Researchers at the Francis Crick Institute have developed a new mass spectrometric acquisition technology, Scanning SWATH, that measures the human proteome substantially faster and at a lower cost than its predecessors. The scientists hope this technology will lead to more effective drug screening and biomarker discovery.

At any one moment, thousands of different proteins are active in our bodies, being used as structural building blocks or to facilitate reactions in our cells. Measuring the activity of these proteins is key to understanding diseases, discovering biomarkers and for drug development. To take these measurements, researchers analyze cells, tissues or blood samples via a technique called mass spectrometry, however, this process is usually time-intensive and expensive.

This new generation of technology opens the door for applications, like exploratory drug screens, where it was difficult to use proteomics before. Markus Ralser

In their study, published in Nature Biotechnology, the scientists developed a new mass spectrometry technology that is drastically quicker and more accurate than existing methods, and used it to uncover key proteins in the body’s response to COVID-19.

The technology modifies electric fields inside mass spectrometer machines to generate more complex and more informative data. It relies on new computer algorithms that the team also developed, to translate this data and allow for thousands of samples to be processed in parallel.

Christoph Messner, lead author and postdoc at the Crick and Charité – Universitätsmedizin Berlin explains: “With this new measurement technique, we have been able to measure the proteome in blood samples from COVID-19 patients at unprecedented speed. This led to the identification of several proteins that change in our bodies as a response to the virus. We further found that certain proteins can predict the severity of the disease and that such measurement could become a viable diagnostic tool in the future.”

Markus Ralser, senior author and group leader of the Molecular Biology of Metabolism Laboratory at the Crick and head of the Institute of Biochemistry at Charité, a leading university hospital in Berlin adds: “This new generation of technology opens the door for applications, like exploratory drug screens, where it was difficult to use proteomics before. A human proteome now costs less than a complete blood count, and provides much more biological information.”

Key to the success of the project was a partnership between academic labs at the Francis Crick Institute, the University of Cambridge, Charité and the mass spectrometry manufacturer SCIEX. This work was in part supported by the BBSRC as an academia-industry partnership ‘LINK’ consortium.