PXD055547

PXD055547 is an original dataset announced via ProteomeXchange.

Title	Maximizing immunopeptidomics-based bacterial epitope discovery by rescoring and integrating the results of multiple search engines
Description	Discovery of human leukocyte antigen (HLA) class I presented peptides of bacterial origin is essential to discover bacterial antigen targets as putative vaccine constituents. However, reliable identification of such HLA-presented bacterial epitopes are extremely low abundant compared to the host proteome. Here, we describe an upgraded bioinformatical workflow to enhance the confident detection of bacterial immunopeptides. Re-analysis of Listeria monocytogenes (Listeria)-infected cell cultures was searched by four search engines in parallel with follow-up by rescoring by MS2Rescore and integration of all search results. Boosting identification by both rescoring and integration, this delivered an additional 18 Listeria peptides (+26.5%) matching 15 different proteins (+35.7%) compared to the initial analysis. Moreover, conflicts between search engine results uncovered ambiguities in spectra-to-peptide assignments, in some cases with spectra assigned to human and Listeria peptides. Finally, we demonstrate how our workflow is compatible with timsTOF data acquisition, incorporating rescoring of ion mobility features using TIMS2Rescore.
HostingRepository	PRIDE
AnnounceDate	2025-02-05
AnnouncementXML	Submission_2025-02-05_01:15:57.194.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Patrick Willems
SpeciesList	scientific name: Listeria monocytogenes EGD; NCBI TaxID: 1334565; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue
Instrument	timsTOF SCP

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-04 08:04:29	ID requested
⏵ 1	2025-02-05 01:15:57	announced

Dataset with its publication pending

submitter keyword: rescoring, search engines, ion mobility., mass spectrometry, Listeria monocytogenes, epitope discovery,immunopeptidomics

Francis Impens
contact affiliation	VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
contact email	Francis.Impens@UGent.be
lab head
Patrick Willems
contact affiliation	Ghent University
contact email	patwille.willems@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/PXD055547

PRIDE project URI

• PRIDE
  1. PXD055547
     1. Label: PRIDE project
     2. Name: Maximizing immunopeptidomics-based bacterial epitope discovery by rescoring and integrating the results of multiple search engines