We have employed a systematic approach to index raw metabolomics data across a diverse range of repositories, namely GNPS/MassIVE, NMDR, and MTBLS, by leveraging the capabilities of their API tools. To facilitate easy retrieval, each supported mass spectrometry file (.raw, .d, .wiff, .cdf, .mzML, and .mzXML) is indexed across all of these public resources and referenced by the MS Run Identifiers (MRI). To achieve this, we have utilized MRIs, a subset of the USI standard, to incorporate not only scans but also the dataset IDs and the file path, serving as a comprehensive unique identifier that enables access to all aforementioned repositories from the GNPS2 ecosystem. The service to translate MRIs to file paths is provided at . Ultimately, MRIs serve as a handle for the download of mass spectrometry files from any repository via a software package that has been implemented in multiple tools in the GNPS2 ecosystem including MassQL and Classical Molecular Networking. Notably, we developed tooling to convert the main proprietary mass spectrometry file formats (.cdf, .raw, .wiff, and .d) into the open mass spectrometry format .mzML . Files can be downloaded by users after a successful conversion.