PXD053748

PXD053748 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-08 03:50:15	ID requested
⏵ 1	2025-02-17 06:03:45	announced

10.1021/ACS.JPROTEOME.4C00609;

submitter keyword: Plasma, data-driven rescoring

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

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/2025/02/PXD053748

PRIDE project URI

• PRIDE
  1. PXD053748
     1. Label: PRIDE project
     2. Name: TIMS²Rescore: A DDA-PASEF optimized data-driven rescoring pipeline based on MS²Rescore - Plasma proteomics