PXD025346

PXD025346 is an original dataset announced via ProteomeXchange.

Title	SPI-ART and the features of cis-spliced peptides in HLA class I immunopeptidomes
Description	The identification of peptides presented by HLA class I molecules to CD8+ T cells – i.e. the HLA-I immunopeptidome - is a useful tool to fish epitopes suitable for vaccinations and immunotherapies against cancer, infection and autoimmunity. These peptides are mainly generated by proteasomes through peptide hydrolysis and peptide splicing. Post-translationally spliced epitopes can enlarge the antigenic landscape and thus immunotherapy efficacy. Their identification is challenging, and the few methods proposed so far hinted toward a controversial broad spectrum of cis-spliced peptide frequencies in HLA-I immunopeptidomes. We here developed a new method named SPI-ART, which can identify cis-spliced peptides in HLA-I immunopeptidomes with precision and recall outperforming all other methods. The benchmark of the methods’ performances provided the proper analytical framework to explain the discordant results published so far. It also allowed to estimate the frequency of cis-spliced peptides in HLA-I immunopeptidomes, and to shed light on the biochemistry of these unconventional peptides and their potential antigenicity.
HostingRepository	PRIDE
AnnounceDate	2022-08-12
AnnouncementXML	Submission_2022-08-12_00:34:50.428.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Michele Mishto
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Orbitrap Fusion Lumos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-04-12 23:01:07	ID requested
⏵ 1	2022-08-12 00:34:51	announced

Gutman I, Gutman R, Sidney J, Chihab L, Mishto M, Liepe J, Chiem A, Greenbaum J, Yan Z, Sette A, Ko, ş, alo, ğ, lu-Yal, ç, ı, n Z, Peters B, Predicting the Success of Fmoc-Based Peptide Synthesis. ACS Omega, 7(27):23771-23781(2022) [pubmed]

submitter keyword: Mass Spectrometry, HLA-I, Immunopeptidome, K562 cell line, peptide splicing, cis-spliced peptides

Juliane Liepe
contact affiliation	Head of research group Quantitative and Systems Biology; Max Planck Institute for Biophysical Chemistry; Goettingen; Germany
contact email	juliane.liepe@mpibpc.mpg.de
lab head
Michele Mishto
contact affiliation	King's College London
contact email	michele.mishto@kcl.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/2022/08/PXD025346

PRIDE project URI

• PRIDE
  1. PXD025346
     1. Label: PRIDE project
     2. Name: SPI-ART and the features of cis-spliced peptides in HLA class I immunopeptidomes