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Related Experiment Video

Updated: Jan 7, 2026

Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis
09:32

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Methods for Isolating and Analyzing the HLA Class I Immunopeptidome.

Martha Nikopaschou1, Georgia Rouni2, Martina Samiotaki3

  • 1Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece.

Methods in Molecular Biology (Clifton, N.J.)
|January 1, 2026
PubMed
Summary

This study presents a simplified immunopeptidomics protocol for analyzing Human Leukocyte Antigen Class I (HLA-I) peptides. The accessible method and in-house antibody production empower researchers to study adaptive immunity and identify disease biomarkers.

Keywords:
Immunoaffinity purificationImmunopeptidomicsLC-MS/MS

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Area of Science:

  • Biochemistry
  • Immunology
  • Mass Spectrometry

Background:

  • Immunopeptidomics characterizes the peptide repertoire presented by Human Leukocyte Antigens Class I (HLA-I), crucial for adaptive immunity.
  • Understanding the immunopeptidome aids in deciphering antigen presentation and identifying biomarkers for diseases like cancer and infections.

Purpose of the Study:

  • To outline a simplified, accessible immunopeptidomics protocol for HLA-I peptide repertoire characterization.
  • To enable researchers with standard laboratory equipment to perform HLA-I immunopeptidomics.
  • To provide guidance on in-house monoclonal antibody production for HLA-I immunopeptidomics.

Main Methods:

  • Mass spectrometry-based immunopeptidomics.
  • Protocol adapted from established workflows for accessibility.
  • In-house production and purification of monoclonal antibodies for HLA-I targeting.
  • Utilization of open-source software for data analysis.

Main Results:

  • A simplified and accessible immunopeptidomics protocol is detailed.
  • Instructions for in-house monoclonal antibody production are provided.
  • Practical considerations and tips are included for researchers.

Conclusions:

  • The presented protocol empowers researchers to apply immunopeptidomics using common laboratory resources.
  • This work facilitates the study of antigen presentation and the discovery of diagnostic markers and therapeutic targets.
  • Accessible immunopeptidomics can advance research in infectious diseases, cancer, and autoimmunity.