Comprehensive Analysis of MHC Ligands in Clinical Material by Immunoaffinity-Mass Spectrometry

  • Kie Kasuga
Part of the Methods in Molecular Biology book series (MIMB, volume 1023)


Major histocompatibility complexes (MHC) are expressed on antigen-presenting cells (APC) that display peptide antigens. This is a crucial step to activate a T-cell response. Since immunogenic ligand of MHC is closely related with autoimmunity, inflammatory diseases, and cancer, comprehensive analysis of MHC ligands (the so-called Ligandome) is essential to unveil disease pathogenesis. Recently, immunotherapies such as vaccination have been focused on as new therapies of cancer, HIV, and infectious diseases. Therefore, the importance of comprehensive analysis of MHC ligands is increasing. Mass spectrometry has been the core technology of ligand identification since the 1990s. The sensitivity of mass spectrometers has been improved dramatically in recent years; thus, it enables to identify MHC ligands in clinical materials. This chapter lays out the workflow of MHC ligand identification in clinical materials, especially human bronchoalveolar (BAL) cells. MHC-ligand complexes are enriched by immunoaffinity extraction and captured ligand peptides are identified by LC-MS/MS. MHC class II ligand in BAL cells is described in this text; however, this approach is applicable to MHC class I and other clinical materials such as tissues.

Key words

Major histocompatibility complexes (MHC) Immunoaffinity extraction Ligand Bronchoalveolar lavage (BAL) Comprehensive analysis 



Dr. Stefan Stevanović (Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany) and Dr. Rui Mamede Branca (Department of Oncology-Pathology, Karolinska Institutet, Science for Life Laboratory Stockholm) are gratefully acknowledged for helpful discussion. The author is a VINNMER fellow supported via VINNMER Marie Curie Chair—a VINNOVA programme cofounded by Marie Curie Actions.


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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Kie Kasuga
    • 1
  1. 1.Science for Life Laboratory, Department of Oncology–PathologyKarolinska InstitutetStockholmSweden

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