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New software toolset advances small molecule analysis

Scientists working in metabolomics, pharmaceuticals, food safety, and environmental and forensic science can now use a new, fully integrated, software toolkit to transform complex, unknown mass spectra generated from small molecule analysis into actionable data.

The new software available from, Thermo Scientific, Compound Discoverer 3.0 is an integrated set of libraries, databases and statistical analysis tools linked in customisable workflows. The software processes the information-rich data generated from high-resolution accurate-mass (HRAM) Orbitrap mass spectrometers and transforms it into meaningful results.

‘Full-scan mass spectrometry systems for small molecule applications create large amounts of information-rich data, making extracting meaningful insights with a high degree of confidence and data processing efficiency challenging,’ said Ken Miller, vice president, omics marketing, chromatography and mass spectrometry, Thermo Fisher. ‘The new Compound Discoverer 3.0 software enables our customers conducting small molecule analysis to seamlessly extract 'compound insights' – from spectra to structure – turning data into actionable knowledge.’

‘Compound Discoverer 3.0 software is a powerful, versatile and easy-to-use solution for MS-based isotopic labelling studies,’ said Juan Moises Sanchez, associate scientist, bioanalytical chemistry, Intrexon. ‘Highly customizable workflows consist of logically connected nodes, including spectral pre-processing, multi-library searches, statistics, in silico fragmentation and isotope labelling patterns, among others. Implementation of this software has reduced our bioinformatics lead time and improved the impact of our research in the areas of high-throughput untargeted metabolomics, structural elucidation of unknowns and carbon fate studies.’

Scientists performing small molecule analysis with the Compound Discoverer 3.0 software can benefit from:

  • A fully integrated, untargeted stable isotope flux workflow and customizable pathway tool
  • Identification of unknowns through the use of MS/MS libraries and online chemical databases
  • Elucidating structures by annotating spectra peaks, designed to enable the quick visualization and interpretation of complex data
  • Customizable workflows designed to reduce processing time, transforming mass spectral data into results with great speed
  • Finding real differences in data through built-in, user-friendly statistical chart visualization and heatmap tools
  • Tailored reporting that facilitates the sharing of data across multiple formats, or its transfer to other informatics solutions, that can save time and help maximize data potential


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