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WebMetabase is more than just a metabolite database. WebMetabase is a server-based application that is used for metabolite identification data storage, reviewing metabolite identification experiments, and extracting the maximum knowledge from the information loaded into the system. In combination with Mass-MetaSite and after the approval of a Met ID expert, WebMetabase speeds up the process of translating the spectral information into chemical structures, transforming the instrument data into information.

The information can then be used with quantitative and qualitative approaches to extract knowledge about clearance or half-life (in the case where incubation kinetics are used) or matrix selectivity when different matrices are analyzed in the experiment. Moreover, MetaDesign has been added as a tool to automatically suggest chemical modifications to improve metabolic properties. In addition to all of these tools to transform information into knowledge based on a single compound analysis, WebMetabase offers an innovative approaches to consider in a single view the metabolic pathways for a number of closely related series of compounds, the Structure Metabolism relationship Table (SMrT).

Discover WebMetaBase:


  • Flexible experimental protocol definition (properties, macros, filters, etc)
  • Automatic uploading of Mass-MetaSite or Metabolite Pilot experiments
  • Treatment of experiments with several samples, i.e. multiple incubation times, matrices, species
  • Expert user for experiment approval and control of the information shared with the rest of the organization
  • User/workgroup management
  • Easy data sharing system
  • Flexible reporting of data with customizable reports
  • Analysis tools:
    • Single compound tool box:
      • MetaDesign
      • Kinetic analysis for parent and metabolites
      • Quan/Qual approach
      • Three2D: Visualization of the interaction of the parent compounds with different cytochrome enzymes considering the structure of the metabolite as starting point
      • Metabolic pathway analysis: The user can easily draw a metabolic pathway keeping the relationship between the different metabolites
      • Reporting system: A totally flexible report system has been implemented
    • Multiple compound tool box:
      • Structure Metabolism relationship Table
      • Clustering View: This analysis tools enables the comparison of the experimental results for the same compound in different experimental setups

WebMetaBase 3.2.0 new features

  • Metabolite Identification tools.
    • Fragmentation Pathway: Representation of the fragmentation tree for the parent.
    • Manual editing of Markush.
  • New Analysis tools:
    • Metabolic pathway kinetic analysis: Being able to check if a metabolic scheme makes kinetic “sense”
  • Peptide mode:
    • Approval process: Chemically aware peptides in the database.
    • Peptide frequency analysis: Automatic analysis of which are the most common amide bonds that get metabolised in a series of experiments.
  • Data sharing and database manager:
    • Export/Import of experiments. Now, one can share experiments between different WebMetabase servers.
    • Import data from external sources (xml).
    • Consolidation tool: A new tool to consolidate the nomenclature of units, properties, protocols and more.

Improvements compared to the 3.1.9 version

  • Metabolite Identification tools:
    • Chromatogram time scale shows the entire range of experiment.
    • Manually edited metabolites keep original MS/MSMS spectra.
    • Manual editing of fragments.
    • Isomorphism creates complete MSomSpot data.
    • Show current prediction number in the ranking chart.
  • Analysis tools:
    • Simplify report pop-up window: Report window has been simplified to make it easier to follow.
  • Information management:
    • Makush system:
      • Revised rules to render markush structures to allow ring openings in oxanes.
      • Changed rules that enable/disable markush rendering of a molecule.
    • New category to control user access to Notebook and Experiment settings.
    • Assign a different owner to an experiment.
    • Improved manual with some advanced sections.
  • Algorithms:
    • Faster kinetic calculation process.
    • Improved internal scheduler to coordinate application tasks.

WebMetabase Report Templates

WebMetabase offers a flexible report system where any information related to Chromatography, mass spectra, structure elucidation (including fragmentation) or analysis tools can be included in the pdf, excel, word or xml report. The WebMetabase uses jasper report to produce the reports, and the templates can be built easily using the iReports tool.

The WebMetabase team can help you to build your own template. In order to import the templates into WebMetabase follow this 6 steps:

  1. Download the desired template report from this webpage.
  2. Uncompress the file.
  3. Connect to the WebMetabase server.
  4. Access to the Analysis tool, but clicking the “Analysis tool” button in the main window.
  5. Select in the reporting option.
  6. A panel where the user add the report template name and the upload of the files will be shown. In each template there is one file that start “main”, this is the first file in the upload template file list. All the other files could be uploaded in any particular order.

The single experiment templates can be used inside each approved experiment in the Atools tab, and jointly with the multi experiment reports in the search results area. We provide here several examples of reporting templates, please select the ones matching your WebMetabase version.

In the single experiment templates you can find the following examples:

  • Experiment: this template provides an output of a typical experiment with the chromatography, the MS spectra, the structural elucidation, the information about the Area, Score, accuracy, etc.. for each metabolite (recommended format pdf).
  • Fragmentation: this template report produces all the MS spectra and the fragmentation used in the metabolites structure elucidation (recommended format pdf).
  • GSH: this is an example to show the ability of the report system to filter the metabolites that contain a GSH adduct (recommended use format pdf).
  • Summary: this is an example to output a summary of an experiment (recommended use format pdf).
  • SoftSpot: this report provides the experiment information and the result of the soft spot identification (recommended use format pdf).
  • Raw Data: exports the areas per peak and experimental conditions in the experiment (recommended use format excel).

The multi experiment examples provided are:

  • Multi Experiment Comparison: outputs the kinetic profiles of substrate and metabolites and the metabolites structures per experiment in a unique report (recommended use format excel).
  • Raw Data: exports all the areas per peak and experimental conditions of all the selected experiments it is specially designed for kinetic experiments and supports the use of internal standards (recommended use format excel).

Templates Download:

Metadesign Tool

Webmetabase offers the possibility to use directly the MetaDesign Tool designed to find biosisoteric replacement of fragments filtered or not by improving metabolic properties like reactivity towards oxidation.

  1. Prepare a database or download a pre-computed one here and uncompress the dowloaded file.
  2. Log in as Administrator and go to the Analysis Tools section.
  3. Select MetaDesign DB management option.
  4. In the new panel give a name to the database and select the uncompressed database file.

Release Notes

A full list of the new features and bugfixes is available here

Please login to see an overview of the WebMetabase capabilities.