DiagnoTop: A computational pipeline for discriminating bacterial pathogens without database search

Detalhes bibliográficos
Autor(a) principal: Lima, Diogo Borges
Data de Publicação: 2021
Outros Autores: Dupré, Mathieu, Santos, Marlon Dias Mariano, Carvalho, Paulo Costa, Chamot-Rooke, Julia
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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spelling 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
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 American Chemical Society
publisher.none.fl_str_mv American Chemical Society
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
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institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
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