PXD047766

PXD047766 is an original dataset announced via ProteomeXchange.

Title	O-GlcNAcome analysis in human placenta
Description	In this study, we expand on this major advancement in O-GlcNAc enrichment protocols by adapting this approach to human-banked samples, which often presents their significant challenges. Indeed, patient samples are often banked without proper washing, thus contaminating cells with abundant O-glycosylated blood protein. These glycoproteins, such as human serum albumin, antibodies, and hemoglobin, pollute MS acquisition, masking the less abundant intracellular proteins and, even more, their O-GlcNAcylated forms. Thus, using freshly banked placentas, we present an adapted method to prepare human placental samples with naturally high blood content (13). We then enriched for O-GlcNAcylated protein using the PTMscan antibodies previously mentioned (12). However, our adapted protocol yielded over 60% of HexNAc peptide on total peptides. Per sample, we obtained up to 2,600 HexNAc-containing PSMs, 1,090 unique HexNAc peptides, and more than 1,000 unique HexNAc proteins using 45mg of starting placenta. Furthermore, we present a bioinformatic workflow to sort these HexNAc PSMs and extract the most confident O-GlcNAcylated proteins and sites. Thus, we confidentially identified 641 O-GlcNAcylated proteins, including up to 146 new proteins and 730 new sites within the 2 placental samples analyzed. Furthermore, we enriched for over 50 placenta-enriched O-GlcNAcylated proteins, such as RPA4, representing a new biomarker of the placental O-GlcNAcylation.
HostingRepository	PRIDE
AnnounceDate	2024-02-14
AnnouncementXML	Submission_2024-02-14_13:11:12.878.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD047766
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Stephanie Olivier-Van Stichelen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	N-acetylhexosaminylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-12-12 14:43:14	ID requested
⏵ 1	2024-02-14 13:11:13	announced

10.1093/glycob/cwae005;

10.6019/PXD047766;

Luna S, Malard F, Pereckas M, Aoki M, Aoki K, Olivier-Van Stichelen S, Studying the O-GlcNAcome of human placentas using banked tissue samples. Glycobiology, 34(4):(2024) [pubmed]

submitter keyword: Placenta, EthcD, O-GlcNAc

Stephanie Olivier-Van Stichelen
contact affiliation	Department of Biochemistry, Medical College of Wisconsin Department of OBGYN, Medical College of Wisconsin
contact email	solivier@mcw.edu
lab head
Stephanie Olivier-Van Stichelen
contact affiliation	Medical College of Wisconsin
contact email	solivier@mcw.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD047766
     1. Label: PRIDE project
     2. Name: O-GlcNAcome analysis in human placenta