Can Progenesis QI impact your research project?

At IMSC 2018, we were lucky to have not one, not two, but three researchers give their presentations at our Progenesis QI lunchtime seminar.

Progenesis–Three personal accounts showing the power of Progenesis QI

  • Untargeted metabolomics using Progenesis QI for small molecules: Developing ion-chromatography-mass spectrometry for the investigation of cancer metabolism – James S.O. McCullagh, University of Oxford, UK
  • Metabolomic profiling of reactive metabolites in toxicology by MSE and Progenesis – Emilien Jamin, Toxalim (Research Centre in Food Toxicology) Toulouse university, INRA, France
  • Novel strategies for discovery of cardiovascular biomarkers in human plasma – Donald JL Jones, Leicester Cancer Research Centre, RKCSB, University of Leicester, UK

These were recorded so we’d like to draw your attention to the interesting and varied presentations over the next few blog posts.

As one of the presenters is awaiting publication, we will present these in reverse order, starting with a lively 23-minute presentation by Prof Don Jones of the University of Leicester.

Below is a short written summary of Don’s talk.  Even better, watch it for yourself and learn which features of Progenesis QI for proteomics Don found so helpful in this ambitious project.  It really is 23 minutes well spent!

Screenshot of the title page for the talk

Novel Strategies for Discovery of Cardiovascular Biomarkers in Human Plasma


Donald JL Jones1,2, Sanjay Bhandari2, Paulene Quinn2, Jatinderpal Sandhu2 and Leong L Ng2

1Leicester Cancer Research Centre, RKCSB, University of Leicester, Leicester, LE2 7LX, United Kingdom

2Department of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, LE3 9QP, United Kingdom

Background: The search for blood-based biomarkers is particularly compelling in the cardiovascular clinical arena. Whilst understanding the genetic basis of cardiovascular disease will provide a clear indication of risk, phenotypic markers represent the pathological changes that occur during disease processes. Methods for investigating the plasma proteome have ostensibly relied on complex pre-analytical protocols that are expensive and limit throughput.

Methods: 100 Coronary heart disease Patients with 20 healthy control were analyzed on the SYNAPT G2-Si, using label-free data-independent acquisition LC-MS with ion mobility optimized (HDMSE). Samples were treated with Calcium Silicate matrix (CSM). Raw data was then analyzed using Progenesis QI for Proteomics. Models of panels of markers were developed using SPSS and RapidMiner.

Results: From 50 µL of plasma, in excess of 1800 proteins are realized that can be reliably observed between samples. Of these, >1100 are quantified. The data shows high reproducibility with known differences predictably demonstrated. New markers are revealed which can be strongly aligned with potential novel mechanisms of coronary artery disease (CAD). The method is shown to be highly reproducible.

Conclusion: We demonstrate that CSM provides sufficient coverage to enable single shot analysis of plasma, historically, a very challenging proteomic sample to analyze, and can provide potential markers for CAD which could feasibly be extended to several classes of disease. This provides a method that can run alongside other omic technologies to profile large-scale numbers of patients individually and thus usher in a new era of precision medicine. Importantly, there are advantageous savings to be made in terms of cost and throughput, which mean that for the first time large scale cardiovascular cohorts, conducted in a realistic timeframe, can be analyzed using proteomics

If you would like to try the Progenesis QI software on your own data then please don’t hesitate to get in touch.


Professor Donald JL Jones