Enhance organic synthesis productivity

MassChemSite is a software dedicated to the structure elucidation of organic molecules produced in chemical reactions based on High Resolution Mass Spectroscopy (HRMS). The application field of MassChemSite is variated: C-H functionalization synthesis, Forced Degradation studies, Agroscience, by-products identification, targeted analysis…



MassChemSite 3.1 includes the fix of some bugs found in MassChemSite 3.0.4 plus some new features:

  • Improved UV detection:

MassChemSite 3.1 includes an improvement of the algorithm aimed for detect UV peaks. This new improvement improves the identification of peaks considering a better treatment from the noise. Additionally, it includes extra settings to allow the user to specify certain anticipation or delay of the UV signal related to the LC-MS one.

  • Improvement of peak detection for saturated signals in UNIFI data:

Saturated data from Waters instrument compatible to UNIFI can now be pre-processed providing better results thanks to the saturation threshold included in MassChemSite.

  • New chemical monitoring workflow for targeted analysis:

Chemical Monitoring workflow present in MassChemSite 3.0 was totally refurbished! The new Chemical Monitoring was thought as a targeted workflow ready to detect and identify more than 1000 compounds in a single run. Results are displayed in a compound-centric view to make an easy identification of the compounds of interest.


The approach consist in the interpretation of Liquid Chromatography in tandem with Mass Spectroscopy (LC-MS) data in order to identify chromatographic peaks related to the compound of interest and the suggestions of chemical structures compatible with the MS data. The application scope of the software are both small molecules and peptides until 5.000 in molecular weight.

The development of the final commercially available product was co-financed by FEDER (Fons Europeu de desenvolupament regional) and the Generalitat de Catalunya via Acció.


To request a copy of MassChemsite, visit Molecular Discovery site.



  1. Enabling Efficient Late Stage Functionalization of Drug-Like Molecules with LC-MS and Reaction Driven Data Processing. Yao H, Liu Y, Tyagarajan S, Streckfuss E, Reibarkh M, Chen K, Zamora I, Fontaine F, Goracci L, Helmy R, Bateman KP, Krska SW, Eur JOC, DOI: 10.1002/ejoc.201701573
  2. Degradation studies of dimethachlor in soils and water by UHPLC-HRMS: putative elucidation of unknown metabolites. López-Ruiz R; Romero-González R; Ortega-Carrasco E; Martínez Vidal JL; Garrido Frenich A, Pest. Manag. Sci. 2020, 76(2), 721-729.
  3. Dissipation kinetic studies of fenamidone and propamocarb in vegetables under greenhouse conditions using liquid and gas chromatography coupled to high-resolution mass spectrometry López-Ruiz R; Romero-González R; Serra B; Garrido Frenich A, Chemosphere 2019, 226, 36-46.
  4. Dissipation studies of famoxadone in vegetables under greenhouse conditions using liquid chromatography coupled to high-resolution mass spectrometry: putative elucidation of a new metabolite. López-Ruiz R; Romero-González R; Ortega-Carrasco E; Garrido Frenich A, J. Sci. Food Agri. 2019, 99(12), 5368-5376
  5. Understanding the Metabolism of Proteolysis Targeting Chimeras (PROTACs): The Next Step toward Pharmaceutical Application. Goracci L; Desantis J; Valeri A; Castellani B; Eleuteri M; Cruciani G, Journal of Medicinal Chemistry, 2020, 63(20), 11615–11638.