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IsoProt: A Complete and Reproducible Workflow To Analyze iTRAQ/TMT Experiments

[Image: see text] Reproducibility has become a major concern in biomedical research. In proteomics, bioinformatic workflows can quickly consist of multiple software tools each with its own set of parameters. Their usage involves the definition of often hundreds of parameters as well as data operatio...

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Autores principales: Griss, Johannes, Vinterhalter, Goran, Schwämmle, Veit
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2019
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456869/
https://www.ncbi.nlm.nih.gov/pubmed/30855969
http://dx.doi.org/10.1021/acs.jproteome.8b00968
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author Griss, Johannes
Vinterhalter, Goran
Schwämmle, Veit
author_facet Griss, Johannes
Vinterhalter, Goran
Schwämmle, Veit
author_sort Griss, Johannes
collection PubMed
description [Image: see text] Reproducibility has become a major concern in biomedical research. In proteomics, bioinformatic workflows can quickly consist of multiple software tools each with its own set of parameters. Their usage involves the definition of often hundreds of parameters as well as data operations to ensure tool interoperability. Hence, a manuscript’s methods section is often insufficient to completely describe and reproduce a data analysis workflow. Here we present IsoProt: A complete and reproducible bioinformatic workflow deployed on a portable container environment to analyze data from isobarically labeled, quantitative proteomics experiments. The workflow uses only open source tools and provides a user-friendly and interactive browser interface to configure and execute the different operations. Once the workflow is executed, the results including the R code to perform statistical analyses can be downloaded as an HTML document providing a complete record of the performed analyses. IsoProt therefore represents a reproducible bioinformatics workflow that will yield identical results on any computer platform.
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spelling pubmed-64568692019-04-11 IsoProt: A Complete and Reproducible Workflow To Analyze iTRAQ/TMT Experiments Griss, Johannes Vinterhalter, Goran Schwämmle, Veit J Proteome Res [Image: see text] Reproducibility has become a major concern in biomedical research. In proteomics, bioinformatic workflows can quickly consist of multiple software tools each with its own set of parameters. Their usage involves the definition of often hundreds of parameters as well as data operations to ensure tool interoperability. Hence, a manuscript’s methods section is often insufficient to completely describe and reproduce a data analysis workflow. Here we present IsoProt: A complete and reproducible bioinformatic workflow deployed on a portable container environment to analyze data from isobarically labeled, quantitative proteomics experiments. The workflow uses only open source tools and provides a user-friendly and interactive browser interface to configure and execute the different operations. Once the workflow is executed, the results including the R code to perform statistical analyses can be downloaded as an HTML document providing a complete record of the performed analyses. IsoProt therefore represents a reproducible bioinformatics workflow that will yield identical results on any computer platform. American Chemical Society 2019-03-11 2019-04-05 /pmc/articles/PMC6456869/ /pubmed/30855969 http://dx.doi.org/10.1021/acs.jproteome.8b00968 Text en Copyright © 2019 American Chemical Society This is an open access article published under a Creative Commons Attribution (CC-BY) License (http://pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html) , which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited.
spellingShingle Griss, Johannes
Vinterhalter, Goran
Schwämmle, Veit
IsoProt: A Complete and Reproducible Workflow To Analyze iTRAQ/TMT Experiments
title IsoProt: A Complete and Reproducible Workflow To Analyze iTRAQ/TMT Experiments
title_full IsoProt: A Complete and Reproducible Workflow To Analyze iTRAQ/TMT Experiments
title_fullStr IsoProt: A Complete and Reproducible Workflow To Analyze iTRAQ/TMT Experiments
title_full_unstemmed IsoProt: A Complete and Reproducible Workflow To Analyze iTRAQ/TMT Experiments
title_short IsoProt: A Complete and Reproducible Workflow To Analyze iTRAQ/TMT Experiments
title_sort isoprot: a complete and reproducible workflow to analyze itraq/tmt experiments
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456869/
https://www.ncbi.nlm.nih.gov/pubmed/30855969
http://dx.doi.org/10.1021/acs.jproteome.8b00968
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