Beyond the identifiable proteome: delving into the proteomics of polymyxin-resistant and non-resistant acinetobacter baumannii from Brazilian hospitals
Autor(a) principal: | |
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Data de Publicação: | 2023 |
Outros Autores: | , , , , , , , , , , , |
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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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 |
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eng |
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eng |
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info:eu-repo/semantics/openAccess |
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openAccess |
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Elsevier |
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Elsevier |
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