Beyond the identifiable proteome: delving into the proteomics of polymyxin-resistant and non-resistant acinetobacter baumannii from Brazilian hospitals

Detalhes bibliográficos
Autor(a) principal: Dal Lin, Amanda
Data de Publicação: 2023
Outros Autores: Fischer, Juliana de Saldanha da Gama, Santos, Marlon D.M., Camillo-Andrade, Amanda Caroline, Kurt, Louise Ulrich, Souza, Tatiana de Arruda Campos Brasil de, Lajas, Ana Beatriz Lyrio, Rivera, Bernardina, Portela, Magdalena, Duran, Rosario, Mira, Marcelo Távora, Pillonetto, Marcelo, Carvalho, Paulo Costa
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/61032
Resumo: Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil / Pontificia Universidade Católica do Paraná. Laboratório Experimental Multiuso. Curitiba, PR, Brasil.
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spelling Dal Lin, AmandaFischer, Juliana de Saldanha da GamaSantos, Marlon D.M.Camillo-Andrade, Amanda CarolineKurt, Louise UlrichSouza, Tatiana de Arruda Campos Brasil deLajas, Ana Beatriz LyrioRivera, BernardinaPortela, MagdalenaDuran, RosarioMira, Marcelo TávoraPillonetto, MarceloCarvalho, Paulo Costa2023-11-06T16:52:21Z2023-11-06T16:52:21Z2023DAL LIN, Amanda et al. Beyond the identifiable proteome: Delving into the proteomics of polymyxin-resistant and non-resistant Acinetobacter baumannii from Brazilian hospitals. Journal of Proteomics. v. 289, n. 105012, p. 1-9, 2023.1874-3919https://www.arca.fiocruz.br/handle/icict/6103210.1016/j.jprot.2023.105012engElsevierBeyond the identifiable proteome: delving into the proteomics of polymyxin-resistant and non-resistant acinetobacter baumannii from Brazilian hospitalsinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil / Pontificia Universidade Católica do Paraná. Laboratório Experimental Multiuso. 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 / Analytical Biochemistry and Proteomics Unit. Institut Pasteur de Montevideo. Montevideo, Uruguay.Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil / Analytical Biochemistry and Proteomics Unit. Institut Pasteur de Montevideo. Montevideo, Uruguay.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.Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.Analytical Biochemistry and Proteomics Unit. Institut Pasteur de Montevideo. Montevideo, Uruguay.Analytical Biochemistry and Proteomics Unit. Institut Pasteur de Montevideo. Montevideo, Uruguay.Analytical Biochemistry and Proteomics Unit. Institut Pasteur de Montevideo. Montevideo, Uruguay.Pontificia Universidade Católica do Paraná. Laboratório Experimental Multiuso. Curitiba, PR, Brasil.Pontificia Universidade Católica do Paraná. Laboratório Experimental Multiuso. Curitiba, PR, Brasil / Laboratório Central do Estado do Paraná. São José dos Pinhais, PR, Brasil.Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.This work discloses a unique, comprehensive proteomic dataset of Acinetobacter baumannii strains, both resistant and non-resistant to polymyxin B, isolated in Brazil generated using Orbitrap Fusion Lumos. From nearly 4 million tandem mass spectra, the software DiagnoMass produced 240,685 quality-filtered mass spectral clusters, of which PatternLab for proteomics identified 44,553 peptides mapping to 3479 proteins. Crucially, DiagnoMass shortlisted 3550 and 1408 unique mass spectral clusters for the resistant and non-resistant strains, respectively, with only about a third with sequences (and PTMs) identified by PatternLab. Further open-search attempts via FragPipe yielded an additional ~20% identifications, suggesting the remaining unidentified spectra likely arise from complex combinations of post-translational modifications and amino-acid substitutions. This highlights the untapped potential of the dataset for future discoveries, particularly given the importance of PTMs, which remain elusive to nucleotide sequencing approaches but are crucial for understanding biological mechanisms. Our innovative approach extends beyond the identifications that are typically subjected to the bias of a search engine; we discern which spectral clusters are differential and subject them to increased scrutiny, akin to spectral library matching by comparing captured spectra to themselves. Our analysis reveals adaptations in the resistant strain, including enhanced detoxification, altered protein synthesis, and metabolic adjustments. Significance: We present comprehensive proteomic profiles of non-resistant and resistant Acinetobacter baumannii from Brazilian Hospitals strains, and highlight the presence of discriminative and yet unidentified mass spectral clusters. Our work emphasizes the importance of exploring this overlooked data, as it could hold the key to understanding the complex dynamics of antibiotic resistance. This approach not only informs antimicrobial stewardship efforts but also paves the way for the development of innovative diagnostic tools. Thus, our findings have profound implications for the field, as far as methods for providing a new perspective on diagnosing antibiotic resistance as well as classifying proteomes in general.DiagnoMassPolymyxinsBacteriaDrug Resistance, BacterialPolimixinasBacteriasFarmacorresistencia BacterianaPolymyxinesBactériesRésistance bactérienne aux médicamentsPolimixinasAcinetobacter baumanniiBactériasFarmacorresistência Bacterianainfo: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/61032/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINAL1-s2.0-S1874391923002014-main.pdf1-s2.0-S1874391923002014-main.pdfapplication/pdf3568696https://www.arca.fiocruz.br/bitstream/icict/61032/2/1-s2.0-S1874391923002014-main.pdf270c8b9ab640dff4db39bfccf96d8affMD52icict/610322023-11-09 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dc.title.en_US.fl_str_mv Beyond the identifiable proteome: delving into the proteomics of polymyxin-resistant and non-resistant acinetobacter baumannii from Brazilian hospitals
title Beyond the identifiable proteome: delving into the proteomics of polymyxin-resistant and non-resistant acinetobacter baumannii from Brazilian hospitals
spellingShingle Beyond the identifiable proteome: delving into the proteomics of polymyxin-resistant and non-resistant acinetobacter baumannii from Brazilian hospitals
Dal Lin, Amanda
DiagnoMass
Polymyxins
Bacteria
Drug Resistance, Bacterial
Polimixinas
Bacterias
Farmacorresistencia Bacteriana
Polymyxines
Bactéries
Résistance bactérienne aux médicaments
Polimixinas
Acinetobacter baumannii
Bactérias
Farmacorresistência Bacteriana
title_short Beyond the identifiable proteome: delving into the proteomics of polymyxin-resistant and non-resistant acinetobacter baumannii from Brazilian hospitals
title_full Beyond the identifiable proteome: delving into the proteomics of polymyxin-resistant and non-resistant acinetobacter baumannii from Brazilian hospitals
title_fullStr Beyond the identifiable proteome: delving into the proteomics of polymyxin-resistant and non-resistant acinetobacter baumannii from Brazilian hospitals
title_full_unstemmed Beyond the identifiable proteome: delving into the proteomics of polymyxin-resistant and non-resistant acinetobacter baumannii from Brazilian hospitals
title_sort Beyond the identifiable proteome: delving into the proteomics of polymyxin-resistant and non-resistant acinetobacter baumannii from Brazilian hospitals
author Dal Lin, Amanda
author_facet Dal Lin, Amanda
Fischer, Juliana de Saldanha da Gama
Santos, Marlon D.M.
Camillo-Andrade, Amanda Caroline
Kurt, Louise Ulrich
Souza, Tatiana de Arruda Campos Brasil de
Lajas, Ana Beatriz Lyrio
Rivera, Bernardina
Portela, Magdalena
Duran, Rosario
Mira, Marcelo Távora
Pillonetto, Marcelo
Carvalho, Paulo Costa
author_role author
author2 Fischer, Juliana de Saldanha da Gama
Santos, Marlon D.M.
Camillo-Andrade, Amanda Caroline
Kurt, Louise Ulrich
Souza, Tatiana de Arruda Campos Brasil de
Lajas, Ana Beatriz Lyrio
Rivera, Bernardina
Portela, Magdalena
Duran, Rosario
Mira, Marcelo Távora
Pillonetto, Marcelo
Carvalho, Paulo Costa
author2_role author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Dal Lin, Amanda
Fischer, Juliana de Saldanha da Gama
Santos, Marlon D.M.
Camillo-Andrade, Amanda Caroline
Kurt, Louise Ulrich
Souza, Tatiana de Arruda Campos Brasil de
Lajas, Ana Beatriz Lyrio
Rivera, Bernardina
Portela, Magdalena
Duran, Rosario
Mira, Marcelo Távora
Pillonetto, Marcelo
Carvalho, Paulo Costa
dc.subject.en.en_US.fl_str_mv DiagnoMass
Polymyxins
Bacteria
Drug Resistance, Bacterial
topic DiagnoMass
Polymyxins
Bacteria
Drug Resistance, Bacterial
Polimixinas
Bacterias
Farmacorresistencia Bacteriana
Polymyxines
Bactéries
Résistance bactérienne aux médicaments
Polimixinas
Acinetobacter baumannii
Bactérias
Farmacorresistência Bacteriana
dc.subject.es.en_US.fl_str_mv Polimixinas
Bacterias
Farmacorresistencia Bacteriana
dc.subject.fr.en_US.fl_str_mv Polymyxines
Bactéries
Résistance bactérienne aux médicaments
dc.subject.decs.en_US.fl_str_mv Polimixinas
Acinetobacter baumannii
Bactérias
Farmacorresistência Bacteriana
description Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil / Pontificia Universidade Católica do Paraná. Laboratório Experimental Multiuso. Curitiba, PR, Brasil.
publishDate 2023
dc.date.accessioned.fl_str_mv 2023-11-06T16:52:21Z
dc.date.available.fl_str_mv 2023-11-06T16:52:21Z
dc.date.issued.fl_str_mv 2023
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 DAL LIN, Amanda et al. Beyond the identifiable proteome: Delving into the proteomics of polymyxin-resistant and non-resistant Acinetobacter baumannii from Brazilian hospitals. Journal of Proteomics. v. 289, n. 105012, p. 1-9, 2023.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/61032
dc.identifier.issn.en_US.fl_str_mv 1874-3919
dc.identifier.doi.none.fl_str_mv 10.1016/j.jprot.2023.105012
identifier_str_mv DAL LIN, Amanda et al. Beyond the identifiable proteome: Delving into the proteomics of polymyxin-resistant and non-resistant Acinetobacter baumannii from Brazilian hospitals. Journal of Proteomics. v. 289, n. 105012, p. 1-9, 2023.
1874-3919
10.1016/j.jprot.2023.105012
url https://www.arca.fiocruz.br/handle/icict/61032
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
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/61032/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/61032/2/1-s2.0-S1874391923002014-main.pdf
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repository.name.fl_str_mv Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)
repository.mail.fl_str_mv repositorio.arca@fiocruz.br
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