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PXD035775

PXD035775 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleDeciphering O-glycoprotease substrate preferences with O-Pair Search
DescriptionO-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.
HostingRepositoryPRIDE
AnnounceDate2023-11-14
AnnouncementXMLSubmission_2023-11-14_08:57:50.677.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterNicholas Riley
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListcomplex glycosylation
InstrumentOrbitrap Fusion
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-08-02 10:52:08ID requested
12023-02-15 14:23:11announced
22023-11-14 08:57:51announced2023-11-14: Updated project metadata.
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: O-glycoproteomics, glycoproteins, cleavage, glycoproteomics, informatics, O-Pair Search, O-glycoprotease
Contact List
Carolyn R. Bertozzi
contact affiliationDepartment of Chemistry, Stanford University
contact emailbertozzi@stanford.edu
lab head
Nicholas Riley
contact affiliationStanford University
contact emailriley.nicholasm@gmail.com
dataset submitter
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Dataset FTP location
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