WebChembase is an application to archive, process, report and explore Product Identification (Prod 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, WebChembase is running on an 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.


WebChembase uses as input the files generated by MassChemSite/Product 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 MassChemSite and the result files are sent to the WebChembase server. Once the file is received by WebChembase they are located in a section of the database call “Pending Experiments” waiting for the review and approval of the Chemist 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 product identifier
  • Markush manual drawing

Chromatography Quality and Multiple signal detection

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

Search engine

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

NMR (Nuclear Magnetic Resonance) data

  • Prediction of NMR chemical shift and multiplicity 
  • Reading and interpretation of NMR data 

Approval process

  •  Formal approve of the experimental results

Single Compound analysis tools

  • Flexible reporting tool based on templates

WBC Training documents

  • Tutorial_WCB_01 WebChembase guided tour: presenting the menus and uploading your first experiment
  • Tutorial_WCB_02 Getting processed files on WebChembase part I: using batch processor connection to WebChembase protocols
  • Tutorial_WCB_03 Getting processed files on WebChembase part I: using batch processor connection to WebChembase protocols
  • Tutorial_WCB_04 Reviewing C-H functionalization experiment results: Approval process, part I
  • Tutorial_WCB_05 Reviewing C-H functionalization experiment results: Approval process, part II
  • Tutorial_WCB_06 Approved experiment: Report and Derivatization pathway analysis tools
  • Tutorial_WCB_07 Processing MassChemSite experiments in WebChembase I: using experiment window
  • Tutorial_WCB_08 Processing MassChemSite experiments in WebChembase II: using templates and sample list
  • Tutorial_WCB_09 Targeted analysis using Chemical Monitoring workflow

Pharma –  Data Analysis –  Compound Degradation



Biopharma –  Data Analysis –  Peptide Degradation



Biopharma –  Data Analysis –  Synthesis



Chemistry –  Compound Degradation



Chemistry –  Synthesis



Food –  Analysis Of Soil And Water For Pesticides



Environmental –  Soil And Water Analysis



Environmental –  Dissipation Analysis For Multiple Pesticides


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