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High-Coverage Immunopeptidomics Using timsTOF Mass Spectrometers with Thunder-DDA-PASEF Boosted by MS2Rescore.

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Methods in Molecular Biology (Clifton, N.J.)
|October 14, 2025
PubMed
Summary
This summary is machine-generated.

This study details an optimized immunopeptidomics workflow for identifying Major Histocompatibility Complex (MHC) ligands. The method enhances deep coverage of immunopeptides for potential immunotherapies.

Keywords:
Human leucocyte antigenImmunopeptidomicsImmunoprecipitationMajor histocompatibility complexMass spectrometryRe-scoringSample preparation

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Area of Science:

  • Immunology
  • Proteomics
  • Mass Spectrometry

Background:

  • Major Histocompatibility Complex (MHC) peptide ligands are crucial for immune response and can be targeted for immunotherapies.
  • Identifying these ligands is key for developing treatments for diseases like cancer and viral infections.
  • Liquid chromatography coupled with mass spectrometry (LC-MS) is the standard for MHC ligand identification.

Purpose of the Study:

  • To describe a detailed, step-by-step workflow for deep-coverage immunopeptidomics.
  • To present an optimized method for comprehensive MHC ligand identification.
  • To validate a robust workflow for immunopeptide discovery.

Main Methods:

  • High-recovery immunopeptidome enrichment.
  • Optimized mass spectrometry (MS) acquisition using Thunder-Data-Dependent Acquisition with Parallel Accumulation-SErial Fragmentation (Thunder-DDA-PASEF) on a timsTOF Pro instrument.
  • Peptide identification via PEAKS XPro software, enhanced with MS2Rescore data-driven rescoring.

Main Results:

  • The workflow enables the identification of over 10,000 MHC class I ligands per cell line.
  • The described process ensures deep coverage of the immunopeptidome.
  • The method integrates sample preparation, MS acquisition, and data analysis for robust identification.

Conclusions:

  • The presented workflow provides a comprehensive approach for deep immunopeptidomics.
  • This optimized method facilitates the discovery of disease-specific immunopeptides for therapeutic development.
  • The workflow is validated for reliable and extensive MHC ligand identification.