Can Progenesis adapt to your application?

Adaptability is a critical factor in research success.  How adaptable is the Progenesis QI and Progenesis QI for proteomics software? The answer is very adaptable. You’ll be surprised to see what different market segments and applications the software has been used for.

Food and environment

In this market sector, the software has been used for food authenticity which is now a major concern across the globe.  This blogpost “Don’t get stung by your Manuka Honey!” Highlights the use of the Progenesis QI software in laboratories that test food to examine the differences between genuine and fraudulent products. For further reading, “Bringing the analysis to the sample: Progenesis QI helps beat food fraud” discusses Professor Chris Elliott’s webinar where he talks about many instances of food fraud including milk, horse meat, oregano, and cumin fraud. Chris speaks about how he works with Progenesis QI to analyze data produced at the Institute for Global Food Security.

Review of standardized abundance profiles and assignment of identity for three markers of Manuka honey as displayed in Progenesis QI software.

Figure 1. Review of standardized abundance profiles and assignment of identity for three markers of Manuka honey as displayed in Progenesis QI software.

Natural products

As with the Food and Environment sector, adulteration is also being seen in the natural products market sector. This blogpost aptly named “Just because it’s natural doesn’t mean it’s safe” describes the webinar on Authenticated Herbal Supplements with a metabolomics approach.  This looks at correctly identifying the marker compounds of each species of Hoodia, Terminalia, and Chamomile to ensure they are the correct substance. The work was carried out with collaboration from Waters and the University of Mississippi. For further reading you can read the relevant paper: Metabolic Profiling of Hoodia, Chamomile, Terminalia Species and Evaluation of Commercial Preparations Using Ultrahigh-Performance Liquid Chromatography Quadrupole-Time-of-Flight Mass Spectrometry.

Screenshot of the Authenticated Herbal Supplements with a metabolomics approach webinar.

Figure 2: Screenshot of the Authenticated Herbal Supplements with a metabolomics approach webinar.

Chemical and materials science

What value can Progenesis QI provide in the world of co-polymer characterization? Polymeric materials are being used more and more in everyday life. They are being used as structural materials for cars and airplanes, fabrics for clothing, packaging materials for food and medicine, to name but a few. These new materials must be properly characterized in order to manufacture the polymers’ reproducibly and thus achieve the required characteristics.

This blogpost explores using Pyrolysis-Gas Chromatography/Mass Spectrometry (Py-GC/MS) coupled with Progenesis QI’s multivariate analysis of the data, to provide novel insight into the polymer structure.

Score plot showing two co-polymer types that are clearly discriminated.

Figure 3. Following replicate analysis of the two co-polymer samples the data was aligned and peak picked using the workflow presented by Progenesis QI. The resulting data was analyzed using an OPLS-DA model to compare the samples. The scores plot resulting from that analysis is shown here where it can be seen that the two co-polymer types are clearly discriminated.


An exciting application is the use of Progenesis QI for proteomics for Host Cell Protein (HCP) analysis. The blogpost, “Progenesis QI for proteomics speeds up biopharmaceutical purification!” , explains how using the software greatly simplifies the user interaction with HCP datasets. Extracting mass chromatograms and calculating peak areas for a multitude of peptide precursors (like the 113 peptides from the MIX-4 spectral library) can be a tedious process. The data from each individual sample replicates need to be compared in order to obtain the peptide level HCP trends. The HCP peptide level results need to be translated into HCP protein levels. All these steps are automated and they are performed rapidly in the Progenesis QI for proteomics software without significant user intervention. This saves a significant amount of time spent on data analysis, producing rapid results.

Four HCPs that were identified by Progenesis QIP in the highly-purified NIST mAb.

Figure 4. Four HCPs (highlighted by red arrows) were identified by Progenesis QIP in the highly-purified NIST mAb.


Dr. Maartens Dhaenens shares his expertise in using the software when he presented his webinar “Proteomics: A peptides Journey to Emergence”. This blogpost of the same name explains his thoughts about understanding how all the different levels of complexity in proteomics data can be unraveled by the different functionalities of Progenesis QI for proteomics. He extols how Progenesis QI for proteomics is a powerful tool for resolving the many challenges in automated data analysis and protein inference.

Screenshot of the title for the Webinar

Figure 5. Screenshot of the title for the Webinar


We have many happy customers, including Dr. Daniel Carrizo, who uses the Progenesis QI software for his metabolomics research. Daniel uses the Progenesis QI software to assess exposure to persistent organic pollutants (POPs). Daniel comments “The data generated is too complex to analyze without specific software like Progenesis. When you have 3000 or 4000 ions of interest and 300 samples, it is impossible to manage this amount of data with normal software. I have found Progenesis QI is robust and easy to use and the technical support is excellent.” He goes on to say “The most important aspect is the power of the analysis and robustness of the data generated, as well the easy design for setting up experiments within the software.” If you would like to see Daniel’s full blogpost you can read it here.


Happy customers mean you have a product to be proud of. We are certainly very proud of the Progenesis QI and Progenesis QI for proteomics software. This blogpost entitled “What are our customers saying?”  highlights how our customers have used the software successfully in their day-to-day research. Comments like “with Progenesis QI for proteomics, we practically started getting publishable data within the first few hours.” from Dr. Lam Yun Wah at the Department of Biology and Chemistry, City University of Hong Kong and “Progenesis QI for proteomics provided me an excellent tool to profile hundreds of proteins with incredible precision to map proteins in cellular compartments of the photoreceptor cells of retina.” from Nikolai Skiba, Assistant Professor at the Albert Eye Research Institute, Duke University in the US, keeps us inspired knowing we are making a difference in people’s research.

More information

Learn more from the resources we have on our website. This useful summary, “Helping you to help yourself”, highlights all the valuable resource we have available, giving you the information you need to use the software more successfully. With user guides, a starter pack and FAQ’s, you can instantly get answers to the more common questions asked about the software.

Were you surprised by the breadth of Progenesis applications?  It’s great to look back but even better to look towards the future. From everyone here at Nonlinear Dynamics, we wish you a successful New Year and look forward to hearing how the Progenesis software has helped you. If you haven’t used the software and would like to, then simply get it touch and we’ll get you started.