Increasing confidence in proteomic spectral deconvolution through mass defect

Detalhes bibliográficos
Autor(a) principal: Clasen, Milan A.
Data de Publicação: 2022
Outros Autores: Kurt, Louise U., Santos, Marlon D. M., Lima, Diogo B., Liu, Fan, Gozzo, Fabio C., Barbosa, Valmir C., Carvalho, Paulo Costa
Tipo de documento: Artigo
Idioma: por
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/55813
Resumo: Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.
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spelling Clasen, Milan A.Kurt, Louise U.Santos, Marlon D. M.Lima, Diogo B.Liu, FanGozzo, Fabio C.Barbosa, Valmir C.Carvalho, Paulo Costa2022-11-28T14:00:33Z2022-11-28T14:00:33Z2022CLASEN, Milan A. et al. Increasing confidence in proteomic spectral deconvolution through mass defect. Bioinformatics, p. 1–2, 2022.1460-2059https://www.arca.fiocruz.br/handle/icict/5581310.1093/bioinformatics/btac638porOxfordY.A.D.A. 3.0ProteomicsMass SpectrometryAlgorithmsProteómicaEspectrometría de MasasAlgoritmosProtéomiqueSpectrométrie de masseAlgorithmesProteômicaEspectrometria de MassasAlgoritmosIncreasing confidence in proteomic spectral deconvolution through mass defectinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.Department of Structural Biology. Leibniz - Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany.Department of Structural Biology. Leibniz - Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany.Universidade Estadual de Campinas. Dalton Mass Spectrometry Laboratory. Campinas, Brasil.Universidade Federal do Rio de Janeiro. Programa em Engenharia de Sistemas e Computação. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.Motivation: Confident deconvolution of proteomic spectra is critical for several applications such as sequencing, cross-linking mass spectrometry and handling chimeric mass spectra. Results: In general, all deconvolution algorithms may eventually report mass peaks that are not compatible with the chemical formula of any peptide. We show how to remove these artifacts by considering their mass defects. We introduce Y.A.D.A. 3.0, a fast deconvolution algorithm that can remove peaks with unacceptable mass defects. Our approach is effective for polypeptides with less than 10 kDa, and its essence can be easily incorporated into any deconvolution algorithm.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/55813/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALbtac638ok.pdfbtac638ok.pdfapplication/pdf845111https://www.arca.fiocruz.br/bitstream/icict/55813/2/btac638ok.pdf1b45d4b08b32c67ff207a5cc154e3f5eMD52icict/558132022-11-29 20:10:47.894oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352022-11-29T23:10:47Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false
dc.title.en_US.fl_str_mv Increasing confidence in proteomic spectral deconvolution through mass defect
title Increasing confidence in proteomic spectral deconvolution through mass defect
spellingShingle Increasing confidence in proteomic spectral deconvolution through mass defect
Clasen, Milan A.
Y.A.D.A. 3.0
Proteomics
Mass Spectrometry
Algorithms
Proteómica
Espectrometría de Masas
Algoritmos
Protéomique
Spectrométrie de masse
Algorithmes
Proteômica
Espectrometria de Massas
Algoritmos
title_short Increasing confidence in proteomic spectral deconvolution through mass defect
title_full Increasing confidence in proteomic spectral deconvolution through mass defect
title_fullStr Increasing confidence in proteomic spectral deconvolution through mass defect
title_full_unstemmed Increasing confidence in proteomic spectral deconvolution through mass defect
title_sort Increasing confidence in proteomic spectral deconvolution through mass defect
author Clasen, Milan A.
author_facet Clasen, Milan A.
Kurt, Louise U.
Santos, Marlon D. M.
Lima, Diogo B.
Liu, Fan
Gozzo, Fabio C.
Barbosa, Valmir C.
Carvalho, Paulo Costa
author_role author
author2 Kurt, Louise U.
Santos, Marlon D. M.
Lima, Diogo B.
Liu, Fan
Gozzo, Fabio C.
Barbosa, Valmir C.
Carvalho, Paulo Costa
author2_role author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Clasen, Milan A.
Kurt, Louise U.
Santos, Marlon D. M.
Lima, Diogo B.
Liu, Fan
Gozzo, Fabio C.
Barbosa, Valmir C.
Carvalho, Paulo Costa
dc.subject.other.en_US.fl_str_mv Y.A.D.A. 3.0
topic Y.A.D.A. 3.0
Proteomics
Mass Spectrometry
Algorithms
Proteómica
Espectrometría de Masas
Algoritmos
Protéomique
Spectrométrie de masse
Algorithmes
Proteômica
Espectrometria de Massas
Algoritmos
dc.subject.en.en_US.fl_str_mv Proteomics
Mass Spectrometry
Algorithms
dc.subject.es.en_US.fl_str_mv Proteómica
Espectrometría de Masas
Algoritmos
dc.subject.fr.en_US.fl_str_mv Protéomique
Spectrométrie de masse
Algorithmes
dc.subject.decs.en_US.fl_str_mv Proteômica
Espectrometria de Massas
Algoritmos
description Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.
publishDate 2022
dc.date.accessioned.fl_str_mv 2022-11-28T14:00:33Z
dc.date.available.fl_str_mv 2022-11-28T14:00:33Z
dc.date.issued.fl_str_mv 2022
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.citation.fl_str_mv CLASEN, Milan A. et al. Increasing confidence in proteomic spectral deconvolution through mass defect. Bioinformatics, p. 1–2, 2022.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/55813
dc.identifier.issn.en_US.fl_str_mv 1460-2059
dc.identifier.doi.none.fl_str_mv 10.1093/bioinformatics/btac638
identifier_str_mv CLASEN, Milan A. et al. Increasing confidence in proteomic spectral deconvolution through mass defect. Bioinformatics, p. 1–2, 2022.
1460-2059
10.1093/bioinformatics/btac638
url https://www.arca.fiocruz.br/handle/icict/55813
dc.language.iso.fl_str_mv por
language por
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Oxford
publisher.none.fl_str_mv Oxford
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/55813/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/55813/2/btac638ok.pdf
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repository.mail.fl_str_mv repositorio.arca@fiocruz.br
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