PXD009652

PXD009652 is an original dataset announced via ProteomeXchange.

Title	LC-MS/MS characterization of xyloside-primed glycosaminoglycans with cell-specific cytotoxic properties reveals structural diversity and novel glycan modifications
Description	Structural characterization of glycosaminoglycans remains a challenge and is essential for determining not only structure-function relationships between glycosaminoglycans and the biomolecules with which they interact, but also to gain insight into the biosynthesis of glycosaminoglycans. We have recently reported cytotoxic effects of xyloside-primed chondroitin/dermatan sulfate derived from a human breast carcinoma cell line, HCC70, and shown that it differs in disaccharide composition from non-toxic chondroitin/dermatan sulfate derived from a human breast fibroblast cell line, CCD-1095Sk. To further investigate the structural requirements for the cytotoxic effect, we have here developed a novel LC-MS/MS approach based on dibutylamine ion-pairing reversed-phase chromatography and negative mode higher-energy collision dissociation (HCD), and used it in combination with cell growth studies and disaccharide fingerprinting. This allowed for detailed structural characterization of linkage regions, internal oligosaccharides, and non-reducing ends, showing not only differences between xyloside-primed chondroitin/dermatan sulfate from HCC70 cells and CCD-1095Sk cells, but also in sialylation of the linkage region as well as previously undescribed methylation and sulfation of the non-reducing ends. Although the xyloside-primed chondroitin/dermatan sulfate from HCC70 cells was less complex in terms of presence and distribution of iduronic acid than that from CCD-1095Sk cells, both glucuronic acid and iduronic acid appeared essential for the cytotoxic effect. Our data have moved us one step closer to understanding the structure of the cytotoxic chondroitin/dermatan sulfate from HCC70 cells primed on xylosides, and demonstrate the suitability of the LC-MS/MS approach for structural characterization of glycosaminoglycans.
HostingRepository	PRIDE
AnnounceDate	2018-05-07
AnnouncementXML	Submission_2018-05-15_05:33:39.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Egor Vorontsov
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	sulfated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2018-05-02 10:57:26	ID requested
1	2018-05-07 00:27:49	announced
⏵ 2	2018-05-15 05:33:40	announced	Updated publication reference for PubMed record(s): 29739851.

Persson A, Gomez Toledo A, Vorontsov E, Nasir W, Will, é, n D, Noborn F, Ellervik U, Mani K, Nilsson J, Larson G, LC-MS/MS characterization of xyloside-primed glycosaminoglycans with cytotoxic properties reveals structural diversity and novel glycan modifications. J Biol Chem, 293(26):10202-10219(2018) [pubmed]

curator keyword: Biological

submitter keyword: Glycosaminoglycan

glycomics

reversed-phase chromatography

ion-pairing chromatography

LC-MS/MS

HCD

negative mode electrospray;

Göran Larson
contact affiliation	Department of Clinical Chemistry and Transfusion Medicine at Institute of Biomedicine, SU Sahlgrenska 413 45 Gothenburg, Sweden
contact email	goran.larson@clinchem.gu.se
lab head
Egor Vorontsov
contact affiliation	Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
contact email	yegor.msu@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/2018/05/PXD009652

PRIDE project URI

• PRIDE
  1. PXD009652
     1. Label: PRIDE project
     2. Name: LC-MS/MS characterization of xyloside-primed glycosaminoglycans with cell-specific cytotoxic properties reveals structural diversity and novel glycan modifications