PXD033868-1

PXD033868 is an original dataset announced via ProteomeXchange.

Title	MS²Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates
Description	Immunopeptidomics aims to identify Major Histocompatibility Complex-presented peptides on every cell that can be used in anti-cancer vaccine development. However, existing immunopeptidomics data analysis pipelines suffer from the non-tryptic nature of immunopeptides, complicating their identification. Previously, peak intensity predictions by MS²PIP and retention time predictions by DeepLC, have been shown to improve tryptic peptide identifications when rescoring peptide-spectrum matches with Percolator. However, as MS²PIP was tailored towards tryptic peptides, we have here retrained MS²PIP to include non-tryptic peptides. Interestingly, the new models not only greatly improve predictions for immunopeptides, but also yield further improvements for tryptic peptides. We show that the integration of new MS²PIP models, DeepLC, and Percolator in one software package, MS²Rescore, increases spectrum identification rate and unique identified peptides with 46% and 36% compared to standard Percolator rescoring at 1% FDR. Moreover, MS²Rescore also outperforms the current state-of-the-art in immunopeptide-specific identification approaches. Integration of immunopeptide MS²PIP models, DeepLC, and Percolator into MS²Rescore thus allows substantial improved identification of novel epitopes from existing immunopeptidomics workflows.
HostingRepository	PRIDE
AnnounceDate	2022-07-11
AnnouncementXML	Submission_2022-07-11_05:52:23.501.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Arthur Declercq
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2022-05-12 09:35:27	ID requested
⏵ 1	2022-07-11 05:52:23	announced
2	2023-05-14 14:58:47	announced	2023-05-14: Updated project metadata.
3	2023-11-14 08:56:05	announced	2023-11-14: Updated project metadata.

10.1016/J.MCPRO.2022.100266;

submitter keyword: immunopeptidomics, human, Q Exactive HF-X

Lennart Martens
contact affiliation	VIB-UGent Center for Medical Biotechnology, VIB, Belgium Department of Biomolecular Medicine, Ghent University, Belgium
contact email	lennart.martens@vib-ugent.be
lab head
Arthur Declercq
contact affiliation	VIB-UGent Center for Medical Biotechnology, VIB, Belgium Department of Biomolecular Medicine, Ghent University, Belgium
contact email	arthur.declercq@ugent.be
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/2022/07/PXD033868

PRIDE project URI

• PRIDE
  1. PXD033868
     1. Label: PRIDE project
     2. Name: MS²Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates