De novo sequencing of proteins by mass spectrometry
Autor(a) principal: | |
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Data de Publicação: | 2020 |
Outros Autores: | , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10773/30814 |
Resumo: | Introduction Proteins are crucial for every cellular activity and unraveling their sequence and structure is a crucial step to fully understand their biology. Early methods of protein sequencing were mainly based on the use of enzymatic or chemical degradation of peptide chains. With the completion of the human genome project and with the expansion of the information available for each protein, various databases containing this sequence information were formed. Areas covered De novo protein sequencing, shotgun proteomics and other mass-spectrometric techniques, along with the various software are currently available for proteogenomic analysis. Emphasis is placed on the methods for de novo sequencing, together with potential and shortcomings using databases for interpretation of protein sequence data. Expert opinion As mass-spectrometry sequencing performance is improving with better software and hardware optimizations, combined with user-friendly interfaces, de-novo protein sequencing becomes imperative in shotgun proteomic studies. Issues regarding unknown or mutated peptide sequences, as well as, unexpected post-translational modifications (PTMs) and their identification through false discovery rate searches using the target/decoy strategy need to be addressed. Ideally, it should become integrated in standard proteomic workflows as an add-on to conventional database search engines, which then would be able to provide improved identification. |
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De novo sequencing of proteins by mass spectrometryAlgorithmsDatabase searchDe novoMass spectrometryMS/MSProteomicsSequence tagsSequencingTandem MSIntroduction Proteins are crucial for every cellular activity and unraveling their sequence and structure is a crucial step to fully understand their biology. Early methods of protein sequencing were mainly based on the use of enzymatic or chemical degradation of peptide chains. With the completion of the human genome project and with the expansion of the information available for each protein, various databases containing this sequence information were formed. Areas covered De novo protein sequencing, shotgun proteomics and other mass-spectrometric techniques, along with the various software are currently available for proteogenomic analysis. Emphasis is placed on the methods for de novo sequencing, together with potential and shortcomings using databases for interpretation of protein sequence data. Expert opinion As mass-spectrometry sequencing performance is improving with better software and hardware optimizations, combined with user-friendly interfaces, de-novo protein sequencing becomes imperative in shotgun proteomic studies. Issues regarding unknown or mutated peptide sequences, as well as, unexpected post-translational modifications (PTMs) and their identification through false discovery rate searches using the target/decoy strategy need to be addressed. Ideally, it should become integrated in standard proteomic workflows as an add-on to conventional database search engines, which then would be able to provide improved identification.Taylor and Francis2021-10-21T00:00:00Z2020-01-01T00:00:00Z2020info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10773/30814eng1478-945010.1080/14789450.2020.1831387Vitorino, RuiGuedes, SofiaTrindade, FabioCorreia, InêsMoura, GabrielaCarvalho, PauloSantos, ManuelAmado, Franciscoinfo:eu-repo/semantics/embargoedAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-02-22T11:59:29Zoai:ria.ua.pt:10773/30814Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:02:47.938849Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
De novo sequencing of proteins by mass spectrometry |
title |
De novo sequencing of proteins by mass spectrometry |
spellingShingle |
De novo sequencing of proteins by mass spectrometry Vitorino, Rui Algorithms Database search De novo Mass spectrometry MS/MS Proteomics Sequence tags Sequencing Tandem MS |
title_short |
De novo sequencing of proteins by mass spectrometry |
title_full |
De novo sequencing of proteins by mass spectrometry |
title_fullStr |
De novo sequencing of proteins by mass spectrometry |
title_full_unstemmed |
De novo sequencing of proteins by mass spectrometry |
title_sort |
De novo sequencing of proteins by mass spectrometry |
author |
Vitorino, Rui |
author_facet |
Vitorino, Rui Guedes, Sofia Trindade, Fabio Correia, Inês Moura, Gabriela Carvalho, Paulo Santos, Manuel Amado, Francisco |
author_role |
author |
author2 |
Guedes, Sofia Trindade, Fabio Correia, Inês Moura, Gabriela Carvalho, Paulo Santos, Manuel Amado, Francisco |
author2_role |
author author author author author author author |
dc.contributor.author.fl_str_mv |
Vitorino, Rui Guedes, Sofia Trindade, Fabio Correia, Inês Moura, Gabriela Carvalho, Paulo Santos, Manuel Amado, Francisco |
dc.subject.por.fl_str_mv |
Algorithms Database search De novo Mass spectrometry MS/MS Proteomics Sequence tags Sequencing Tandem MS |
topic |
Algorithms Database search De novo Mass spectrometry MS/MS Proteomics Sequence tags Sequencing Tandem MS |
description |
Introduction Proteins are crucial for every cellular activity and unraveling their sequence and structure is a crucial step to fully understand their biology. Early methods of protein sequencing were mainly based on the use of enzymatic or chemical degradation of peptide chains. With the completion of the human genome project and with the expansion of the information available for each protein, various databases containing this sequence information were formed. Areas covered De novo protein sequencing, shotgun proteomics and other mass-spectrometric techniques, along with the various software are currently available for proteogenomic analysis. Emphasis is placed on the methods for de novo sequencing, together with potential and shortcomings using databases for interpretation of protein sequence data. Expert opinion As mass-spectrometry sequencing performance is improving with better software and hardware optimizations, combined with user-friendly interfaces, de-novo protein sequencing becomes imperative in shotgun proteomic studies. Issues regarding unknown or mutated peptide sequences, as well as, unexpected post-translational modifications (PTMs) and their identification through false discovery rate searches using the target/decoy strategy need to be addressed. Ideally, it should become integrated in standard proteomic workflows as an add-on to conventional database search engines, which then would be able to provide improved identification. |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020-01-01T00:00:00Z 2020 2021-10-21T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10773/30814 |
url |
http://hdl.handle.net/10773/30814 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
1478-9450 10.1080/14789450.2020.1831387 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/embargoedAccess |
eu_rights_str_mv |
embargoedAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Taylor and Francis |
publisher.none.fl_str_mv |
Taylor and Francis |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
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RCAAP |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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1799137683169083392 |