PXD048006

PXD048006 is an original dataset announced via ProteomeXchange.

Title	pXg: Comprehensive identification of noncanonical MHC-I-associated peptides from de novo peptide sequencing using RNA-Seq reads
Description	Discovering noncanonical peptides has been a common application of proteogenomics. Recent studies suggest that certain noncanonical peptides, known as ncMAPs (noncanonical MHC-I-associated peptides), that bind to major histocompatibility complex I may make good immunotherapeutic targets. De novo peptide sequencing is a great way to find ncMAPs since it can detect peptide sequences from their tandem mass spectra without using any sequence databases. However, this strategy hasn’t been widely applied for ncMAP identification because there is not a good way to estimate its false-positive rates. In order to completely and accurately identify immunopeptides using de novo peptide sequencing, we describe a unique pipeline called pXg. In contrast to current pipelines, it makes use of genomic data, RNA-Seq abundance and sequencing quality, in addition to proteomic features to increase the sensitivity and specificity of peptide identification. We show that the peptide-spectrum match quality and genetic traits have a clear relationship, showing that they can be utilized to evaluate peptide-spectrum matches. From ten samples, we found 24,449 cMAPs (canonical MHC-I-associated peptides) and 956 ncMAPs by using a target-decoy competition. 387 ncMAPs and 1,611 cMAPs were novel identifications that had not yet been published. We discovered 11 ncMAPs produced from a squirrel monkey retrovirus in human cell lines in addition to the 2 ncMAPs originating from a complementarity determining region 3 in an antibody thanks to the unrestricted search space assumed by de novo sequencing. These entirely new identifications show that pXg can make the most of de novo peptide sequencing's advantages and its potential use in the search for new immunotherapeutic targets.
HostingRepository	PRIDE
AnnounceDate	2024-02-28
AnnouncementXML	Submission_2024-02-28_02:37:26.245.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Seunghyuk Choi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF; Orbitrap Fusion; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2023-12-20 07:41:32	ID requested
⏵ 1	2024-02-28 02:37:28	announced

10.1016/j.celrep.2021.108815;

Pandey K, Mifsud NA, Lim Kam Sian TCC, Ayala R, Ternette N, Ramarathinam SH, Purcell AW, In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementary ligand enrichment and data acquisition strategies. Mol Immunol, 123():7-17(2020) [pubmed]

10.1016/j.molimm.2020.04.008;

10.1016/J.MCPRO.2024.100743;

Granados DP, Sriranganadane D, Daouda T, Zieger A, Laumont CM, Caron-Lizotte O, Boucher G, Hardy MP, Gendron P, C, ô, t, é C, Lemieux S, Thibault P, Perreault C, Impact of genomic polymorphisms on the repertoire of human MHC class I-associated peptides. Nat Commun, 5():3600(2014) [pubmed]

Ruiz Cuevas MV, Hardy MP, Holl, ý J, Bonneil É, Durette C, Courcelles M, Lanoix J, C, ô, t, é C, Staudt LM, Lemieux S, Thibault P, Perreault C, Yewdell JW, Most non-canonical proteins uniquely populate the proteome or immunopeptidome. Cell Rep, 34(10):108815(2021) [pubmed]

10.1038/ncomms4600;

submitter keyword: immunopeptidomics

Eunok Paek
contact affiliation	1 Department of Computer Science, Hanyang University, Seoul 04763, Republic of Korea 2 Institute for Artificial Intelligence Research, Hanyang University, Seoul 04763, Republic of Korea
contact email	eunokpaek@hanyang.ac.kr
lab head
Seunghyuk Choi
contact affiliation	Hanyang University
contact email	progistar@gmail.com
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/2024/02/PXD048006

PRIDE project URI

• PRIDE
  1. PXD048006
     1. Label: PRIDE project
     2. Name: pXg: Comprehensive identification of noncanonical MHC-I-associated peptides from de novo peptide sequencing using RNA-Seq reads