PXD033868 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 | 2023-11-14 |
AnnouncementXML | Submission_2023-11-14_08:56:05.228.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 |
Dataset History
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. |
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 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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD033868
- Label: PRIDE project
- Name: MS²Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates