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

Prathyusha Konda, J. Patrick Murphy, Morten Nielsen, Shashi Gujar*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

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).
Original languageEnglish
Title of host publicationImmunoproteomics: Methods and protocols
EditorsKelly M. Fulton, Susan M. Twine
Number of pages7
Volume2024
PublisherSpringer
Publication date2019
Pages301-307
Chapter19
ISBN (Print)978-1-4939-9596-7
ISBN (Electronic)978-1-4939-9597-4
DOIs
Publication statusPublished - 2019
SeriesMethods in Molecular Biology
ISSN1064-3745

Keywords

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

Cite this

Konda, P., Murphy, J. P., Nielsen, M., & Gujar, S. (2019). Enhancing Mass Spectrometry-Based MHC-I Peptide Identification Through a Targeted Database Search Approach. In K. M. Fulton, & S. M. Twine (Eds.), Immunoproteomics: Methods and protocols (Vol. 2024, pp. 301-307). Springer. Methods in Molecular Biology https://doi.org/10.1007/978-1-4939-9597-4_19
Konda, Prathyusha ; Murphy, J. Patrick ; Nielsen, Morten ; Gujar, Shashi. / Enhancing Mass Spectrometry-Based MHC-I Peptide Identification Through a Targeted Database Search Approach. Immunoproteomics: Methods and protocols. editor / Kelly M. Fulton ; Susan M. Twine. Vol. 2024 Springer, 2019. pp. 301-307 (Methods in Molecular Biology).
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Konda, P, Murphy, JP, Nielsen, M & Gujar, S 2019, Enhancing Mass Spectrometry-Based MHC-I Peptide Identification Through a Targeted Database Search Approach. in KM Fulton & SM Twine (eds), Immunoproteomics: Methods and protocols. vol. 2024, Springer, Methods in Molecular Biology, pp. 301-307. https://doi.org/10.1007/978-1-4939-9597-4_19

Enhancing Mass Spectrometry-Based MHC-I Peptide Identification Through a Targeted Database Search Approach. / Konda, Prathyusha; Murphy, J. Patrick; Nielsen, Morten; Gujar, Shashi.

Immunoproteomics: Methods and protocols. ed. / Kelly M. Fulton; Susan M. Twine. Vol. 2024 Springer, 2019. p. 301-307 (Methods in Molecular Biology).

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

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AB - 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).

KW - Bioinformatics

KW - Immuno-informatics

KW - MHC ligandome

KW - MHC peptides

KW - Mass spectrometry

KW - NetMHC

KW - SpectMHC

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Konda P, Murphy JP, Nielsen M, Gujar S. Enhancing Mass Spectrometry-Based MHC-I Peptide Identification Through a Targeted Database Search Approach. In Fulton KM, Twine SM, editors, Immunoproteomics: Methods and protocols. Vol. 2024. Springer. 2019. p. 301-307. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-9597-4_19