PXD006223

PXD006223 is an original dataset announced via ProteomeXchange.

Title	The proteomic landscape of patient-derived CD4+ T cells in recent-onset type 1 diabetes
Description	The pathophysiology underlying the autoimmune disease type 1 diabetes (T1D) is poorly understood. Obtaining an accurate proteomic profile of the T helper cell population is essential for understanding the pathogenesis of T1D. Here, we performed in-depth proteomic profiling of peripheral CD4+ T cells in a pediatric cohort in order to identify cellular signatures associated with the onset of T1D. Using only 250,000 CD4+ T cells per patient, isolated from biobanked PBMC samples, we identified nearly 6,000 proteins using deep-proteome profiling with LC-MS/MS data-independent acquisition. Our analysis revealed an inflammatory signature in patients with T1D; this signature is characterized by circulating mediators of neutrophils, platelets, and the complement system. This signature likely reflects the inflammatory extracellular milieu, suggesting that activation of the innate immune system plays an important role in disease onset. Our results emphasize the potential value of using high-resolution LC-MS/MS to investigate limited quantities of biobanked samples in order to identify disease-relevant proteomic patterns. The deposited data set is the shotgun proteomic part of our two-phase study.
HostingRepository	PRIDE
AnnounceDate	2017-12-06
AnnouncementXML	Submission_2017-12-06_07:39:06.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Marlen Lepper
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	carbamoylated residue; N-acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2017-03-31 00:07:36	ID requested
⏵ 1	2017-12-06 07:39:07	announced

Lepper MF, Ohmayer U, von Toerne C, Maison N, Ziegler AG, Hauck SM, Proteomic Landscape of Patient-Derived CD4+ T Cells in Recent-Onset Type 1 Diabetes. J Proteome Res, 17(1):618-634(2018) [pubmed]

curator keyword: Biomedical

submitter keyword: CD4+ T-cells, human, Type 1 Diabetes, autoimmune, shotgun proteomics, LC-MS/MS DDA, Orbitrap XL

Stefanie M. Hauck
contact affiliation	Research Unit Protein Science, Helmholtz Center Munich, Research Center for Environmental Health (GmbH), Neuherberg,Germany
contact email	hauck@helmholtz-muenchen.de
lab head
Marlen Lepper
contact affiliation	Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH)
contact email	marlen.lepper@helmholtz-muenchen.de
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/2017/11/PXD006223

PRIDE project URI

• PRIDE
  1. PXD006223
     1. Label: PRIDE project
     2. Name: The proteomic landscape of patient-derived CD4+ T cells in recent-onset type 1 diabetes