Rapid dereplication of small molecules by high-resolution mass spectrometry (HRMS) relies on efficiently connecting experimental spectral data with information available across chemical databases. However, many existing databases provide limited support for direct m/z-based searches and integrated spectral analysis. To address this challenge, we developed OctoChemDB, an open-source platform that aggregates and harmonizes chemical, biological, and mass spectrometry data from resources including PubChem, MassBank, and GNPS. A REST API provides programmatic access to the database and enables its integration into external tools and analytical workflows. Building on this infrastructure, we developed a web application that allows researchers to perform m/z-based searches, predict molecular formulas, compare isotopic patterns, analyze MS/MS fragments, and retrieve related literature and patents. Case studies with MDMA and caffeine demonstrate how OctoChemDB can support structural hypothesis generation and streamline small-molecule dereplication. The platform provides a unified and accessible environment for accelerating compound identification using HRMS data.
Link to the paper:
https://doi.org/10.1021/acs.analchem.5c06761
OctoChemDB:
