WebMetabase is an application to archive, process, report and explore Metabolite Identification (Met ID) data from different experimental sources. Technically, it is a Java application that runs on a Java application server that connects to a database server, which is accessible to the user by a web browser. Therefore, WebMetabase is running on a internal server that should be reachable by anyone in the organization through the Intranet.

Since the application has been developed as independent of the database server, it can run in multiple systems (MySQL, Oracle, Microsoft SQL, etc..). Once the Java application and database servers are set up the deployment of the application is simple, reducing the maintenance time.

WebMetabase uses as input the files generated by MassMetaSite/Metabolite Pilot/Manually generated XML that can be automatically or manually upload to the server. The instruments are connected to a computer, where the raw data files are processed by Mass-MetaSite and the result files are sent to the WebMetabase server. Once the file is received by WebMetabase they are located in a section of the database call “Pending Experiments” waiting for the review and approval of the Met ID experts.

After the save and approval of the expert the state of the experiments is moved from “Pending” to “approved” and they are then visible to the rest of the organization.


  • Data integrity
  • Audit trail
  • SQL database and Standard data formats 
  • Licensing and Free/easy access to your data 

Automated workflow

  • From raw data to process information in the same interface 
  • Automation mechanisms
  • Flexible experiment definition 

Original data browsing

  • A system independent of the vendor or acquisition mode
  • Extracting Ion Chromatograms (EIC)
  • Manual addition of new peaks

Structure elucidation

  • Fragment visualization and flexible expert decision tools
  • Flexibility to edit the proposed structure
  • Unique metabolite identifier
  • Markush manual drawing

Chromatography Quality and Multiple signal detection:

  • MS (Mass Spectrometry)
  • Ultraviolet
  • Radio
  • Fluorescent 
  • Peak quality analysis

Multiple compounds analysis tool

  • Comparison of multiple experiments of a single compound 
  • Met ID comparison for a con-generic series of compounds
  • Comparing results from different condition

Single Compound analysis tools

  • Flexible reporting tool based on templates
  • Docking of the compounds in CYPS, FMO or AOx (Aldehyde oxidase) enzyme cavities
  • MetaDesign: suggestion of structural modifications 
  • Metabolic pathway drawing tool
  • Fragmentation Tree
  • Kinetic analysis

Search engine

  • Experiment parameters
  • Compound parameters

Approval process

  • Formal approve of the experimental results.

Connectivity to other systems

  • To UNIFI from Waters
  • To Compound Library Module 
  • Import process data from Metabolite Pilot from Sciex 

WMB Training Documents:

Pharma – Data Analysis – Met ID





Pharma –  Data Analysis –  Reactive Metabolite Screening



Biopharma –  Data Analysis –  Peptide Metabolite Identification



Biopharma –  Data Analysis –  Peptide Degradation



Biopharma –  Data Analysis –  Synthesis



Biopharma –  Prediction –  Catalysis Prediction


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