PXD037990

PXD037990 is an original dataset announced via ProteomeXchange.

Title	Mapping the human chondroitin sulfate glycoproteome reveals an unexpected correlation between glycan sulfation and attachment site characteristics
Description	Chondroitin sulfate proteoglycans (CSPGs), an important class of carbohydrate-modified proteins, are composed of chondroitin sulfate (CS) polysaccharide(s) attached to different core proteins. CS polysaccharides interact with a multitude of protein ligands to control key events in homeostasis and development. Much effort has been devoted to CS structural characterization, as the specificities of the interactions are considered to be determined by the distribution of sulfate groups along the polysaccharide chains. Owing to their structural complexity however, CS chains are typically characterized after they have been released from their core proteins, which precludes site-specific structural information. Such information would likely assist in assigning CSPG-related functions and provide insights to potential differences in CS structures for different core proteins and their glycosites. Here we utilize a novel glycoproteomic approach for the site-specific sequencing of CS modifications of CSPGs from human urine using a combination of biochemical enrichments, enzymatic digestions, and positive mode nano-scale liquid chromatography tandem mass spectrometry (nLC-MS/MS) analysis. Trypsin-derived CS-glycopeptides were partially depolymerized with chondroitinase ABC, yielding peptide-attached CS chains, ranging from 6 - 18 monosaccharides in length. Software-assisted- and manual analysis revealed that certain core proteins carried CS with abundant sulfate modifications, while others carried CS with lower levels of sulfation. Inspection of the amino acid sequences surrounding the attachment sites indicated that acidity of the attachment site motifs influenced the levels of CS sulfation and statistical analysis confirmed this relationship. These results demonstrate attachment site-specific CS polysaccharides of CSPGs in human urine and indicate that this novel method may assist in elucidating the biosynthesis and functional roles of CSPGs in cellular physiology.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:07:24.440.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jonas Nilsson
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2022-11-07 09:00:18	ID requested
1	2023-10-24 11:18:24	announced
⏵ 2	2023-11-14 09:07:31	announced	2023-11-14: Updated project metadata.

Noborn F, Nilsson J, Sihlbom C, Nikpour M, Kjell, é, n L, Larson G, Mapping the Human Chondroitin Sulfate Glycoproteome Reveals an Unexpected Correlation Between Glycan Sulfation and Attachment Site Characteristics. Mol Cell Proteomics, 22(8):100617(2023) [pubmed]

submitter keyword: glycosaminoglycans

proteoglycans

glycoproteomics

glycopeptides

Fredrik Noborn
contact affiliation	Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
contact email	fredrik.noborn@clinchem.gu.se
lab head
Jonas Nilsson
contact affiliation	University of Gothenburg
contact email	jonas.nilsson@clinchem.gu.se
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD037990
     1. Label: PRIDE project
     2. Name: Mapping the human chondroitin sulfate glycoproteome reveals an unexpected correlation between glycan sulfation and attachment site characteristics