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Enhancing Mass Spectrometry-Based MHC-I Peptide Identification Through a Targeted Database Search Approach

  • Prathyusha Konda
  • J. Patrick Murphy
  • Morten Nielsen
  • Shashi GujarEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2024)

Abstract

MHC-bound peptide ligands dictate the activation and specificity of CD8+ T- cells-based and thus are important for devising T-cell immunotherapies. In recent times, advances in mass spectrometry (MS) have enabled the precise identification of these peptides, wherein MS/MS spectra are compared against a reference proteome. Unfortunately, matching immunopeptide MS/MS to reference proteome databases is hindered by inflated search spaces attributed to the number of matches that need to be considered due to a lack of enzyme restriction. These large search spaces limit the efficiency with which MHC-I peptides are identified. Here we offer a solution to this problem whereby we describe a targeted database search approach and accompanying tool SpectMHC that is based on a priori predicted MHC-I peptides (Murphy et al., J Proteome Res 16:1806–1816, 2017).

Key words

MHC ligandome Mass spectrometry Bioinformatics Immuno-informatics MHC peptides NetMHC SpectMHC 

Notes

Acknowledgments

We gratefully acknowledge 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 Ms. Youra Kim for her support with editing of this document. We 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 2019

Authors and Affiliations

  • Prathyusha Konda
    • 1
  • J. Patrick Murphy
    • 2
  • Morten Nielsen
    • 3
    • 4
  • Shashi Gujar
    • 1
    • 2
    • 5
    • 6
    Email author
  1. 1.Department of Microbiology and ImmunologyDalhousie UniversityHalifaxCanada
  2. 2.Department of PathologyDalhousie UniversityHalifaxCanada
  3. 3.Department of Bio and Health InformaticsTechnical University of DenmarkLyngbyDenmark
  4. 4.Instituto de Investigaciones BiotecnológicasUniversidad Nacional de San MartínSan Martín, Buenos AiresArgentina
  5. 5.Department of BiologyDalhousie UniversityHalifaxCanada
  6. 6.Centre for Innovative and Collaborative Health Services ResearchIWK Health CentreHalifaxCanada

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