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Updated: Jan 30, 2026

Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics
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Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics

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High-Throughput, Fast, and Sensitive Immunopeptidomics Sample Processing for Mass Spectrometry

Fabio Marino1,2, Chloe Chong1,2, Justine Michaux1,2

  • 1Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland.

Methods in Molecular Biology (Clifton, N.J.)
|January 23, 2019
PubMed

Comprehensive knowledge of the HLA class I and class II peptides presented to T cells is crucial for designing innovative therapeutics against cancer and other diseases. So far, methodologies for recovery of HLA class I and II peptides for subsequent mass spectrometry-based analysis have been a major limitation. In this chapter we describe a detailed protocol for a high-throughput, reproducible, and sensitive immunoaffinity-purification of HLA-I and HLA-II peptides from up to 96 samples in a plate format, suitable for tissue samples and cell lines. Our methodology reduces sample handling, has a competitive peptide yield, and can be completed within 5 h. This simplified pipeline is applicable for basic and clinical applications.

Keywords:
Affinity purificationAntigen processing and presentationHLA class I and HLA class IIHuman leukocyte antigenImmunopeptidomicsMass spectrometry

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