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Capture Compound Mass Spectrometry - A Powerful Tool to Identify Novel c-di-GMP Effector Proteins

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OctoChemDB: An Aggregated Database for Small Molecule Identification Using High-Resolution MS Data.

Ricardo Silvestre^1,2, Rémi Martinent¹, Laure Menin²

¹School of Engineering and Architecture, Institute of Chemical Technology, HES-SO University of Applied Sciences and Arts Western Switzerland, Fribourg 1700, Switzerland.

Analytical Chemistry

|February 16, 2026

Summary

This summary is machine-generated.

OctoChemDB centralizes chemical, biological, and spectral data, enhancing small molecule identification. Its REST API and web application enable rapid m/z-based searches and spectral matching for streamlined dereplication.

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Area of Science:

Computational chemistry and cheminformatics
Analytical chemistry and mass spectrometry
Bioinformatics and data science

Background:

High-resolution mass spectrometry (HRMS) is crucial for small molecule dereplication using chemical databases.
Existing databases often lack direct m/z-based search capabilities and robust spectral data processing.
This limits the efficiency of rapid compound identification workflows.

Purpose of the Study:

To develop OctoChemDB, a centralized database integrating diverse chemical, biological, and spectral data.
To provide programmatic access via a REST API for seamless integration into research workflows.
To create a user-friendly web application for advanced small molecule identification and dereplication.

Main Methods:

Aggregated and harmonized data from open-access resources (PubChem, MassBank, GNPS).
Implemented a REpresentational State Transfer Application Program Interface (REST API) for data querying.
Developed a web application featuring m/z-based searches, formula prediction, isotopic similarity, fragmentation analysis, and literature retrieval.

Main Results:

OctoChemDB successfully integrates and harmonizes disparate chemical and spectral datasets.
The REST API enables efficient programmatic access and custom querying of the integrated data.
The web application demonstrated effective small molecule identification through case studies (e.g., MDMA, caffeine).

Conclusions:

OctoChemDB and its associated API/web application significantly accelerate small molecule identification and dereplication.
The platform provides a powerful, user-friendly tool for researchers leveraging HRMS data.
The open-source availability fosters further development and integration into diverse cheminformatics workflows.