PXD000332

PXD000332 is an original dataset announced via ProteomeXchange.

Title	N-linked glycosylation enrichment for in-depth cell surface proteomics and the classification of diffuse large B-cell lymphoma subtypes
Description	The classification of histologically similar yet molecularly distinct tumors into specific subtypes remains a clinically challenging task. Classification of such tumors into distinct entities based on their cell surface protein expression profiles has been hindered by the lack of an unbiased global approach. Here we use N-glyco FASP, a recently developed mass spectrometric approach based on lectin-enrichment of N-linked glycoproteins, in conjunction with a super-SILAC based quantitative strategy, on patient derived diffuse large B-cell lymphoma cell lines. We mapped 2383 glycosites on more than 1300 proteins, which were highly enriched for cell membrane proteins. The resulting sub-proteome was highly enriched for cell membrane proteins. This N-glyco sub-proteome alone allowed the segregation of the ABC from the GCB subtypes of diffuse large B-cell lymphoma, which before gene expression studies had been considered one disease entity. Encouragingly, many of the glycopeptides driving the segregation belong to proteins previously characterized as segregators in a deep proteome study of these subtypes (S. J. Deeb et al MCP 2012 PMID 22442255). This conforms to the high correlation that we observed between the expression level of the glycosites and their corresponding proteins. Detailed examination of glycosites and glycoprotein expression levels uncovered, amongst other interesting findings, enrichment of transcription factor binding motifs, including known NF-kappa-B related ones. Thus, enrichment of a class of post-translationally modified peptides can classify cancer types as well as reveal cancer specific mechanistic changes.
HostingRepository	PRIDE
AnnounceDate	2016-08-26
AnnouncementXML	Submission_2016-08-26_00:33:13.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mario Oroshi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	deamidated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2013-07-10 01:43:01	ID requested
1	2016-08-25 00:56:28	announced
⏵ 2	2016-08-26 00:33:14	announced	Updated project metadata.

Deeb SJ, Cox J, Schmidt-Supprian M, Mann M, N-linked glycosylation enrichment for in-depth cell surface proteomics of diffuse large B-cell lymphoma subtypes. Mol Cell Proteomics, 13(1):240-51(2014) [pubmed]

curator keyword: Biomedical, Biological

submitter keyword: diffuse large B-cell lymphoma, glycoproteome, N-linked glycosylation

Matthias Mann
contact affiliation	Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry
contact email	mmann@biochem.mpg.de
lab head
Mario Oroshi
contact affiliation	Proteomics
contact email	oroshi@biochem.mpg.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000332
     1. Label: PRIDE project
     2. Name: N-linked glycosylation enrichment for in-depth cell surface proteomics and the classification of diffuse large B-cell lymphoma subtypes