We developed a set of command-line Python tools, reproducible Nextflow workflows, web infrastructure as application programming interfaces (APIs), and user interfaces. At the heart of this ecosystem, the web infrastructure periodically aggregates and harmonizes metadata (into controlled ontologies ) from all supported repositories. Additionally, all raw data files are indexed and made downloadable via MS Run Identifiers (MRI), a subset of the Universal Spectrum Identifiers (USI) . Finally, all data and metadata are integrated into the Pan-ReDU search engine which is the data portal for the community to find data, download data, and/or co-analyze data across multiple data repositories. This lays the foundations to facilitate fragmentation spectra (MS/MS) searches across all supported repositories. Overall, the Pan-ReDU effort has grown the number of datafiles in ReDU-compatible harmonized metadata format from ~54,800 to >605,000 (>1100% increase, Figure ).. Briefly, all supported metabolomics raw data formats (.mzML, .mzXML, .raw, .wiff, .cdf, and .d) that could be associated with sufficient metadata [meaning that at least one piece of sample-specific metadata was available (e.g., analyzed organism or body part)] were added to Pan-ReDU. At the time of this work, 04/2024, MTBLS made up 39% of Pan-ReDU compatible raw data, representing ~95% of MTBLS supported raw data; NMDR made up 42% representing ~67% of raw data in NMDR; and GNPS contributed 19% representing ~15% of all GNPS raw data that had Pan-ReDU compatible metadata. Although the three repositories have some overlap between the communities they serve, they do reach different audiences with different preferences regarding sample types and data acquisition modes (Figure ). NMDR, funded by the National Institutes of Health (NIH), supports data deposition of clinical studies and contributed the majority (73%) of human plasma/blood data to Pan-ReDU. This data is often collected without MS/MS spectra for untargeted discoveries (Figure ). MTBLS showed similar proportions of raw data regarding MS/MS spectra and is a global general-purpose metabolomics repository, while GNPS/MassIVE serves a worldwide community that uses mainly untargeted MS/MS-based metabolomics (Figure ), often to discover novel natural products and microbiome-derived molecules. This is reflected in GNPS/MassIVE having the largest diversity of represented organisms (Figure ). Overall, these three repositories complement each other with diverse sample types as well as analyzed body parts within the same organisms (Figure ).