| Author | Santos, Marlon D. M. | |
| Author | Lima, Diogo B. | |
| Author | Fischer, Juliana S. G. | |
| Author | Clasen, Milan A. | |
| Author | Kurt, Louise U. | |
| Author | Andrade, Amanda Caroline Camillo | |
| Author | Monteiro, Leandro C. | |
| Author | Aquino, Priscila F. de | |
| Author | Ferreira, Ana G. C. Neves | |
| Author | Valente, Richard H. | |
| Author | Trugilho, Monique R. O. | |
| Author | Brunoro, Giselle V. F. | |
| Author | Souza, Tatiana A. C. B. | |
| Author | Santos, Renata M. | |
| Author | Batista, Michel | |
| Author | Gozzo, Fabio C. | |
| Author | Durán, Rosario | |
| Author | Yates III, John R. | |
| Author | Barbosa, Valmir C. | |
| Author | Carvalho, Paulo C. | |
| Access date | 2022-05-12T13:13:16Z | |
| Available date | 2022-05-12T13:13:16Z | |
| Document date | 2015 | |
| Citation | SANTOS, Marlon D. M. et al. Simple, efficient and thorough shotgun proteomic analysis with PatternLab V, Nature Protocols, v. 11, p. 102-117, 2015. | pt_BR |
| ISSN | 1754-2189 | pt_BR |
| URI | https://www.arca.fiocruz.br/handle/icict/52628 | |
| Language | eng | pt_BR |
| Publisher | Nature Protocols | pt_BR |
| Rights | open access | |
| Subject in Portuguese | Análise proteômica | pt_BR |
| Subject in Portuguese | Espingarda simples, eficiente e completa | pt_BR |
| Subject in Portuguese | PatternLab V | pt_BR |
| Title | Simple, efficient and thorough shotgun proteomic analysis with PatternLab V | pt_BR |
| Type | Article | |
| DOI | 10.1038/nprot.2015.133 | |
| Abstract | 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. | pt_BR |
| Affilliation | Fiocruz Paraná. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil. | pt_BR |
| Affilliation | Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP). Berlin, Germany. | pt_BR |
| Affilliation | Fiocruz Paraná. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil. | pt_BR |
| Affilliation | Fiocruz Paraná. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil. | pt_BR |
| Affilliation | Fiocruz Paraná. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil. | pt_BR |
| Affilliation | Fiocruz Paraná. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil. | pt_BR |
| Affilliation | Fiocruz Paraná. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil. | pt_BR |
| Affilliation | Fiocruz Amazonas. Instituto Leonidas e Maria Deane. Manaus, AM, Brasil. | pt_BR |
| Affilliation | Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. . Rio de Janeiro, RJ, Brasil. | pt_BR |
| Affilliation | Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. . Rio de Janeiro, RJ, Brasil. | pt_BR |
| Affilliation | 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. | pt_BR |
| Affilliation | Blau Farmacêutica S/A. Pesquisa e Desenvolvimento em Biotecnologia. Cotia, SP, Brasil. | pt_BR |
| Affilliation | Fiocruz Paraná. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil. | pt_BR |
| Affilliation | 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. | pt_BR |
| Affilliation | Fiocruz Paraná. Instituto Carlos Chagas. Instalação de espectrometria de massa. Curitiba, PR, Brasil. | pt_BR |
| Affilliation | Universidade de Campinas. Dalton Laboratório Espectrometria de Massa. Campinas, SP, Brasil. | pt_BR |
| Affilliation | Instituto Pasteur. Analytical Biochemistry and Proteomics Unit, Instituto de Investigaciones Biológicas Clemente Estable. MOntevideo, Uruguay. | pt_BR |
| Affilliation | Laboratory for Biological Mass Spectrometry, The Scripps Research Institute. La Jolla, CA, USA. | pt_BR |
| Affilliation | Universidade Federal do Rio de Janeiro. Programa de Engenharia de Sistemas e Ciência da Computação. Rio de Janeiro, RJ, Brasil. | pt_BR |
| Affilliation | Fiocruz Paraná. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil. | pt_BR |
| Subject | PatternLab V | pt_BR |
| Subject | Proteomic analysis | pt_BR |
| Subject | Simple, efficient and thorough shotgun | pt_BR |
