PXD015240

PXD015240 is an original dataset announced via ProteomeXchange.

Title	NNAlign_MA; MHC peptidome deconvolution for accurate MHC binding motif characterization and improved T cell epitope predictions
Description	Current mass spectrometry technologies allow for identification of MHC-associated peptide ligands. Studies have proven these data to be a rich source of information for learning the rules of MHC-mediated antigen presentation. Such immunopeptidomes are usually poly-specific, containing multiple sequence motifs matching the MHC molecules expressed in the system under investigation. Motif deconvolution -the process of associating each ligand to its presenting MHC molecule(s)- is a critical and challenging step in the analysis of MS-eluted MHC ligand data. Here, we describe NNAlign_MA, a computational method designed to address this challenge. NNAlign_MA simultaneously performs the tasks of i) clustering peptides into individual specificities; ii) automatic annotation of each cluster to an MHC molecule; and iii) training of a prediction model covering all MHCs present in the training set. NNAlign_MA was benchmarked on large and diverse datasets, covering class I and class II data. In all cases, the method was demonstrated to outperform state-of-the-art methods, effectively expanding the coverage of alleles for which accurate predictions can be made, resulting in improved identification of both eluted ligands and T cellepitopes. Given its high flexibility and ease of use, we expect NNAlign_MA to serve as an effective tool to increase our understanding of the rules of MHC antigen presentation and guide the development of novel T cell-based therapeutics.
HostingRepository	PRIDE
AnnounceDate	2024-10-08
AnnouncementXML	Submission_2024-10-08_11:38:36.189.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD015240
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Nicola Ternette
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913;
ModificationList	GG; Crotonaldehyde; Amidated; Diethyl; Cys->Dha; Hex; Thiazolidine; Methylphosphonate; Ethanolyl; Propionamide; Phospho; Deamidated; Acetyl; Trp->Oxolactone; Myristoyl; Cation:Ni[II]; Methylthio; Carboxymethyl; HexNAc; Glycosyl; Carbamidomethyl; Cysteinyl; Gln->pyro-Glu; Met->Hsl; Trioxidation; Guanidinyl; Glu->pyro-Glu; DAET; Carboxyethyl; Hydroxymethyl; Dehydro; Trimethyl; Ethyl; Ammonia-loss; AEBS; Pyridylacetyl; Oxidation; AEC-MAEC; Carboxy; Pyridylethyl; O-pinacolylmethylphosphonate; MolybdopterinGD; Ethanolamine; Didehydro; Cation:Na; Trp->Kynurenin; Hydroxytrimethyl; Pro->Pyrrolidinone; Sulfo; Iminobiotin; SMA; Deoxy; HexN; Methyl+Deamidated; Nmethylmaleimide; Glutathione; Formyl; Carbamyl; Lys->Allysine; 3-deoxyglucosone; Amidine; Amino; Ammonium; Dehydrated; Biotin; Dioxidation; Xlink:DTSSP[88]; Lipoyl; glycidamide; Pro->Pyrrolidone
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2019-08-30 02:05:58	ID requested
⏵ 1	2024-10-08 11:38:37	announced

10.6019/PXD015240;

Alvarez B, Reynisson B, Barra C, Buus S, Ternette N, Connelley T, Andreatta M, Nielsen M, NNAlign_MA

MHC Peptidome Deconvolution for Accurate MHC Binding Motif Characterization and Improved T-cell Epitope Predictions. Mol Cell Proteomics, 18(12):2459-2477(2019) [pubmed]

10.1074/mcp.tir119.001658;

submitter keyword: Immunopeptidomics, BoLA ligandome

Nicola Ternette
contact affiliation	University of Oxford
contact email	nicola.ternette@ndm.ox.ac.uk
lab head
Nicola Ternette
contact affiliation	University of Oxford
contact email	nicola.ternette@ndm.ox.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/2019/10/PXD015240

PRIDE project URI

• PRIDE
  1. PXD015240
     1. Label: PRIDE project
     2. Name: NNAlign_MA; MHC peptidome deconvolution for accurate MHC binding motif characterization and improved T cell epitope predictions