Progenesis CoMet v2.0 released for LC-MS-based metabolomics

Early last year we announced a beta version of Progenesis CoMet v2.0 was available so we could get feedback on a radical new workflow we introduced.  After showing it to many metabolomics researchers and finalising the development work we have now released Progenesis CoMet v2.0.

The latest version has new features but retains the benefits you need for metabolomics data analysis:

  • One streamlined package to quantify-then-identify the  significantly changing compounds in a complex mixture
  • An objective approach to analysis, using a complete matrix of data with no missing values for reliable multivariate statistics
  • Easily export analysis results for further bioinformatics or generate a list of interesting compounds that you can review and share

The new version of Progenesis CoMet is a big step forward for discovery-focussed quantitative metabolomics data analysis. It was developed to meet the specific challenges of metabolomics data visualisation and analysis compared to the needs of peptide and protein analysis for proteomics. You can read about the features introduced into the beta version of Progenesis CoMet v2.0 in our earlier blog post.

The improvements to the workflow have been well received. The main feature that has made an impact, which we hoped it would, is the automatic deconvolution of compound ions for more accurate and reliable quantification and identification results.


Progenesis CoMet v2.0 automatically deconvolutes compound ions to generate a list of quantified and identified compounds. You can also visualise and edit compound ion deconvolution for quality assurance and improve precision of ion abundance measurements respectively.

You can download a demonstration version to see how all the features and workflows give you a single unified workflow for metabolomics analysis.

What has been added to the final version of Progenesis CoMet v2.0?

There has been work to enhance the beta version including:

  • Improvements to the automatic peak picking algorithm for detecting single isotopes and overlapping ions
  • Expanding data export options, including raw abundance of every isotope peak for every adduct
  • Adding support for SDF database searches to display chemical structures alongside compound identification and quantification results
  • An ion map, mass spectra and chromatogram displayed for each compound ion on all runs
  • Improved views of  peak picking and alignment of a compound adduct, with the ability to edit detection on one run and make the same change to the same feature across all runs
  • The option to import experiment design files that instantly create the groups you need for relative quantification of compounds across hundreds of runs


Select compound ions to view as ion intensity map, mass spectrum and chromatogram. You can also visualise peak picking and alignment of a compound adduct as well as having the ability to edit detection on one run and make the same change to the same feature across all runs.

Supporting your metabolomics data analysis in the future

Progenesis CoMet enables you to reliably quantify-then-identify relative differences in compound abundance for discovery-based metabolomics. It will support your existing research now as well as options for the future, including:

  • The same simple workflow for data from all the common MS instruments that you are likely to install (Thermo, Agilent, Bruker, Waters ) as well as supporting cross-vendor file formats (mzXML, mzML, NetCDF)
  • Easily export raw data and analysis results into your bioinformatics pipelines e.g. KEGG pathway analysis software
  • Ability to develop plug-ins that support new data import and database search options without requiring a major software release

Download and try our demonstration version of Progenesis CoMet v2.0 to see how it can help you analyse metabolomics data now and in the future.