DiagnoTop: A computational pipeline for discriminating bacterial pathogens without database search
Autor(a) principal: | |
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Data de Publicação: | 2021 |
Outros Autores: | , , , |
Tipo de documento: | Artigo |
Idioma: | por |
Título da fonte: | Repositório Institucional da FIOCRUZ (ARCA) |
Texto Completo: | https://www.arca.fiocruz.br/handle/icict/47063 |
Resumo: | Mass Spectrometry for Biology Unit. Institut Pasteur. Paris, France. |
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Lima, Diogo BorgesDupré, MathieuSantos, Marlon Dias MarianoCarvalho, Paulo CostaChamot-Rooke, Julia2021-05-05T20:28:59Z2021-05-05T20:28:59Z2021LIMA, Diogo Borges et al. DiagnoTop: A computational pipeline for discriminating bacterial pathogens without database search. Scientific Reports, p. 1–5, 2021.1879-1123https://www.arca.fiocruz.br/handle/icict/4706310.1021/jasms.1c00014porAmerican Chemical SocietyDiagnoTop: A computational pipeline for discriminating bacterial pathogens without database searchinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleMass Spectrometry for Biology Unit. Institut Pasteur. Paris, France.Mass Spectrometry for Biology Unit. Institut Pasteur. Paris, France.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.Mass Spectrometry for Biology Unit. Institut Pasteur. Paris, France.Pathogen identification is crucial to confirm bacterial infections and guide antimicrobial therapy. Although MALDI-TOF mass spectrometry (MS) serves as foundation for tools that enable rapid microbial identification, some bacteria remain challenging to identify. We recently showed that top-down proteomics (TDP) could be used to discriminate closely related enterobacterial pathogens (Escherichia coli, Shigella, and Salmonella) that are indistinguishable with tools rooted in the MALDI-TOF MS approach. Current TDP diagnostic relies on the identification of specific proteoforms for each species through a database search. However, microbial proteomes are often poorly annotated, which complicates the large-scale identification of proteoforms and leads to many unidentified high-quality mass spectra. Here, we describe a new computational pipeline called DiagnoTop that lists discriminative spectral clusters found in TDP data sets that can be used for microbial diagnostics without database search. Applied to our enterobacterial TDP data sets, DiagnoTop could easily shortlist highquality discriminative spectral clusters, leading to increased diagnostic power. This pipeline opens new perspectives in clinical microbiology and biomarker discovery using TDP.ProteomicsEnterobacteriaceae InfectionsClinical DiagnosisProteómicaInfecciones por EnterobacteriaceaeDiagnóstico ClínicoProtéomiqueInfections à EnterobacteriaceaeDiagnostic CliniqueProteômicaInfecções por EnterobacteriaceaeDiagnóstico Clínicoinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-83084https://www.arca.fiocruz.br/bitstream/icict/47063/1/license.txt783568c2893d2e25a99990b126be1772MD51ORIGINALjasms.1c000ok.pdfjasms.1c000ok.pdfapplication/pdf1104212https://www.arca.fiocruz.br/bitstream/icict/47063/2/jasms.1c000ok.pdf28f622e3318367f06f76289e00cdbe20MD52TEXTjasms.1c000ok.pdf.txtjasms.1c000ok.pdf.txtExtracted 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dc.title.pt_BR.fl_str_mv |
DiagnoTop: A computational pipeline for discriminating bacterial pathogens without database search |
title |
DiagnoTop: A computational pipeline for discriminating bacterial pathogens without database search |
spellingShingle |
DiagnoTop: A computational pipeline for discriminating bacterial pathogens without database search Lima, Diogo Borges Proteomics Enterobacteriaceae Infections Clinical Diagnosis Proteómica Infecciones por Enterobacteriaceae Diagnóstico Clínico Protéomique Infections à Enterobacteriaceae Diagnostic Clinique Proteômica Infecções por Enterobacteriaceae Diagnóstico Clínico |
title_short |
DiagnoTop: A computational pipeline for discriminating bacterial pathogens without database search |
title_full |
DiagnoTop: A computational pipeline for discriminating bacterial pathogens without database search |
title_fullStr |
DiagnoTop: A computational pipeline for discriminating bacterial pathogens without database search |
title_full_unstemmed |
DiagnoTop: A computational pipeline for discriminating bacterial pathogens without database search |
title_sort |
DiagnoTop: A computational pipeline for discriminating bacterial pathogens without database search |
author |
Lima, Diogo Borges |
author_facet |
Lima, Diogo Borges Dupré, Mathieu Santos, Marlon Dias Mariano Carvalho, Paulo Costa Chamot-Rooke, Julia |
author_role |
author |
author2 |
Dupré, Mathieu Santos, Marlon Dias Mariano Carvalho, Paulo Costa Chamot-Rooke, Julia |
author2_role |
author author author author |
dc.contributor.author.fl_str_mv |
Lima, Diogo Borges Dupré, Mathieu Santos, Marlon Dias Mariano Carvalho, Paulo Costa Chamot-Rooke, Julia |
dc.subject.en.pt_BR.fl_str_mv |
Proteomics Enterobacteriaceae Infections Clinical Diagnosis |
topic |
Proteomics Enterobacteriaceae Infections Clinical Diagnosis Proteómica Infecciones por Enterobacteriaceae Diagnóstico Clínico Protéomique Infections à Enterobacteriaceae Diagnostic Clinique Proteômica Infecções por Enterobacteriaceae Diagnóstico Clínico |
dc.subject.es.pt_BR.fl_str_mv |
Proteómica Infecciones por Enterobacteriaceae Diagnóstico Clínico |
dc.subject.fr.pt_BR.fl_str_mv |
Protéomique Infections à Enterobacteriaceae Diagnostic Clinique |
dc.subject.decs.pt_BR.fl_str_mv |
Proteômica Infecções por Enterobacteriaceae Diagnóstico Clínico |
description |
Mass Spectrometry for Biology Unit. Institut Pasteur. Paris, France. |
publishDate |
2021 |
dc.date.accessioned.fl_str_mv |
2021-05-05T20:28:59Z |
dc.date.available.fl_str_mv |
2021-05-05T20:28:59Z |
dc.date.issued.fl_str_mv |
2021 |
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 |
LIMA, Diogo Borges et al. DiagnoTop: A computational pipeline for discriminating bacterial pathogens without database search. Scientific Reports, p. 1–5, 2021. |
dc.identifier.uri.fl_str_mv |
https://www.arca.fiocruz.br/handle/icict/47063 |
dc.identifier.issn.pt_BR.fl_str_mv |
1879-1123 |
dc.identifier.doi.none.fl_str_mv |
10.1021/jasms.1c00014 |
identifier_str_mv |
LIMA, Diogo Borges et al. DiagnoTop: A computational pipeline for discriminating bacterial pathogens without database search. Scientific Reports, p. 1–5, 2021. 1879-1123 10.1021/jasms.1c00014 |
url |
https://www.arca.fiocruz.br/handle/icict/47063 |
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por |
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por |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
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openAccess |
dc.publisher.none.fl_str_mv |
American Chemical Society |
publisher.none.fl_str_mv |
American Chemical Society |
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