Mass spectrometric analysis of the HLA class I peptidome of melanoma cell lines as a promising tool for the identification of putative tumor-associated HLA epitopes

Cancer Immunol Immunother. 2016 Nov;65(11):1377-1393. doi: 10.1007/s00262-016-1897-3. Epub 2016 Sep 6.


Melanoma is one of the most immunogenic tumors, and extensive lists of potential tumor rejection antigens have been collected during the last decades. By isolating human leukocyte antigen (HLA) class I complexes from five melanoma cell lines (FM-82, FM-93/2, Mel-624, MeWo and SK-Mel-5) and sequencing HLA-eluted peptides by mass spectrometry, we identified over 10,000 unique peptides with high confidence. The majority of the peptides were 8-11 amino acids in length and were predicted to bind to the respective HLA alleles. Over 250 epitopes, corresponding to previously described tumor-associated antigens, were identified, suggesting that HLA peptidome analysis may facilitate the characterization of putative tumor rejection antigens. MeWo and SK-Mel-5 cell lines were further interrogated for neo-epitopes, revealing one peptide from MeWo cells carrying an amino acid mutation. We also observed a remarkable overlap between A*03:01 peptides eluted from Mel-624 cells and A*03:01 peptides recovered from soluble HLA complexes purified from two melanoma patients, shedding light on the similarity of the HLA peptidome in cell lines and in patient-derived material. The reliable characterization of the HLA class I peptidome in melanoma promises to facilitate the identification of tumor rejection antigens and the development of immunotherapeutic strategies.

Keywords: HLA; Immunocapture; Immunopeptidome; Mass spectrometry; Melanoma; Tumor-associated antigen.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Antigens, Neoplasm / metabolism*
  • Cell Line, Tumor
  • Cytotoxicity, Immunologic
  • Epitope Mapping / methods*
  • Epitopes, T-Lymphocyte / metabolism*
  • HLA Antigens / metabolism
  • Histocompatibility Antigens Class I / metabolism
  • Humans
  • Immunotherapy / methods*
  • Mass Spectrometry / methods
  • Melanoma / immunology*
  • Peptides / metabolism*
  • Protein Binding
  • T-Lymphocytes, Cytotoxic / immunology*


  • Antigens, Neoplasm
  • Epitopes, T-Lymphocyte
  • HLA Antigens
  • Histocompatibility Antigens Class I
  • Peptides