LC-MSMS software for small molecule identification with confidence

SmileMS software is designed to identify analyses from mass spectrometry (MS) spectra of fragmented molecules via a spectral library search approach. It can be used both for targeted and untargeted screening methods.


LC-MSMS is a recognized powerful analytical technique used to screen and identify a wide range of chemical compounds. It is used routinely in many laboratories in fields such as Laboratory Medicine, Forensic Toxicology, Doping Control, Food Testing, and Metabolomics research. SmileMS proposes a unique LC-MSMS library search solution. It is designed to identify analytes from MS spectra of fragmented molecules via a spectral library search approach. It can be used both for targeted and untargeted screening methods.

Key features

  • Outstanding compound identification with highest levels of confidence
  • Easy to use and intuitive interface
  • Two-step workflow designed for routine technicians
  • Interactive result review for in-depth analysis
  • Filters for identification of metabolites and other unknown compounds
  • Compatible with LC-MSMS instruments from major vendors (AB Sciex, Agilent, Bruker, Thermo, Waters)
  • Library search against multiple LC-MSMS libraries, provided by NIST, AB Sciex, Wiley, as well as home made libraries

Advanced functionalities

  • Take advantage of accurate mass MSMS from high resolution instruments, e.g. QqTOF, FT, etc.
  • Efficient spectra library management (edition, visualization, sharing, etc.)
  • Analysis workspace for organization of results and analyses
  • Login system and user rights for enhanced traceability and privileges
  • Automation with “SmileMS submission module” for greater productivity with Bruker and Thermo instruments

Main advantages

SmileMS is a unique software tool for rapid screening of large sets of molecules by LC-MS/MS. It provides a robust, reliable, easy-to-use and MS vendor-independent solution.


  • Calculator for low precision isotopic ratio distribution
  • Calculator for high precision isotopic ratio distribution
  • Mass based Pubchem (toxicology) content search tool


A multi-target screening analysis in human plasma using fast liquid chromatography-hybrid tandem mass spectrometry (Part I and II)
Clinical Biochemistry, 2010 Aug 10; Viette V, Guillarme D, Mylonas R, Mauron Y, Fathi M, Rudaz S, Hochstrasser D, Veuthey JL
Department of Genetics and Laboratory Medicine, Service of Laboratory Medicine, Toxicology Laboratory, Geneva University Hospital, Geneva 14, Switzerland; Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland; ADMed Laboratoires, La Chaux-de-Fonds, Switzerland; Swiss Center of Applied Human Toxicology, University of Geneva, Geneva, Switzerland DOI:10.1016/j.clinbiochem.2010.07.021

X-Rank: A robust algorithm for small molecule identification using tandem mass spectrometry
Analytical Chem. 2009 Sep 15;81(18):7604-10 Roman Mylonas, Yann Mauron, Alexandre Masselot, Pierre-Alain Binz, Nicolas Budin, Marc Fathi, Véronique Viette, Denis F Hochstrasser and Frederique Lisacek


SmileMS is developed and copyrighted by SIB Swiss Institute of Bioinformatics and its exclusive commercial representative GeneBio.
Access is subject to the licensing conditions outlined in the GeneBio License Agreement (PDF).

Please contact us for further details.