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Pitfalls in HLA Ligandomics—How to Catch a Li(e)gand
Knowledge about the peptide repertoire presented by human leukocyte antigens (HLA) holds the key to unlock target-specific cancer immunotherapies such as adoptive cell therapies or bispecific T cell engaging receptors. Therefore, comprehensive and accurate characterization of HLA peptidomes by mass...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Society for Biochemistry and Molecular Biology
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8313844/ https://www.ncbi.nlm.nih.gov/pubmed/34129939 http://dx.doi.org/10.1016/j.mcpro.2021.100110 |
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author | Fritsche, Jens Kowalewski, Daniel J. Backert, Linus Gwinner, Frederik Dorner, Sonja Priemer, Martin Tsou, Chih-Chiang Hoffgaard, Franziska Römer, Michael Schuster, Heiko Schoor, Oliver Weinschenk, Toni |
author_facet | Fritsche, Jens Kowalewski, Daniel J. Backert, Linus Gwinner, Frederik Dorner, Sonja Priemer, Martin Tsou, Chih-Chiang Hoffgaard, Franziska Römer, Michael Schuster, Heiko Schoor, Oliver Weinschenk, Toni |
author_sort | Fritsche, Jens |
collection | PubMed |
description | Knowledge about the peptide repertoire presented by human leukocyte antigens (HLA) holds the key to unlock target-specific cancer immunotherapies such as adoptive cell therapies or bispecific T cell engaging receptors. Therefore, comprehensive and accurate characterization of HLA peptidomes by mass spectrometry (immunopeptidomics) across tissues and disease states is essential. With growing numbers of immunopeptidomics datasets and the scope of peptide identification strategies reaching beyond the canonical proteome, the likelihood for erroneous peptide identification as well as false annotation of HLA-independent peptides as HLA ligands is increasing. Such “fake ligands” can lead to selection of nonexistent targets for immunotherapeutic development and need to be recognized as such as early as possible in the preclinical pipeline. Here we present computational and experimental methods that enable the identification of “fake ligands” that might be introduced at different steps of the immunopeptidomics workflow. The statistics presented herein allow discrimination of true HLA ligands from coisolated HLA-independent proteolytic fragments. In addition, we describe necessary steps to ensure system suitability of the chromatographic system. Furthermore, we illustrate an algorithm for detection of source fragmentation events that are introduced by electrospray ionization during mass spectrometry. For confirmation of peptide sequences, we present an experimental pipeline that enables high-throughput sequence verification through similarity of fragmentation pattern and coelution of synthetic isotope-labeled internal standards. Based on these methods, we show the overall high quality of existing datasets but point out limitations and pitfalls critical for individual peptides and how they can be uncovered in order to identify true ligands. |
format | Online Article Text |
id | pubmed-8313844 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | American Society for Biochemistry and Molecular Biology |
record_format | MEDLINE/PubMed |
spelling | pubmed-83138442021-07-28 Pitfalls in HLA Ligandomics—How to Catch a Li(e)gand Fritsche, Jens Kowalewski, Daniel J. Backert, Linus Gwinner, Frederik Dorner, Sonja Priemer, Martin Tsou, Chih-Chiang Hoffgaard, Franziska Römer, Michael Schuster, Heiko Schoor, Oliver Weinschenk, Toni Mol Cell Proteomics Technological Innovation and Resources Knowledge about the peptide repertoire presented by human leukocyte antigens (HLA) holds the key to unlock target-specific cancer immunotherapies such as adoptive cell therapies or bispecific T cell engaging receptors. Therefore, comprehensive and accurate characterization of HLA peptidomes by mass spectrometry (immunopeptidomics) across tissues and disease states is essential. With growing numbers of immunopeptidomics datasets and the scope of peptide identification strategies reaching beyond the canonical proteome, the likelihood for erroneous peptide identification as well as false annotation of HLA-independent peptides as HLA ligands is increasing. Such “fake ligands” can lead to selection of nonexistent targets for immunotherapeutic development and need to be recognized as such as early as possible in the preclinical pipeline. Here we present computational and experimental methods that enable the identification of “fake ligands” that might be introduced at different steps of the immunopeptidomics workflow. The statistics presented herein allow discrimination of true HLA ligands from coisolated HLA-independent proteolytic fragments. In addition, we describe necessary steps to ensure system suitability of the chromatographic system. Furthermore, we illustrate an algorithm for detection of source fragmentation events that are introduced by electrospray ionization during mass spectrometry. For confirmation of peptide sequences, we present an experimental pipeline that enables high-throughput sequence verification through similarity of fragmentation pattern and coelution of synthetic isotope-labeled internal standards. Based on these methods, we show the overall high quality of existing datasets but point out limitations and pitfalls critical for individual peptides and how they can be uncovered in order to identify true ligands. American Society for Biochemistry and Molecular Biology 2021-06-12 /pmc/articles/PMC8313844/ /pubmed/34129939 http://dx.doi.org/10.1016/j.mcpro.2021.100110 Text en © 2021 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Technological Innovation and Resources Fritsche, Jens Kowalewski, Daniel J. Backert, Linus Gwinner, Frederik Dorner, Sonja Priemer, Martin Tsou, Chih-Chiang Hoffgaard, Franziska Römer, Michael Schuster, Heiko Schoor, Oliver Weinschenk, Toni Pitfalls in HLA Ligandomics—How to Catch a Li(e)gand |
title | Pitfalls in HLA Ligandomics—How to Catch a Li(e)gand |
title_full | Pitfalls in HLA Ligandomics—How to Catch a Li(e)gand |
title_fullStr | Pitfalls in HLA Ligandomics—How to Catch a Li(e)gand |
title_full_unstemmed | Pitfalls in HLA Ligandomics—How to Catch a Li(e)gand |
title_short | Pitfalls in HLA Ligandomics—How to Catch a Li(e)gand |
title_sort | pitfalls in hla ligandomics—how to catch a li(e)gand |
topic | Technological Innovation and Resources |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8313844/ https://www.ncbi.nlm.nih.gov/pubmed/34129939 http://dx.doi.org/10.1016/j.mcpro.2021.100110 |
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