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Cancer Exome-Based Identification of Tumor Neo-Antigens Using Mass Spectrometry

  • Shelly Kalaora
  • Yardena SamuelsEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1884)

Abstract

Neo-antigens expressed on tumors are targets for development of cancer immunotherapy strategies. Use of prediction algorithms to identify neo-antigens yields a significant number of peptides that must be validated in laborious and time-consuming methods; many prove to be false-positive identifications. The use of HLA peptidomics allows the isolation of the HLA-peptide complexes directly from cells and can be done on fresh tumor, patient-derived xerographs, or cell lines when the tissue sample is limited. This method can be used to identify both HLA class I and HLA class II or any different MHC from different species. Here we describe the steps to create the immune-affinity columns used from the process, the immunoprecipitation procedure, and also the isolation of the peptides that will be analyzed by mass spectrometry.

Key words

Neo-antigens HLA peptidomics MHC peptides Exome sequencing Mass spectrometry 

Notes

Acknowledgments

YS is supported by the Israel Science Foundation grant number 696/17. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 754282), the ERC (StG-335377), the MRA (#402024), the Knell Family and the Hamburger Family , by the Henry Chanoch Krenter Institute for Biomedical Imaging and Genomics and the estates of Alice Schwarz-Gardos and John Hunter.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Molecular Cell Biology DepartmentWeizmann Institute of ScienceRehovotIsrael

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