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PXD033868-1

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
AnnounceDate2022-07-11
AnnouncementXMLSubmission_2022-07-11_05:52:23.501.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
10.1016/J.MCPRO.2022.100266;
Keyword List
submitter keyword: immunopeptidomics, human, Q Exactive HF-X
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
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PRIDE project URI
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