Simple, efficient and thorough shotgun proteomic analysis with PatternLab V
| Autor(a) principal: | |
|---|---|
| Data de Publicação: | 2015 |
| 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/52628 |
Resumo: | Fiocruz Paraná. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil. |
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Santos, Marlon D. M.Lima, Diogo B.Fischer, Juliana S. G.Clasen, Milan A.Kurt, Louise U.Andrade, Amanda Caroline CamilloMonteiro, Leandro C.Aquino, Priscila F. deFerreira, Ana G. C. NevesValente, Richard H.Trugilho, Monique R. O.Brunoro, Giselle V. F.Souza, Tatiana A. C. B.Santos, Renata M.Batista, MichelGozzo, Fabio C.Durán, RosarioYates III, John R.Barbosa, Valmir C.Carvalho, Paulo C.2022-05-12T13:13:16Z2022-05-12T13:13:16Z2015SANTOS, Marlon D. M. et al. Simple, efficient and thorough shotgun proteomic analysis with PatternLab V, Nature Protocols, v. 11, p. 102-117, 2015.1754-2189https://www.arca.fiocruz.br/handle/icict/5262810.1038/nprot.2015.133engNature ProtocolsAnálise proteômicaEspingarda simples, eficiente e completaPatternLab VPatternLab VProteomic analysisSimple, efficient and thorough shotgunSimple, efficient and thorough shotgun proteomic analysis with PatternLab Vinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFiocruz Paraná. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP). Berlin, Germany.Fiocruz Paraná. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.Fiocruz Paraná. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.Fiocruz Paraná. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.Fiocruz Paraná. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.Fiocruz Paraná. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.Fiocruz Amazonas. Instituto Leonidas e Maria Deane. Manaus, AM, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. . Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. . Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. . Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Centro de Desenvolvimento Tecnológico em Saúde. Rio de Janeiro, RJ, Brasil.Blau Farmacêutica S/A. Pesquisa e Desenvolvimento em Biotecnologia. Cotia, SP, Brasil.Fiocruz Paraná. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.Fiocruz Paraná. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil / Universidade Federal do Rio de Janeiro. Instituto de Química. Rio de Janeiro, RJ, Brasil.Fiocruz Paraná. Instituto Carlos Chagas. Instalação de espectrometria de massa. Curitiba, PR, Brasil.Universidade de Campinas. Dalton Laboratório Espectrometria de Massa. Campinas, SP, Brasil.Instituto Pasteur. Analytical Biochemistry and Proteomics Unit, Instituto de Investigaciones Biológicas Clemente Estable. MOntevideo, Uruguay.Laboratory for Biological Mass Spectrometry, The Scripps Research Institute. La Jolla, CA, USA.Universidade Federal do Rio de Janeiro. Programa de Engenharia de Sistemas e Ciência da Computação. Rio de Janeiro, RJ, Brasil.Fiocruz Paraná. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.Shotgun proteomics aims to identify and quantify the thousands of proteins in complex mixtures such as cell and tissue lysates and biological fluids. This approach uses liquid chromatography coupled with tandem mass spectrometry and typically generates hundreds of thousands of mass spectra that require specialized computational environments for data analysis. PatternLab for proteomics is a unified computational environment for analyzing shotgun proteomic data. PatternLab V (PLV) is the most comprehensive and crucial update so far, the result of intensive interaction with the proteomics community over several years. All PLV modules have been optimized and its graphical user interface has been completely updated for improved user experience. Major improvements were made to all aspects of the software, ranging from boosting the number of protein identifications to faster extraction of ion chromatograms. PLV provides modules for preparing sequence databases, protein identification, statistical filtering and in-depth result browsing for both labeled and label-free quantitation. The PepExplorer module can even pinpoint de novo sequenced peptides not already present in the database. PLV is of broad applicability and therefore suitable for challenging experimental setups, such as time-course experiments and data handling from unsequenced organisms. PLV interfaces with widely adopted software and community initiatives, e.g., Comet, Skyline, PEAKS and PRIDE. It is freely available at http://www.patternlab forproteomics.org.info: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/52628/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALMoniqueTrujilo_AnaNevesFerreira_etal_IOC_2022.pdfMoniqueTrujilo_AnaNevesFerreira_etal_IOC_2022.pdfapplication/pdf6469494https://www.arca.fiocruz.br/bitstream/icict/52628/2/MoniqueTrujilo_AnaNevesFerreira_etal_IOC_2022.pdfa308e019f854427a42195de883d9e827MD52icict/526282022-05-12 10:13:16.141oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352022-05-12T13:13:16Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false |
| dc.title.pt_BR.fl_str_mv |
Simple, efficient and thorough shotgun proteomic analysis with PatternLab V |
| title |
Simple, efficient and thorough shotgun proteomic analysis with PatternLab V |
| spellingShingle |
Simple, efficient and thorough shotgun proteomic analysis with PatternLab V Santos, Marlon D. M. Análise proteômica Espingarda simples, eficiente e completa PatternLab V PatternLab V Proteomic analysis Simple, efficient and thorough shotgun |
| title_short |
Simple, efficient and thorough shotgun proteomic analysis with PatternLab V |
| title_full |
Simple, efficient and thorough shotgun proteomic analysis with PatternLab V |
| title_fullStr |
Simple, efficient and thorough shotgun proteomic analysis with PatternLab V |
| title_full_unstemmed |
Simple, efficient and thorough shotgun proteomic analysis with PatternLab V |
| title_sort |
Simple, efficient and thorough shotgun proteomic analysis with PatternLab V |
| author |
Santos, Marlon D. M. |
| author_facet |
Santos, Marlon D. M. Lima, Diogo B. Fischer, Juliana S. G. Clasen, Milan A. Kurt, Louise U. Andrade, Amanda Caroline Camillo Monteiro, Leandro C. Aquino, Priscila F. de Ferreira, Ana G. C. Neves Valente, Richard H. Trugilho, Monique R. O. Brunoro, Giselle V. F. Souza, Tatiana A. C. B. Santos, Renata M. Batista, Michel Gozzo, Fabio C. Durán, Rosario Yates III, John R. Barbosa, Valmir C. Carvalho, Paulo C. |
| author_role |
author |
| author2 |
Lima, Diogo B. Fischer, Juliana S. G. Clasen, Milan A. Kurt, Louise U. Andrade, Amanda Caroline Camillo Monteiro, Leandro C. Aquino, Priscila F. de Ferreira, Ana G. C. Neves Valente, Richard H. Trugilho, Monique R. O. Brunoro, Giselle V. F. Souza, Tatiana A. C. B. Santos, Renata M. Batista, Michel Gozzo, Fabio C. Durán, Rosario Yates III, John R. Barbosa, Valmir C. Carvalho, Paulo C. |
| author2_role |
author author author author author author author author author author author author author author author author author author author |
| dc.contributor.author.fl_str_mv |
Santos, Marlon D. M. Lima, Diogo B. Fischer, Juliana S. G. Clasen, Milan A. Kurt, Louise U. Andrade, Amanda Caroline Camillo Monteiro, Leandro C. Aquino, Priscila F. de Ferreira, Ana G. C. Neves Valente, Richard H. Trugilho, Monique R. O. Brunoro, Giselle V. F. Souza, Tatiana A. C. B. Santos, Renata M. Batista, Michel Gozzo, Fabio C. Durán, Rosario Yates III, John R. Barbosa, Valmir C. Carvalho, Paulo C. |
| dc.subject.other.pt_BR.fl_str_mv |
Análise proteômica Espingarda simples, eficiente e completa PatternLab V |
| topic |
Análise proteômica Espingarda simples, eficiente e completa PatternLab V PatternLab V Proteomic analysis Simple, efficient and thorough shotgun |
| dc.subject.en.pt_BR.fl_str_mv |
PatternLab V Proteomic analysis Simple, efficient and thorough shotgun |
| description |
Fiocruz Paraná. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil. |
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2015 |
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2015 |
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2022-05-12T13:13:16Z |
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2022-05-12T13:13:16Z |
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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. Simple, efficient and thorough shotgun proteomic analysis with PatternLab V, Nature Protocols, v. 11, p. 102-117, 2015. |
| dc.identifier.uri.fl_str_mv |
https://www.arca.fiocruz.br/handle/icict/52628 |
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1754-2189 |
| dc.identifier.doi.none.fl_str_mv |
10.1038/nprot.2015.133 |
| identifier_str_mv |
SANTOS, Marlon D. M. et al. Simple, efficient and thorough shotgun proteomic analysis with PatternLab V, Nature Protocols, v. 11, p. 102-117, 2015. 1754-2189 10.1038/nprot.2015.133 |
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Nature Protocols |
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Nature Protocols |
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