Improving MHC-I Ligand Identification by Incorporating Targeted Searches of Mass Spectrometry Data

  • Prathyusha Konda
  • J. Patrick Murphy
  • Shashi GujarEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2120)


Effective immunotherapies rely on specific activation of immune cells. Class I major histocompatibility complex (MHC-I) bound peptide ligands play a major role in dictating the specificity and activation of CD8+ T cells and hence are important in developing T cell-based immunotherapies. Mass spectrometry-based approaches are most commonly used for identifying these MHC-bound peptides, wherein the MS/MS spectra are compared against a reference proteome database. Unfortunately, the effectiveness of matching the immunopeptide MS/MS spectra to a reference proteome database is hindered by inflated search spaces attributed to a lack of enzyme restriction in searches. These large search spaces limit the efficiency with which MHC-I peptides are identified. Here, we describe the implementation of a targeted database search approach and accompanying tool, SpectMHC, that is based on a priori-predicted MHC-I peptides. We have previously shown that this targeted search strategy improved peptide identifications for both mouse and human MHC ligands by greater than two-fold and is superior to traditional “no enzyme” search of reference proteomes (Murphy et al. J Res Proteome 16:1806–1816, 2017).

Key words

Mass spectrometry Bioinformatics MHC ligandome 



We gratefully acknowledge Dr. Steven Gygi (Department of Cell Biology, Harvard Medical School), Dr. Stefan Stevanovic, Dr. Dan Kowalewski, and Dr. Heiko Schuster (Department of Immunology, Institute for Cell Biology, University of Tubingen) for helpful discussions in devising the targeted database search approach. We also acknowledge financial support from the Canadian Institutes of Health Research (CIHR), Canadian Cancer Society Research Institute (CCSRI), the Beatrice Hunter Cancer Research Institute (BHCRI), and the Dalhousie Medical Research Foundation (DMRF).


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  • Prathyusha Konda
    • 1
  • J. Patrick Murphy
    • 2
  • Shashi Gujar
    • 1
    • 2
    • 3
    • 4
    Email author
  1. 1.Department of Microbiology and ImmunologyDalhousie UniversityHalifaxCanada
  2. 2.Department of PathologyDalhousie UniversityHalifaxCanada
  3. 3.Department of BiologyDalhousie UniversityHalifaxCanada
  4. 4.Beatrice Hunter Cancer Research InstituteHalifaxCanada

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