PXD016476

PXD016476 is an original dataset announced via ProteomeXchange.

Title	A sensitive S-trap-based approach to the analysis of T-cell raft proteome
Description	The development of sensitive technologies for T cell-raft proteomics is highly challenging. We explored an innovative strategy, based on suspension trapping (S-trap) sample preparation. Mouse splenocytes were subjected to negative immunoselection for T cell preparation. Rafts were isolated by a detergent-free method and Optiprep gradient ultracentrifugation. Flotillin-1-, LAT- and cholesterol-rich microdomains were subjected to proteomic analysis through an optimized protocol based on S-Trap and high pH fractionation, followed by nano-LC-MS/MS. We identified 2680 proteins in the raft-rich fraction and established a database of 894 bona fide T cell-raft proteins. We performed a differential analysis on the raft-rich fraction from non-stimulated vs. anti-CD3/CD28 TCR-stimulated T cells. Our results revealed 42 proteins present in one condition and absent in the other, such as Akt2 and Nck1. For the first time a proteomic analysis is performed on rafts from ex-vivo T cells obtained from individual mice, before and after TCR activation. Our results show an increased specificity and sensitivity of the proposed method.
HostingRepository	PRIDE
AnnounceDate	2020-08-13
AnnouncementXML	Submission_2020-08-13_04:31:42.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Cerina Chhuon
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-11-27 03:43:42	ID requested
⏵ 1	2020-08-13 04:31:43	announced

Chhuon C, Zhang SY, Jung V, Lewandowski D, Lipecka J, Pawlak A, Sahali D, Ollero M, Guerrera IC, A sensitive S-Trap-based approach to the analysis of T cell lipid raft proteome. J Lipid Res, 61(11):1512-1523(2020) [pubmed]

submitter keyword: detergent-free, FASP, S-trap, OptiPrep, raftomics, T cell

Ida Chiara Guerrera
contact affiliation	Proteomic Platform Necker, PPN-3P5, Structure Fédérative de Recherche SFR Necker US24, 75015, Paris, France
contact email	chiara.guerrera@inserm.fr
lab head
Cerina Chhuon
contact affiliation	Proteomics Platform Necker, PPN-3P5, Structure Fédérative de Recherche SFR Necker, Université Paris Descartes, Paris, France
contact email	cerina.chhuon@inserm.fr
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/2020/08/PXD016476

PRIDE project URI

• PRIDE
  1. PXD016476
     1. Label: PRIDE project
     2. Name: A sensitive S-trap-based approach to the analysis of T-cell raft proteome