PXD038165-1

PXD038165 is an original dataset announced via ProteomeXchange.

Title	Immune response disfunction in chronic lymphocytic leukemia: Dissecting molecular mechanism by multipronged functional proteomics approaches. Crucial parameters for the evaluation of Immunopeptidomic analysis.
Description	The main goal of the current project is to design and develop a multipronged functional proteomics strategy, with translation into the clinic, for deciphering all the microenvironment protein factors involved in the dysfunction of the immune system in MBLhi and CLL patients in order to understand the disease better and design effective treatment and management strategies. This novel strategy will be performed by a systematic and comprehensive integration of complementary functional proteomics approaches which include antigen presentation and recognition by Immunopeptidomics. In this work, different protein extraction methods (Protocol A and Protocol B) and different immunoprecipitation (IP) solid supports (Protocol #1 and Protocol #2) are performed, using four tumor cell lines as a model. The study samples will be identified by the name of the cell line, followed by the number of the IP protocol used, followed by the letter corresponding to the protein extraction protocol used. H460_1A: 0520_1_2 H460_1B: 0520_2_1 JURKAT_1A: 0520_3_1 JURKAT_1B: 0520_4_1 H460_2B: 0520_5_1 CACO-2_2B: 0520_6_1 MDA-MB-231_2B: 0520_7_1
HostingRepository	PRIDE
AnnounceDate	2024-10-17
AnnouncementXML	Submission_2024-10-17_02:40:34.416.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD038165
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Pablo Juanes-Velasco
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	cysteinylation (disulfide with free L-cysteine); monohydroxylated residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2022-11-15 07:45:50	ID requested
⏵ 1	2024-10-17 02:40:35	announced

10.6019/PXD038165;

Juanes-Velasco P, Arias-Hidalgo C, Garc, í, a-Vaquero ML, Sotolongo-Ravelo J, Pa, í, no T, L, é, crevisse Q, Landeira-Vi, ñ, uela A, G, ó, ngora R, Hern, á, ndez Á P, Fuentes M, Crucial Parameters for Immunopeptidome Characterization: A Systematic Evaluation. Int J Mol Sci, 25(17):(2024) [pubmed]

10.3390/ijms25179564;

submitter keyword: Immunopeptidomics, Immunopeptidome, LC-MS/MS

Manuel Fuentes García
contact affiliation	Department of Medicine and General Service of Cytometry, Cancer Research Centre-IBMCC, IBSAL. University of Salamanca-CSIC, Campus Miguel de Unamuno s/n, 37007 Salamanca, Spain
contact email	mfuentes@usal.es
lab head
Pablo Juanes-Velasco
contact affiliation	Department of Medicine and General Service of Cytometry, Cancer Research Centre, IBSAL. University of Salamanca-CSIC, Campus Miguel de Unamuno s/n, 37007 Salamanca, Spain
contact email	pablojuanesvelasco@usal.es
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/2024/10/PXD038165

PRIDE project URI

• PRIDE
  1. PXD038165
     1. Label: PRIDE project
     2. Name: Immune response disfunction in chronic lymphocytic leukemia: Dissecting molecular mechanism by multipronged functional proteomics approaches. Crucial parameters for the evaluation of Immunopeptidomic analysis.