PXD046370-2

PXD046370 is an original dataset announced via ProteomeXchange.

Title	A complete peptidome workflow for neoantigen identification and validation by mass spectrometry-based immunopeptidomics
Description	We proposed a complete workflow for neoantigen identification and validation based solely on MS immunopeptidomics.We first developed a new Neo DiscoveryTM immunopeptidome enrichment Kit, which can be used for HLA peptide purification from a small amount of biopsied tissue as low as 18mg. To achieve high sensitivity with such a low amount of sample, we leveraged the power of deep learning and a massive amount of MS-based immunopeptidomics data to build DeepNovo-HLA, a de novo sequencing model specialized for HLA peptides. We also developed DeepImmu, a personalized model for immunogenicity prediction based on the central tolerance of T cells, i.e. the positive and negative selection of T cells in an individual patient.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:38:04.004.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ngoc Hieu Tran
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-24 20:48:55	ID requested
1	2024-05-03 19:43:04	announced
⏵ 2	2024-10-22 06:38:04	announced	2024-10-22: Updated project metadata.

10.21203/RS.3.RS-3520814/V1;

submitter keyword: neoantigen, immunopeptidomics, LC-MS/MS

Baozhen Shan
contact affiliation	Bioinformatics Solutions Inc., Waterloo, Ontario, Canada
contact email	bshan@bioinfor.com
lab head
Ngoc Hieu Tran
contact affiliation	Bioinformatics Solutions Inc.
contact email	htran@bioinfor.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/2024/05/PXD046370

PRIDE project URI

• PRIDE
  1. PXD046370
     1. Label: PRIDE project
     2. Name: A complete peptidome workflow for neoantigen identification and validation by mass spectrometry-based immunopeptidomics