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Related Experiment Video

Updated: Jan 31, 2026

$Liquid Chromatography Coupled to Refractive Index or Mass Spectrometric Detection for Metabolite Profiling in Lysate-based Cell-free Systems$

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Published on: September 23, 2021

CEU Mass Mediator 3.0: A Metabolite Annotation Tool.

Alberto Gil-de-la-Fuente^1,2, Joanna Godzien², Sergio Saugar¹

¹Department of Information Technology, Escuela Politécnica Superior , Universidad San Pablo-CEU, CEU Universities, Campus Montepríncipe , Boadilla del Monte, Madrid 28668 , Spain.

Journal of Proteome Research

|December 22, 2018

Summary

CEU Mass Mediator (CMM) version 3.0 enhances metabolite identification with an expanded knowledge base and new expert system services. This advanced tool supports researchers in annotating and identifying metabolites, improving metabolomic data analysis.

Keywords:

REST annotation databases identification knowledge representation mass spectrometry metabolomics software tool web services

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Area of Science:

Metabolomics
Bioinformatics
Computational Biology

Background:

CEU Mass Mediator (CMM) has evolved from a simple database query tool (CMM 1.0) to an integrated expert system (CMM 2.0).
Continuous development has focused on expanding its knowledge base and services for metabolite annotation and identification.

Purpose of the Study:

To present the novel functionalities incorporated into version 3.0 of the CEU Mass Mediator (CMM).
To highlight improvements in metabolite data integration, annotation, and identification support for researchers.

Main Methods:

Expansion of the expert system's knowledge base and integration of an in-house oxidized lipid library.
Implementation of new services: oxidized glycerophosphocholine annotation, MS2 spectral comparison, and spectral quality assessment.
Development of a RESTful API for enhanced collaboration and integration with external metabolomic platforms.

Main Results:

Increased metabolite entries to 332,665 experimental and 681,198 predicted.
Incorporation of new taxonomy and ontology metadata.
Successful integration of the RESTful API into the Human Metabolome Database (HMDB).

Conclusions:

CMM 3.0 offers significantly enhanced capabilities for metabolite annotation and identification.
The new features and API integration improve the tool's utility and interoperability within the metabolomics community.
CMM 3.0 represents a substantial advancement in supporting metabolomic research.