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Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow
Proteogenomics enable the discovery of novel peptides (from unannotated genomic protein-coding loci) and single amino acid variant peptides (derived from single-nucleotide polymorphisms and mutations). Increasing the reliability of these identifications is crucial to ensure their usefulness for geno...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5834625/ https://www.ncbi.nlm.nih.gov/pubmed/29500430 http://dx.doi.org/10.1038/s41467-018-03311-y |
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author | Zhu, Yafeng Orre, Lukas M. Johansson, Henrik J. Huss, Mikael Boekel, Jorrit Vesterlund, Mattias Fernandez-Woodbridge, Alejandro Branca, Rui M. M. Lehtiö, Janne |
author_facet | Zhu, Yafeng Orre, Lukas M. Johansson, Henrik J. Huss, Mikael Boekel, Jorrit Vesterlund, Mattias Fernandez-Woodbridge, Alejandro Branca, Rui M. M. Lehtiö, Janne |
author_sort | Zhu, Yafeng |
collection | PubMed |
description | Proteogenomics enable the discovery of novel peptides (from unannotated genomic protein-coding loci) and single amino acid variant peptides (derived from single-nucleotide polymorphisms and mutations). Increasing the reliability of these identifications is crucial to ensure their usefulness for genome annotation and potential application as neoantigens in cancer immunotherapy. We here present integrated proteogenomics analysis workflow (IPAW), which combines peptide discovery, curation, and validation. IPAW includes the SpectrumAI tool for automated inspection of MS/MS spectra, eliminating false identifications of single-residue substitution peptides. We employ IPAW to analyze two proteomics data sets acquired from A431 cells and five normal human tissues using extended (pH range, 3–10) high-resolution isoelectric focusing (HiRIEF) pre-fractionation and TMT-based peptide quantitation. The IPAW results provide evidence for the translation of pseudogenes, lncRNAs, short ORFs, alternative ORFs, N-terminal extensions, and intronic sequences. Moreover, our quantitative analysis indicates that protein production from certain pseudogenes and lncRNAs is tissue specific. |
format | Online Article Text |
id | pubmed-5834625 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-58346252018-03-06 Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow Zhu, Yafeng Orre, Lukas M. Johansson, Henrik J. Huss, Mikael Boekel, Jorrit Vesterlund, Mattias Fernandez-Woodbridge, Alejandro Branca, Rui M. M. Lehtiö, Janne Nat Commun Article Proteogenomics enable the discovery of novel peptides (from unannotated genomic protein-coding loci) and single amino acid variant peptides (derived from single-nucleotide polymorphisms and mutations). Increasing the reliability of these identifications is crucial to ensure their usefulness for genome annotation and potential application as neoantigens in cancer immunotherapy. We here present integrated proteogenomics analysis workflow (IPAW), which combines peptide discovery, curation, and validation. IPAW includes the SpectrumAI tool for automated inspection of MS/MS spectra, eliminating false identifications of single-residue substitution peptides. We employ IPAW to analyze two proteomics data sets acquired from A431 cells and five normal human tissues using extended (pH range, 3–10) high-resolution isoelectric focusing (HiRIEF) pre-fractionation and TMT-based peptide quantitation. The IPAW results provide evidence for the translation of pseudogenes, lncRNAs, short ORFs, alternative ORFs, N-terminal extensions, and intronic sequences. Moreover, our quantitative analysis indicates that protein production from certain pseudogenes and lncRNAs is tissue specific. Nature Publishing Group UK 2018-03-02 /pmc/articles/PMC5834625/ /pubmed/29500430 http://dx.doi.org/10.1038/s41467-018-03311-y Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Zhu, Yafeng Orre, Lukas M. Johansson, Henrik J. Huss, Mikael Boekel, Jorrit Vesterlund, Mattias Fernandez-Woodbridge, Alejandro Branca, Rui M. M. Lehtiö, Janne Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow |
title | Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow |
title_full | Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow |
title_fullStr | Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow |
title_full_unstemmed | Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow |
title_short | Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow |
title_sort | discovery of coding regions in the human genome by integrated proteogenomics analysis workflow |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5834625/ https://www.ncbi.nlm.nih.gov/pubmed/29500430 http://dx.doi.org/10.1038/s41467-018-03311-y |
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