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HSPVdb—the Human Short Peptide Variation Database for improved mass spectrometry-based detection of polymorphic HLA-ligands

T cell epitopes derived from polymorphic proteins or from proteins encoded by alternative reading frames (ARFs) play an important role in (tumor) immunology. Identification of these peptides is successfully performed with mass spectrometry. In a mass spectrometry-based approach, the recorded tandem...

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Autores principales: Nijveen, Harm, Kester, Michel G. D., Hassan, Chopie, Viars, Aurélie, de Ru, Arnoud H., de Jager, Machiel, Falkenburg, J. H. Fred, Leunissen, Jack A. M., van Veelen, Peter A.
Formato: Texto
Lenguaje:English
Publicado: Springer-Verlag 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035791/
https://www.ncbi.nlm.nih.gov/pubmed/21125265
http://dx.doi.org/10.1007/s00251-010-0497-1
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author Nijveen, Harm
Kester, Michel G. D.
Hassan, Chopie
Viars, Aurélie
de Ru, Arnoud H.
de Jager, Machiel
Falkenburg, J. H. Fred
Leunissen, Jack A. M.
van Veelen, Peter A.
author_facet Nijveen, Harm
Kester, Michel G. D.
Hassan, Chopie
Viars, Aurélie
de Ru, Arnoud H.
de Jager, Machiel
Falkenburg, J. H. Fred
Leunissen, Jack A. M.
van Veelen, Peter A.
author_sort Nijveen, Harm
collection PubMed
description T cell epitopes derived from polymorphic proteins or from proteins encoded by alternative reading frames (ARFs) play an important role in (tumor) immunology. Identification of these peptides is successfully performed with mass spectrometry. In a mass spectrometry-based approach, the recorded tandem mass spectra are matched against hypothetical spectra generated from known protein sequence databases. Commonly used protein databases contain a minimal level of redundancy, and thus, are not suitable data sources for searching polymorphic T cell epitopes, either in normal or ARFs. At the same time, however, these databases contain much non-polymorphic sequence information, thereby complicating the matching of recorded and theoretical spectra, and increasing the potential for finding false positives. Therefore, we created a database with peptides from ARFs and peptide variation arising from single nucleotide polymorphisms (SNPs). It is based on the human mRNA sequences from the well-annotated reference sequence (RefSeq) database and associated variation information derived from the Single Nucleotide Polymorphism Database (dbSNP). In this process, we removed all non-polymorphic information. Investigation of the frequency of SNPs in the dbSNP revealed that many SNPs are non-polymorphic “SNPs”. Therefore, we removed those from our dedicated database, and this resulted in a comprehensive high quality database, which we coined the Human Short Peptide Variation Database (HSPVdb). The value of our HSPVdb is shown by identification of the majority of published polymorphic SNP- and/or ARF-derived epitopes from a mass spectrometry-based proteomics workflow, and by a large variety of polymorphic peptides identified as potential T cell epitopes in the HLA-ligandome presented by the Epstein–Barr virus cells. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00251-010-0497-1) contains supplementary material, which is available to authorized users.
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spelling pubmed-30357912011-03-16 HSPVdb—the Human Short Peptide Variation Database for improved mass spectrometry-based detection of polymorphic HLA-ligands Nijveen, Harm Kester, Michel G. D. Hassan, Chopie Viars, Aurélie de Ru, Arnoud H. de Jager, Machiel Falkenburg, J. H. Fred Leunissen, Jack A. M. van Veelen, Peter A. Immunogenetics Original Paper T cell epitopes derived from polymorphic proteins or from proteins encoded by alternative reading frames (ARFs) play an important role in (tumor) immunology. Identification of these peptides is successfully performed with mass spectrometry. In a mass spectrometry-based approach, the recorded tandem mass spectra are matched against hypothetical spectra generated from known protein sequence databases. Commonly used protein databases contain a minimal level of redundancy, and thus, are not suitable data sources for searching polymorphic T cell epitopes, either in normal or ARFs. At the same time, however, these databases contain much non-polymorphic sequence information, thereby complicating the matching of recorded and theoretical spectra, and increasing the potential for finding false positives. Therefore, we created a database with peptides from ARFs and peptide variation arising from single nucleotide polymorphisms (SNPs). It is based on the human mRNA sequences from the well-annotated reference sequence (RefSeq) database and associated variation information derived from the Single Nucleotide Polymorphism Database (dbSNP). In this process, we removed all non-polymorphic information. Investigation of the frequency of SNPs in the dbSNP revealed that many SNPs are non-polymorphic “SNPs”. Therefore, we removed those from our dedicated database, and this resulted in a comprehensive high quality database, which we coined the Human Short Peptide Variation Database (HSPVdb). The value of our HSPVdb is shown by identification of the majority of published polymorphic SNP- and/or ARF-derived epitopes from a mass spectrometry-based proteomics workflow, and by a large variety of polymorphic peptides identified as potential T cell epitopes in the HLA-ligandome presented by the Epstein–Barr virus cells. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00251-010-0497-1) contains supplementary material, which is available to authorized users. Springer-Verlag 2010-12-02 2011 /pmc/articles/PMC3035791/ /pubmed/21125265 http://dx.doi.org/10.1007/s00251-010-0497-1 Text en © The Author(s) 2010 https://creativecommons.org/licenses/by-nc/4.0/ This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.
spellingShingle Original Paper
Nijveen, Harm
Kester, Michel G. D.
Hassan, Chopie
Viars, Aurélie
de Ru, Arnoud H.
de Jager, Machiel
Falkenburg, J. H. Fred
Leunissen, Jack A. M.
van Veelen, Peter A.
HSPVdb—the Human Short Peptide Variation Database for improved mass spectrometry-based detection of polymorphic HLA-ligands
title HSPVdb—the Human Short Peptide Variation Database for improved mass spectrometry-based detection of polymorphic HLA-ligands
title_full HSPVdb—the Human Short Peptide Variation Database for improved mass spectrometry-based detection of polymorphic HLA-ligands
title_fullStr HSPVdb—the Human Short Peptide Variation Database for improved mass spectrometry-based detection of polymorphic HLA-ligands
title_full_unstemmed HSPVdb—the Human Short Peptide Variation Database for improved mass spectrometry-based detection of polymorphic HLA-ligands
title_short HSPVdb—the Human Short Peptide Variation Database for improved mass spectrometry-based detection of polymorphic HLA-ligands
title_sort hspvdb—the human short peptide variation database for improved mass spectrometry-based detection of polymorphic hla-ligands
topic Original Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035791/
https://www.ncbi.nlm.nih.gov/pubmed/21125265
http://dx.doi.org/10.1007/s00251-010-0497-1
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