Evidence map›Paper›PMID 41085619›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2026

High-Coverage Immunopeptidomics Using timsTOF Mass Spectrometers with Thunder-DDA-PASEF Boosted by MS

David Gomez-Zepeda, Julian Beyrle, Annica Preikschat, Arthur Declercq, Yannic Chen, Ralf Gabriels, Lennart Martens, Ute Distler, Stefan Tenzer

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

9 authors.

David Gomez-ZepedaHelmholtz Institute for Translational Oncology Mainz (HI-TRON Mainz) - A Helmholtz Institute of the DKFZ, Mainz, Germany. david.gomez-zepeda@dkfz-heidelberg.de.
Julian BeyrleHelmholtz Institute for Translational Oncology Mainz (HI-TRON Mainz) - A Helmholtz Institute of the DKFZ, Mainz, Germany.
Annica PreikschatInstitute of Immunology, University Medical Center Mainz, Mainz, Germany.
Arthur DeclercqGhent University, Ghent, Belgium.
Yannic ChenHelmholtz Institute for Translational Oncology Mainz (HI-TRON Mainz) - A Helmholtz Institute of the DKFZ, Mainz, Germany.
Ralf GabrielsGhent University, Ghent, Belgium.
Lennart MartensGhent University, Ghent, Belgium.
Ute DistlerInstitute of Immunology, University Medical Center Mainz, Mainz, Germany.
Stefan TenzerHelmholtz Institute for Translational Oncology Mainz (HI-TRON Mainz) - A Helmholtz Institute of the DKFZ, Mainz, Germany. tenzer@uni-mainz.de.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Major histocompatibility complex (MHC, or human leukocyte antigen, HLA) peptide ligands can be exploited to develop immunotherapies targeting immunogenic disease-specific immunopeptides, such as virus- or cancer mutation-derived peptides. Liquid chromatography coupled with mass spectrometry (LC-MS)-based immunopeptidomics is the gold standard for identifying MHC ligands. We previously optimized a workflow enabling the identification of more than 10,000 MHC class I ligands per cell line. This process comprises three major steps: (I) a high-recovery immunopeptidome enrichment, (II) an optimized MS acquisition in the timsTOF Pro called Thunder-Data-Dependent Acquisition with Parallel Accumulation-SErial Fragmentation (Thunder-DDA-PASEF), and (III) peptide identification using PEAKS XPro boosted by MS

Indexed as

Mass SpectrometryPeptidesProteomicsChromatography, LiquidHistocompatibility Antigens Class IHumansLigandsTandem Mass SpectrometryWorkflowHistocompatibility Antigens Class ILigandsPeptidesHuman leucocyte antigenImmunopeptidomicsImmunoprecipitationMajor histocompatibility complexMass spectrometryRe-scoringSample preparation

Identifiers

PMID41085619

What OpenQuestion holds

Textmetadata
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.