Untargeted Metabolomics

Untargeted metabolomics is the method of choice to characterize samples of unknown content. This workflow is used for example to identify biomarkers and metabolites. The information obtained can be mapped onto biological pathways which helps to understand the complex regulation of systems biology. As the metabolome cannot be computed from the genome or proteome alone, high resolution mass spectrometry together with data-dependent and –independent fragmentation and sophisticated bioinformatics methods are needed to identify specific compounds. In recent years several metabolite database and open-source software became available.

BayBioMS supports the whole workflow from data acquisition and extensive statistical and bioinformatics analysis.

Feel free to contact us with any question!


Available metabolite databases:

· ChemSpider Database 

· European MassBank 

· FooDB 

· GNPS: Global Natural Products Social Molecular Networking 

· Human Metabolome Database 

· Japanese MassBank 

· KEGG Compound Database 

· LipidMaps Database 

· METLIN Database 


· Phenol-Explorer 

· PlantCyc Database 

· PubChem Compound Database 

· ReSpect for Phytochemicals 

· Yeast Metabolome Database 


Useful open source tools to analyze MS-data:


· ProteoWizard to convert files 


· MZmine2 


· Cytoscape 


Literature Example

Kleigrewe, K.; Almaliti, J.; Tian, I. Y.; Kinnel, R. B.; Korobeynikov, A.; Monroe, E. A.; Duggan, B. M.; Di Marzo, V.; Sherman, D. H.; Dorrestein, P. C.; Gerwick, L.; Gerwick, W. H., Combining Mass Spectrometric Metabolic Profiling with Genomic Analysis: A Powerful Approach for Discovering Natural Products from Cyanobacteria. J. Nat. Prod. 201578, 1671-82.

Stark, T. D.; Lösch, S.; Wakamatsu, J.; Balemba, O. B.; Frank, O.; Hofmann, T., UPLC-ESI-TOF MS-Based Metabolite Profiling of the Antioxidative Food Supplement Garcinia buchananiiJ. Agri. Food Chem. 201563, 7169-7179.