http://pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.htmlJohannes GrissVeit SchwämmleGoran VinterhalterJohannes Griss2025-06-192025-06-192018-10-171535-38931535-390710.1021/acs.jproteome.8b0096810.1101/446070https://ror.circle-u.eu/handle/123456789/1324460<jats:title>Abstract</jats:title><jats:p>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 analyse 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 or PDF 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.</jats:p>OPENProteomicsDatabases, FactualProteomeworkflowMalaria, CerebralMiceTandem Mass SpectrometryAnimalsprotocolProtProtocolsreproducibilityDockerReproducibility of ResultsbioinformaticsJupyteriTRAQIsotope LabelingTMTisobaric labelingSoftwarepublication0206 medical engineering02 engineering and technology03 medical and health sciences0303 health sciencesdoi_dedup___:f6f690bbe5bb1ff1988b978fff50c9f4PMC645686930855969