Evidence map›Paper›PMID 40983925›Full record

ArticleGenome biology2025

MHCquant2 refines immunopeptidomics tumor antigen discovery.

Jonas Scheid, Steffen Lemke, Naomi Hoenisch-Gravel, Anna Dengler, Timo Sachsenberg, Arthur Declerq, Ralf Gabriels, Jens Bauer, Marcel Wacker, Leon Bichmann and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 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. Review
  2. Review
  3. Review
  4. Article
  5. Article
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

14 authors.

Jonas ScheidDepartment of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany.
Steffen LemkeDepartment of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany.
Naomi Hoenisch-GravelDepartment of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany.
Anna DenglerDepartment of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany.
Timo SachsenbergInstitute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany.
Arthur DeclerqCompOmics, VIB Center for Medical Biotechnology, VIB, Ghent, Belgium.
Ralf GabrielsCompOmics, VIB Center for Medical Biotechnology, VIB, Ghent, Belgium.
Jens BauerDepartment of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany.
Marcel WackerDepartment of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany.
Leon BichmannCenter for Systems and Engineering Immunology (CSEI), School of Medicine, Yale University, New Haven, CT, USA.
Lennart MartensCompOmics, VIB Center for Medical Biotechnology, VIB, Ghent, Belgium.
Marissa L Dubbelaar *Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany.
Sven Nahnsen *Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.
Juliane S Walz *Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany. juliane.walz@med.uni-tuebingen.de.

Funding

CHIST-ERA ODEEP-EUDeutsche Forschungsgemeinschaft EXC2180-390900677Deutsche Krebshilfe 70114948Else Kröner-Fresenius-Stiftung 2022_EKSE.79Fonds Wetenschappelijk Onderzoek,Belgium 12B7123N, G010023N, G028821N, 1SE3724NHORIZON EUROPE Project BAXERNA 2.0 101080544Invest BW Innovation grant BW1_4064/03/TruVac
6 · The paper itself

Abstract

Confident identification of human leukocyte antigen (HLA)-presented peptides is crucial for advancing cancer immunotherapy. We present MHCquant2, a scalable and modular Nextflow pipeline integrated into nf-core as a reproducible, portable, and standardized workflow for immunopeptidomics. This integration allows a community-driven, robust solution for high-throughput analyses across operating systems and cloud infrastructures. MHCquant2 integrates open-source tools including OpenMS, DeepLC, and MS

Indexed as

Antigens, NeoplasmPeptidesProteomicsSoftwareHLA AntigensHumansNeoplasmsAntigens, NeoplasmHLA AntigensPeptidesHLAImmunopeptidomicsImmunotherapyMass spectrometryNextflowNf-coreOpen-sourcePipeline

Identifiers

PMID40983925
PMCPMC12455830

What OpenQuestion holds

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LicenceCC BY
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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.