Metabolomics data analysis of herbicide susceptible and resistant populations of black-grass using Progenesis software

We have a new application note describing metabolite profiling of black-grass (Alopecurus myosuroides) using Progenesis software generated by Michael Dickinson, Research LCMS Specialist at The Food and Environment Research Agency here in the UK.

The challenge was to characterise the metabolites showing significant abundance changes between strains of black-grass with varying degrees of herbicide resistance at various time-points after  spraying.  The results will allow development of diagnostic approaches for farmers to determine optimal weed control strategy within a growing season.  For example, recognizing the appearance of multiple-herbicide (MHR) black-grass early-on would inform the choice of which, if any, herbicides should be applied.

You can read the application note and others here but several features of Progenesis were highlighted as being particularly helpful, including:

  • Simple, directed workflow allowed 42 high-resolution LC-MS runs to be processed in <2 hours.
  • Rapid, versatile way that LC-MS runs could be re-grouped to report relative compound abundances within the same experiment i.e. there was no need to re-analyse the whole experiment in order to compare different time-points or different strains at this exploratory phase.
  • The in-built multivariate statistical tools, especially PCA, to quickly visualise which panel of metabolites provide the best discrimination between the different strains and at which time-point.
  • Running searches against an in-house plant metabolite database using MetaScope to putatively identify compounds for confirmation by NMR or MS/MS fragmentation.


PCA showing the metabolic relationship between black-grass plants of varying herbicide resistance 13 days after the herbicide application based on data-analysis with Progenesis™ software. Key: (A) Herbicide Susceptible (SUS); (B) Multiple herbicide resistance (MHR) and (C) Target site resistant (TSR).  Compounds having significant abundance were selected for validation using NMR and / or MS/MS.

The Progenesis software also allowed visualisation of the data at each step within the analysis and in particular to validate any specific compound abundance changes of interest. For example, the 3D peak montage below was used to interrogate a significant ion abundance change across the three strains of black-grass; (SUS) non-resistant to herbicide, (TSR) Target-site resistant i.e. selectively resistant to herbicide and (MHR) multiply-resistant to herbicide 8 days after spraying with herbicide.

Figure 5

If you would like to see how the features of Progenesis can support metabolomics profiling of your own samples get in touch and we can arrange a demo on your own LC-MS runs.