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PXD053748

PXD053748 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleTIMS²Rescore: A DDA-PASEF optimized data-driven rescoring pipeline based on MS²Rescore - Plasma proteomics
DescriptionThe 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.
HostingRepositoryPRIDE
AnnounceDate2025-02-17
AnnouncementXMLSubmission_2025-02-17_06:03:45.161.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterArthur Declercq
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListacetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
InstrumenttimsTOF HT
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-07-08 03:50:15ID requested
12025-02-17 06:03:45announced
Publication List
10.1021/ACS.JPROTEOME.4C00609;
Keyword List
submitter keyword: Plasma, data-driven rescoring
Contact List
Claudia Martelli
contact affiliationBruker Switzerland AG, Faellanden, Switzerland
contact emailclaudia.martelli@bruker.com
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
Repository Record List
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