ProteoRE, a Galaxy-based infrastructure for visualizing and interpreting proteomics data.

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ProteoRE (Proteomics Research Environment) is a Galaxy-based platform for reproducibly analyzing proteomics and transcriptomics data in biomedical research. ProteoRE enables researchers to apply a wide range of bioinformatics tools and tailored workflows to their data using Galaxy's capabilities. It comprises a large set of tools for manipulating, visualizing, annotating, and conducting enrichment and pathway analyses, specifically designed for visualizing and interpreting MS-based proteomics results. The platform also incorporates Galaxy generic tools and select tools from the GalaxyP project for (re)processing MS-based proteomics data, such as peptide/protein identification. Using output files from quantitative proteomics software (e.g., MaxQuant, Proline) as input, ProteoRE's tools and interfaces facilitate : i. functional analysis of MS/MS proteomics samples, ii. interpretation of differentially expressed proteins, iii. selection of candidate proteomics biomarkers. As part of the Galaxy Training Network (GTN), ProteoRE offers publicly accessible online training resources (tutorials, datasets, recorded videos, and pre-prepared workflows) to help users learn and utilize the software tools and workflows. ProteoRE is freely accessible: https://proteore.org

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