<<< Full experiment listing

PXD033868

PXD033868 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleMS²Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates
DescriptionImmunopeptidomics 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.
HostingRepositoryPRIDE
AnnounceDate2023-11-14
AnnouncementXMLSubmission_2023-11-14_08:56:05.228.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterArthur Declercq
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue
InstrumentQ Exactive HF-X
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-05-12 09:35:27ID requested
12022-07-11 05:52:23announced
22023-05-14 14:58:47announced2023-05-14: Updated project metadata.
32023-11-14 08:56:05announced2023-11-14: Updated project metadata.
Publication List
Dataset with its publication pending
Keyword List
ProteomeXchange project tag: EPIC-XS
submitter keyword: Q Exactive HF-X, human,immunopeptidomics
Contact List
Lennart Martens
contact affiliationVIB-UGent Center for Medical Biotechnology, VIB, Belgium Department of Biomolecular Medicine, Ghent University, Belgium
contact emaillennart.martens@vib-ugent.be
lab head
Arthur Declercq
contact affiliationVIB-UGent Center for Medical Biotechnology, VIB, Belgium Department of Biomolecular Medicine, Ghent University, Belgium
contact emailarthur.declercq@ugent.be
dataset submitter
Full Dataset Link List
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
Repository Record List
[ + ]