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

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.