Evidence map›Paper›PMID 40080147›Full record

ArticleJournal of proteome research2025

Maximizing Immunopeptidomics-Based Bacterial Epitope Discovery by Multiple Search Engines and Rescoring.

Patrick Willems, Fabien Thery, Laura Van Moortel, Margaux De Meyer, An Staes, Adillah Gul, Lyudmila Kovalchuke, Arthur Declercq, Robbe Devreese, Robbin Bouwmeester and 3 more

Abstract read
In one paragraph

Article in Journal of proteome research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Article
  2. Review
  3. Article
  4. Article
  5. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors.

Patrick WillemsVIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium.ORCID 0000-0003-4667-2294
Fabien TheryVIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium.
Laura Van MoortelVIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium.
Margaux De MeyerVIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium.
An StaesVIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium.ORCID 0000-0001-8767-8508
Adillah GulVIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium.
Lyudmila KovalchukeVIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium.
Arthur DeclercqVIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium.ORCID 0000-0002-9376-1399
Robbe DevreeseVIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium.ORCID 0000-0002-3432-1502
Robbin BouwmeesterVIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium.ORCID 0000-0001-6807-7029
Ralf GabrielsVIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium.ORCID 0000-0002-1679-1711
Lennart MartensVIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium.
Francis ImpensVIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium.ORCID 0000-0003-2886-9616

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Mass spectrometry-based discovery of bacterial immunopeptides presented by infected cells allows untargeted discovery of bacterial antigens that can serve as vaccine candidates. However, reliable identification of bacterial epitopes is challenged by their extremely low abundance. Here, we describe an optimized bioinformatic framework to enhance the confident identification of bacterial immunopeptides. Immunopeptidomics data of cell cultures infected with

Indexed as

Antigens, BacterialBacterial ProteinsEpitopesListeria monocytogenesPeptidesProteomicsSearch EngineComputational BiologyHumansAntigens, BacterialBacterial ProteinsEpitopesPeptidesimmunopeptidesion mobilityListeria monocytogenesmass spectrometrysearch enginesTIMS2Rescore

Identifiers

PMID40080147
PMCPMC11976845

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.