PXD012797

PXD012797 is an original dataset announced via ProteomeXchange.

Title	Validation of a high-performance liquid chromatography-tandem mass spectrometry immunopeptidomics assay for the identification of HLA ligands suitable for pharmaceutical therapies
Description	For more than two decades naturally presented, human leukocyte antigen (HLA)-restricted peptides (immunopeptidome) have been eluted and sequenced using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Since, identified disease-associated HLA ligands have been characterized and evaluated as potential active substances. Treatments based on HLA-presented peptides have shown promising results in clinical application as personalized T cell-based immunotherapy. Peptide vaccination cocktails are produced as investigational medicinal products under GMP conditions. In order to support clinical trials based on HLA-presented tumor-associated antigens, in this study the sensitive LC-MS/MS antigen identification pipeline was fully validated according to the current US Food and Drug Administration (FDA) and European Medicines Agency (EMA) guidelines. The immunopeptidomes of JY cells with or without spiked-in, isotope labeled peptides, were reliably identified using a data-dependent acquisition method. As the LC-MS/MS pipeline is used for identification purposes, the validation parameters include accuracy, precision, specificity, limit of detection and robustness.
HostingRepository	PRIDE
AnnounceDate	2020-01-15
AnnouncementXML	Submission_2020-02-17_03:18:53.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Michael Ghosh
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2019-02-20 04:01:39	ID requested
1	2020-01-15 00:38:51	announced
⏵ 2	2020-02-17 03:18:55	announced	2020-02-17: Updated publication reference for PubMed record(s): 31937595.

Ghosh M, Gauger M, Marcu A, Nelde A, Denk M, Schuster H, Rammensee HG, Stevanovi, ć S, Guidance Document: Validation of a High-Performance Liquid Chromatography-Tandem Mass Spectrometry Immunopeptidomics Assay for the Identification of HLA Class I Ligands Suitable for Pharmaceutical Therapies. Mol Cell Proteomics, 19(3):432-443(2020) [pubmed]

submitter keyword: Immunopeptidome, mass spectrometry, cancer immunotherapy, GMP, LC–MS/MS, validation

Stefan Stevanovic
contact affiliation	University of Tübingen Interfaculty Institute for Cell Biology Department of Immunology Auf der Morgenstelle 15 72076 Tuebingen Germany
contact email	stefan.stevanovic@uni-tuebingen.de
lab head
Michael Ghosh
contact affiliation	Department of Immunology, Tübingen
contact email	Michaelghosh@gmx.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/2020/01/PXD012797

PRIDE project URI

• PRIDE
  1. PXD012797
     1. Label: PRIDE project
     2. Name: Validation of a high-performance liquid chromatography-tandem mass spectrometry immunopeptidomics assay for the identification of HLA ligands suitable for pharmaceutical therapies