DiagnoMass: A proteomics hub for pinpointing discriminative spectral clusters
| Autor(a) principal: | |
|---|---|
| Data de Publicação: | 2023 |
| 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/57700 https://doi.org/10.1016/j.jprot.2023.104853 |
Resumo: | Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil. |
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Santos, Marlon D.M.Camillo-Andrade, Amanda C.Lima, Diogo B.Souza, Tatiana de Arruda Campos Brasil deFischer, Juliana de Saldanha da GamaValente, Richard H.Gozzo, Fabio C.Barbosa, Valmir C.Batthyany, CarlosChamot-Rooke, JuliaDuran, RosarioCarvalho, Paulo Costa2023-04-06T16:33:12Z2023-04-06T16:33:12Z2023SANTOS, Marlon D. M. et al. DiagnoMass: A proteomics hub for pinpointing discriminative spectral clusters. Journal of Proteomics, v. 277, n. 104853, p. 1–3, 2023.1874-3919https://www.arca.fiocruz.br/handle/icict/57700https://doi.org/10.1016/j.jprot.2023.104853porElsevierDiagnoMass: A proteomics hub for pinpointing discriminative spectral clustersinfo: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.Department of Structural Biology. Leibniz - Forschungsinstitut für Molekulare Pharmakologie. Berlin, Germany.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 Oswaldo Cruz. Laboratório de Toxinologia. Rio de Janeiro, RJ, Brasil.Universidade de Campinas. Campinas, SP, Brasil.Universidade Federal do Rio de Janeiro. Programa de Engenharia de Sistemas e Computação. Rio de Janeiro, RJ, Brasil.Analytical Biochemistry and Proteomics Unit. Institut Pasteur de Montevideo. Montevideo, Uruguay.Institut Pasteur. University de Paris Cité. Mass Spectrometry for Biology. Paris, France.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.There are several well-established paradigms for identifying and pinpointing discriminative peptides/ proteins using shotgun proteomic data; examples are peptide-spectrum matching, de novo sequencing, open searches, and even hybrid approaches. Such an arsenal of complementary paradigms can provide deep data coverage, albeit some unidentified discriminative peptides remain. We present DiagnoMass, software tool that groups similar spectra into spectral clusters and then shortlists those clusters that are discriminative for biological conditions. DiagnoMass then communicates with proteomic tools to attempt the identification of such clusters. We demonstrate the effectiveness of DiagnoMass by analyzing proteomic data from Escherichia coli, Salmonella, and Shigella, listing many high-quality discriminative spectral clusters that had thus far remained unidentified by widely adopted proteomic tools. DiagnoMass can also classify proteomic profiles. We anticipate the use of DiagnoMass as a vital tool for pinpointing biomarkers.PeptidesProteinsBiomarkersProteomicsPeptídeosProteínasBiomarcadoresProteômicainfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZORIGINAL1-s2.0-S1874391923000428-main.pdf1-s2.0-S1874391923000428-main.pdfapplication/pdf714631https://www.arca.fiocruz.br/bitstream/icict/57700/2/1-s2.0-S1874391923000428-main.pdf22770dc383e3682d1812e607419111faMD52LICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/57700/1/license.txt5a560609d32a3863062d77ff32785d58MD51icict/577002023-04-06 13:33:14.323oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352023-04-06T16:33:14Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false |
| dc.title.en_US.fl_str_mv |
DiagnoMass: A proteomics hub for pinpointing discriminative spectral clusters |
| title |
DiagnoMass: A proteomics hub for pinpointing discriminative spectral clusters |
| spellingShingle |
DiagnoMass: A proteomics hub for pinpointing discriminative spectral clusters Santos, Marlon D.M. Peptides Proteins Biomarkers Proteomics Peptídeos Proteínas Biomarcadores Proteômica |
| title_short |
DiagnoMass: A proteomics hub for pinpointing discriminative spectral clusters |
| title_full |
DiagnoMass: A proteomics hub for pinpointing discriminative spectral clusters |
| title_fullStr |
DiagnoMass: A proteomics hub for pinpointing discriminative spectral clusters |
| title_full_unstemmed |
DiagnoMass: A proteomics hub for pinpointing discriminative spectral clusters |
| title_sort |
DiagnoMass: A proteomics hub for pinpointing discriminative spectral clusters |
| author |
Santos, Marlon D.M. |
| author_facet |
Santos, Marlon D.M. Camillo-Andrade, Amanda C. Lima, Diogo B. Souza, Tatiana de Arruda Campos Brasil de Fischer, Juliana de Saldanha da Gama Valente, Richard H. Gozzo, Fabio C. Barbosa, Valmir C. Batthyany, Carlos Chamot-Rooke, Julia Duran, Rosario Carvalho, Paulo Costa |
| author_role |
author |
| author2 |
Camillo-Andrade, Amanda C. Lima, Diogo B. Souza, Tatiana de Arruda Campos Brasil de Fischer, Juliana de Saldanha da Gama Valente, Richard H. Gozzo, Fabio C. Barbosa, Valmir C. Batthyany, Carlos Chamot-Rooke, Julia Duran, Rosario Carvalho, Paulo Costa |
| author2_role |
author author author author author author author author author author author |
| dc.contributor.author.fl_str_mv |
Santos, Marlon D.M. Camillo-Andrade, Amanda C. Lima, Diogo B. Souza, Tatiana de Arruda Campos Brasil de Fischer, Juliana de Saldanha da Gama Valente, Richard H. Gozzo, Fabio C. Barbosa, Valmir C. Batthyany, Carlos Chamot-Rooke, Julia Duran, Rosario Carvalho, Paulo Costa |
| dc.subject.en.en_US.fl_str_mv |
Peptides Proteins Biomarkers Proteomics |
| topic |
Peptides Proteins Biomarkers Proteomics Peptídeos Proteínas Biomarcadores Proteômica |
| dc.subject.decs.en_US.fl_str_mv |
Peptídeos Proteínas Biomarcadores Proteômica |
| description |
Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil. |
| publishDate |
2023 |
| dc.date.accessioned.fl_str_mv |
2023-04-06T16:33:12Z |
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2023-04-06T16:33:12Z |
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2023 |
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info:eu-repo/semantics/publishedVersion |
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info:eu-repo/semantics/article |
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article |
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publishedVersion |
| dc.identifier.citation.fl_str_mv |
SANTOS, Marlon D. M. et al. DiagnoMass: A proteomics hub for pinpointing discriminative spectral clusters. Journal of Proteomics, v. 277, n. 104853, p. 1–3, 2023. |
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https://www.arca.fiocruz.br/handle/icict/57700 |
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1874-3919 |
| dc.identifier.doi.none.fl_str_mv |
https://doi.org/10.1016/j.jprot.2023.104853 |
| identifier_str_mv |
SANTOS, Marlon D. M. et al. DiagnoMass: A proteomics hub for pinpointing discriminative spectral clusters. Journal of Proteomics, v. 277, n. 104853, p. 1–3, 2023. 1874-3919 |
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https://www.arca.fiocruz.br/handle/icict/57700 https://doi.org/10.1016/j.jprot.2023.104853 |
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