PXD004894-3

PXD004894 is an original dataset announced via ProteomeXchange.

Title	Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry
Description	Although mutations may represent attractive targets for immunotherapy, direct identification of mutated peptide ligands isolated from human leukocyte antigens (HLA) on the surface of native tumor tissue has so far not been successful. Using advanced mass spectrometry (MS) analysis, we survey the melanoma-associated immunopeptidome to a depth of 95,500 patient-presented peptides. We thereby discover a large spectrum of attractive target antigen candidates including cancer testis antigens and phosphopeptides. Most importantly, we identify peptide ligands presented on native tumor tissue samples harboring somatic mutations. Four of eleven mutated ligands prove to be immunogenic by neoantigen-specific T-cell responses. Moreover, tumor-reactive T cells with specificity for selected neoantigens identified by MS are detected in the patient`s tumor and peripheral blood. We conclude that direct identification of mutated peptide ligands from primary tumor material by MS is possible and yields true neoepitopes with high relevance for immunotherapeutic strategies in cancer.
HostingRepository	PRIDE
AnnounceDate	2017-06-06
AnnouncementXML	Submission_2017-06-06_00:30:36.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Michal Bassani-Sternberg
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-08-25 00:03:08	ID requested
1	2016-11-30 08:33:14	announced
2	2017-04-20 06:21:52	announced	Updated project metadata.
⏵ 3	2017-06-06 00:30:37	announced	Updated project metadata.
4	2017-10-24 04:03:28	announced	Updated project metadata.
5	2024-10-22 04:31:55	announced	2024-10-22: Updated project metadata.

Bassani-Sternberg M, Br, ä, unlein E, Klar R, Engleitner T, Sinitcyn P, Audehm S, Straub M, Weber J, Slotta-Huspenina J, Specht K, Martignoni ME, Werner A, Hein R, H Busch D, Peschel C, Rad R, Cox J, Mann M, Krackhardt AM, Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry. Nat Commun, 7():13404(2016) [pubmed]

ProteomeXchange project tag: Human Immuno-Peptidome Project (HUPO-HIPP), Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project

curator keyword: Biomedical

submitter keyword: Immunopeptidomics, LC-MS/MS, cancer antigens, neoantigens

Michal Bassani-Sternberg
contact affiliation	Head / Immunopeptidomics unit Department of Oncology UNIL/CHUV Ludwig Cancer Research Center Biopole III, Chemin des Boversses 155 Epalinges, 1066 Switzerland
contact email	michal.bassani@chuv.ch
lab head
Michal Bassani-Sternberg
contact affiliation	UNIL/CHUV
contact email	michal.bassani@chuv.ch
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/2017/04/PXD004894

PRIDE project URI

• PRIDE
  1. PXD004894
     1. Label: PRIDE project
     2. Name: Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry