New insights into functional regulation in MS-based drug profiling

Detalhes bibliográficos
Autor(a) principal: Carvalho, A.S.
Data de Publicação: 2016
Outros Autores: Molina, H., Matthiesen, Rune
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10400.18/3818
Resumo: We present a novel data analysis strategy which combined with subcellular fractionation and liquid chromatography-mass spectrometry (LC-MS) based proteomics provides a simple and effective workflow for global drug profiling. Five subcellular fractions were obtained by differential centrifugation followed by high resolution LC-MS and complete functional regulation analysis. The methodology combines functional regulation and enrichment analysis into a single visual summary. The workflow enables improved insight into perturbations caused by drugs. We provide a statistical argument to demonstrate that even crude subcellular fractions leads to improved functional characterization. We demonstrate this data analysis strategy on data obtained in a MS-based global drug profiling study. However, this strategy can also be performed on other types of large scale biological data.
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spelling New insights into functional regulation in MS-based drug profilingLC-MSProteomicsBiochemistryCell BiologyCancerComputational biology and bioinformaticsChromatography–mass SpectrometryGenomica FuncionalGenómica Funcional e EstruturalWe present a novel data analysis strategy which combined with subcellular fractionation and liquid chromatography-mass spectrometry (LC-MS) based proteomics provides a simple and effective workflow for global drug profiling. Five subcellular fractions were obtained by differential centrifugation followed by high resolution LC-MS and complete functional regulation analysis. The methodology combines functional regulation and enrichment analysis into a single visual summary. The workflow enables improved insight into perturbations caused by drugs. We provide a statistical argument to demonstrate that even crude subcellular fractions leads to improved functional characterization. We demonstrate this data analysis strategy on data obtained in a MS-based global drug profiling study. However, this strategy can also be performed on other types of large scale biological data.We thank Dr. Fridtjof Lund-Johansen for critical comments on the manuscript text. The Proteomics Resource Center at The Rockefeller University acknowledges funding from the Leona M. and Harry B. Helmsley Charitable Trust for mass spectrometer instrumentation. Cost of all experiments including MS analysis were supported by the Portuguese Foundation for Science and Technology (EXPL/DTP-PIC/0616/2013). R.M. is supported FCT investigator program 2012. A.S.C. is supported by the Portuguese Foundation for Science and Technology (FCT), financed by the European Social Funds (COMPETE-FEDER) and national funds of the Portuguese Ministry of Education and Science (POPH-QREN) fellowship SFRH/85569/2012.Nature Publishing GroupRepositório Científico do Instituto Nacional de SaúdeCarvalho, A.S.Molina, H.Matthiesen, Rune2016-05-24T16:33:03Z2016-01-082016-01-08T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.18/3818engSci Rep. 2016 Jan 8;6:18826. doi: 10.1038/srep188262045-2322doi: 10.1038/srep18826.info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-20T15:40:00Zoai:repositorio.insa.pt:10400.18/3818Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T18:38:38.680942Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv New insights into functional regulation in MS-based drug profiling
title New insights into functional regulation in MS-based drug profiling
spellingShingle New insights into functional regulation in MS-based drug profiling
Carvalho, A.S.
LC-MS
Proteomics
Biochemistry
Cell Biology
Cancer
Computational biology and bioinformatics
Chromatography–mass Spectrometry
Genomica Funcional
Genómica Funcional e Estrutural
title_short New insights into functional regulation in MS-based drug profiling
title_full New insights into functional regulation in MS-based drug profiling
title_fullStr New insights into functional regulation in MS-based drug profiling
title_full_unstemmed New insights into functional regulation in MS-based drug profiling
title_sort New insights into functional regulation in MS-based drug profiling
author Carvalho, A.S.
author_facet Carvalho, A.S.
Molina, H.
Matthiesen, Rune
author_role author
author2 Molina, H.
Matthiesen, Rune
author2_role author
author
dc.contributor.none.fl_str_mv Repositório Científico do Instituto Nacional de Saúde
dc.contributor.author.fl_str_mv Carvalho, A.S.
Molina, H.
Matthiesen, Rune
dc.subject.por.fl_str_mv LC-MS
Proteomics
Biochemistry
Cell Biology
Cancer
Computational biology and bioinformatics
Chromatography–mass Spectrometry
Genomica Funcional
Genómica Funcional e Estrutural
topic LC-MS
Proteomics
Biochemistry
Cell Biology
Cancer
Computational biology and bioinformatics
Chromatography–mass Spectrometry
Genomica Funcional
Genómica Funcional e Estrutural
description We present a novel data analysis strategy which combined with subcellular fractionation and liquid chromatography-mass spectrometry (LC-MS) based proteomics provides a simple and effective workflow for global drug profiling. Five subcellular fractions were obtained by differential centrifugation followed by high resolution LC-MS and complete functional regulation analysis. The methodology combines functional regulation and enrichment analysis into a single visual summary. The workflow enables improved insight into perturbations caused by drugs. We provide a statistical argument to demonstrate that even crude subcellular fractions leads to improved functional characterization. We demonstrate this data analysis strategy on data obtained in a MS-based global drug profiling study. However, this strategy can also be performed on other types of large scale biological data.
publishDate 2016
dc.date.none.fl_str_mv 2016-05-24T16:33:03Z
2016-01-08
2016-01-08T00:00:00Z
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.uri.fl_str_mv http://hdl.handle.net/10400.18/3818
url http://hdl.handle.net/10400.18/3818
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Sci Rep. 2016 Jan 8;6:18826. doi: 10.1038/srep18826
2045-2322
doi: 10.1038/srep18826.
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Nature Publishing Group
publisher.none.fl_str_mv Nature Publishing Group
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
repository.mail.fl_str_mv
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