PatternLab V handles multiplex spectra in shotgun proteomic searches and increases identification
| 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/57829 https://doi.org/10.1021/jasms.3c00063 |
Resumo: | Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil. |
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Clasen, Milan A.Santos, Marlon D. M.Kurt, Louise UlrichFischer, JulianaCamillo-Andrade, Amanda C.Sales, Lucas AlbuquerqueSouza, Tatiana de Arruda Campos Brasil deLima, Diogo BorgesGozzo, Fabio C.Valente, Richard HemmiDuran, RosarioBarbosa, Valmir C.Carvalho, Paulo Costa2023-04-17T17:41:43Z2023-04-17T17:41:43Z2023CLASEN, Milan A. et al. PatternLab V handles multiplex spectra in shotgun proteomic searches and increases identification. Journal of the American Society for Mass Spectrometry, p. 1-3, 2023.1879-1123https://www.arca.fiocruz.br/handle/icict/57829https://doi.org/10.1021/jasms.3c00063porAmerican Chemical SocietyPatternLab VProteomicsProteinsPeptidesProteómicaProteínasPéptidosProtéomiqueProtéinesPeptidesProteômicaProteínasPeptídeosPatternLab V handles multiplex spectra in shotgun proteomic searches and increases identificationinfo: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.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.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.Department of Structural Biology. Leibniz Forschungsinstitut für Molekulare Pharmakologie. Berlin, Germany.Universidade Estadual de Campinas. Dalton Mass Spectrometry Laboratory. Campinas, SP, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. Rio de Janeiro, RJ, Brasil.Analytical Biochemistry and Proteomics Unit. Institut Pasteur de Montevideo. Montevideo, Uruguay.Universidade Federal do Rio de Janeiro. Programa de Engenharia de Sistemas e Computação. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.Complex protein mixtures typically generate many tandem mass spectra produced by different peptides coisolated in the gas phase. Widely adopted proteomic data analysis environments usually fail to identify most of these spectra, succeeding at best in identifying only one of the multiple cofragmenting peptides. We present PatternLab V (PLV), an updated version of PatternLab that integrates the YADA 3 deconvolution algorithm to handle such cases efficiently. In general, we expect an increase of 10% in spectral identifications when dealing with complex proteomic samples.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZORIGINALjasms.3c00063OK.pdfjasms.3c00063OK.pdfapplication/pdf2282815https://www.arca.fiocruz.br/bitstream/icict/57829/2/jasms.3c00063OK.pdf7fe4f2e7db3bf79d9cdffa4dc4168ca4MD52LICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/57829/1/license.txt5a560609d32a3863062d77ff32785d58MD51icict/578292023-04-17 14:41:44.608oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352023-04-17T17:41:44Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false |
| dc.title.en_US.fl_str_mv |
PatternLab V handles multiplex spectra in shotgun proteomic searches and increases identification |
| title |
PatternLab V handles multiplex spectra in shotgun proteomic searches and increases identification |
| spellingShingle |
PatternLab V handles multiplex spectra in shotgun proteomic searches and increases identification Clasen, Milan A. PatternLab V Proteomics Proteins Peptides Proteómica Proteínas Péptidos Protéomique Protéines Peptides Proteômica Proteínas Peptídeos |
| title_short |
PatternLab V handles multiplex spectra in shotgun proteomic searches and increases identification |
| title_full |
PatternLab V handles multiplex spectra in shotgun proteomic searches and increases identification |
| title_fullStr |
PatternLab V handles multiplex spectra in shotgun proteomic searches and increases identification |
| title_full_unstemmed |
PatternLab V handles multiplex spectra in shotgun proteomic searches and increases identification |
| title_sort |
PatternLab V handles multiplex spectra in shotgun proteomic searches and increases identification |
| author |
Clasen, Milan A. |
| author_facet |
Clasen, Milan A. Santos, Marlon D. M. Kurt, Louise Ulrich Fischer, Juliana Camillo-Andrade, Amanda C. Sales, Lucas Albuquerque Souza, Tatiana de Arruda Campos Brasil de Lima, Diogo Borges Gozzo, Fabio C. Valente, Richard Hemmi Duran, Rosario Barbosa, Valmir C. Carvalho, Paulo Costa |
| author_role |
author |
| author2 |
Santos, Marlon D. M. Kurt, Louise Ulrich Fischer, Juliana Camillo-Andrade, Amanda C. Sales, Lucas Albuquerque Souza, Tatiana de Arruda Campos Brasil de Lima, Diogo Borges Gozzo, Fabio C. Valente, Richard Hemmi Duran, Rosario Barbosa, Valmir C. Carvalho, Paulo Costa |
| author2_role |
author author author author author author author author author author author author |
| dc.contributor.author.fl_str_mv |
Clasen, Milan A. Santos, Marlon D. M. Kurt, Louise Ulrich Fischer, Juliana Camillo-Andrade, Amanda C. Sales, Lucas Albuquerque Souza, Tatiana de Arruda Campos Brasil de Lima, Diogo Borges Gozzo, Fabio C. Valente, Richard Hemmi Duran, Rosario Barbosa, Valmir C. Carvalho, Paulo Costa |
| dc.subject.other.en_US.fl_str_mv |
PatternLab V |
| topic |
PatternLab V Proteomics Proteins Peptides Proteómica Proteínas Péptidos Protéomique Protéines Peptides Proteômica Proteínas Peptídeos |
| dc.subject.en.en_US.fl_str_mv |
Proteomics Proteins Peptides |
| dc.subject.es.en_US.fl_str_mv |
Proteómica Proteínas Péptidos |
| dc.subject.fr.en_US.fl_str_mv |
Protéomique Protéines Peptides |
| dc.subject.decs.en_US.fl_str_mv |
Proteômica Proteínas Peptídeos |
| description |
Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil. |
| publishDate |
2023 |
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2023-04-17T17:41:43Z |
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2023-04-17T17:41:43Z |
| dc.date.issued.fl_str_mv |
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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| dc.identifier.citation.fl_str_mv |
CLASEN, Milan A. et al. PatternLab V handles multiplex spectra in shotgun proteomic searches and increases identification. Journal of the American Society for Mass Spectrometry, p. 1-3, 2023. |
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https://www.arca.fiocruz.br/handle/icict/57829 |
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1879-1123 |
| dc.identifier.doi.none.fl_str_mv |
https://doi.org/10.1021/jasms.3c00063 |
| identifier_str_mv |
CLASEN, Milan A. et al. PatternLab V handles multiplex spectra in shotgun proteomic searches and increases identification. Journal of the American Society for Mass Spectrometry, p. 1-3, 2023. 1879-1123 |
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https://www.arca.fiocruz.br/handle/icict/57829 https://doi.org/10.1021/jasms.3c00063 |
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American Chemical Society |
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American Chemical Society |
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