPa) from Pseudomonas aeruginosa and show that IMPa is a favorable O-glycoprotease for characterizing densely O-glycosylated mucin-domain glycoproteins.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:57:50.677.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nicholas Riley
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	complex glycosylation
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2022-08-02 10:52:08	ID requested
1	2023-02-15 14:23:11	announced
⏵ 2	2023-11-14 08:57:51	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: O-glycoproteomics, glycoproteins, cleavage, glycoproteomics, informatics, O-Pair Search, O-glycoprotease

Carolyn R. Bertozzi
contact affiliation	Department of Chemistry, Stanford University
contact email	bertozzi@stanford.edu
lab head
Nicholas Riley
contact affiliation	Stanford University
contact email	riley.nicholasm@gmail.com
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/2023/02/PXD035775

PRIDE project URI

• PRIDE
  1. PXD035775
     1. Label: PRIDE project
     2. Name: Deciphering O-glycoprotease substrate preferences with O-Pair Search