PXD053748 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | TIMS²Rescore: A DDA-PASEF optimized data-driven rescoring pipeline based on MS²Rescore - Plasma proteomics |
Description | The high throughput analysis of proteins with mass spectrometry (MS) is highly valuable for understanding human biology, discovering disease biomarkers, identifying therapeutic targets, and exploring pathogen interactions. To achieve these goals, specialized proteomics subfields – such as plasma proteomics, immunopeptidomics, and metaproteomics – must tackle specific analytical challenges, such as an increased identification ambiguity compared to routine proteomics experiments. Technical advancements in MS instrumentation can counter these issues by acquiring more discerning information at higher sensitivity levels, as is exemplified by the incorporation of ion mobility and parallel accumulation - serial fragmentation (PASEF) technologies in timsTOF instruments. In addition, AI-based bioinformatics solutions can help overcome ambiguity issues by integrating more data into the identification workflow. Here, we introduce TIMS²Rescore, a data-driven rescoring workflow optimized for DDA-PASEF data from timsTOF instruments. This platform includes new timsTOF MS²PIP spectrum prediction models and IM2Deep, a new deep learning-based peptide ion mobility predictor. Furthermore, to fully streamline data throughput, TIMS²Rescore directly accepts Bruker raw mass spectrometry data, and search results from ProteoScape and many other search engines, including MS Amanda and PEAKS. We showcase TIMS²Rescore performance on plasma proteomics, immunopeptidomics (HLA class I and II), and metaproteomics data sets. TIMS²Rescore is open-source and freely available at https://github.com/compomics/tims2rescore. |
HostingRepository | PRIDE |
AnnounceDate | 2025-02-17 |
AnnouncementXML | Submission_2025-02-17_06:03:45.161.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 | acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | timsTOF HT |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2024-07-08 03:50:15 | ID requested | |
⏵ 1 | 2025-02-17 06:03:45 | announced | |
Publication List
Keyword List
submitter keyword: Plasma, data-driven rescoring |
Contact List
Claudia Martelli |
contact affiliation | Bruker Switzerland AG, Faellanden, Switzerland |
contact email | claudia.martelli@bruker.com |
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
- PXD053748
- Label: PRIDE project
- Name: TIMS²Rescore: A DDA-PASEF optimized data-driven rescoring pipeline based on MS²Rescore - Plasma proteomics