PXD028990

PXD028990 is an original dataset announced via ProteomeXchange.

Title	Immunopeptidomics guided identification of neoantigens in non-small cell lung cancer
Description	Discovery of tumour specific peptides (neoantigens) generating target specific personalised T cell therapies is difficult because of the complex relationship between genetic mutations and neoantigen presentation. Studies predicting neoantigens have a 5% success rate, and direct observations of neoantigens are even rarer. We have developed a mass spectrometry proteomics guided approach to identify neoantigens in non-small cell lung cancer (NSCLC). We hypothesised that by characterising the observable peptides presented by HLA molecules (the immunopeptidome) we might better predict which mutations lead to neoantigens. From a cohort of 24 NSCLC patients, we performed a detailed analysis of 3 adenocarcinoma and 3 squamous cell carcinoma samples. Our workflow identified neoantigens generating functional T cell responses in 5 out of 6 patients, with one directly observed neoantigen, and an overall response rate of 20% of predicted neoantigens.
HostingRepository	PRIDE
AnnounceDate	2026-07-03
AnnouncementXML	Submission_2026-07-03_13:31:12.651.xml
DigitalObjectIdentifier	https://doi.org/10.6019/PXD028990
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Alistair Bailey
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetic acid derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2021-10-07 08:57:55	ID requested
⏵ 1	2026-07-03 13:31:13	announced

Nicholas B, Bailey A, McCann KJ, Wood O, Currall E, Johnson P, Elliott T, Ottensmeier C, Skipp P, Immunopeptidomics-guided identification of functional neoantigens in non-small cell lung cancer. NPJ Precis Oncol, ():(2026) [pubmed]

10.6019/PXD028990;

10.1038/s41698-026-01539-2;

submitter keyword: cancer, HLA,Lung, neoantigen, peptidome

Paul J Skipp
contact affiliation	Centre for Proteomic Research B85, Life Sciences Building University of Southampton University Road Highfield Southampton, Hants. SO17 1BJ United Kingdom
contact email	pjss@soton.ac.uk
lab head
Alistair Bailey
contact affiliation	University of Southampton
contact email	ab604@soton.ac.uk
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/2026/07/PXD028990

PRIDE project URI

• PRIDE
  1. PXD028990
     1. Label: PRIDE project
     2. Name: Immunopeptidomics guided identification of neoantigens in non-small cell lung cancer