New Scanning SWATH Technology Enables Faster Identification of Proteins

Researchers from the University of Berlin and the Francis Crick Institute have developed a mass spectrometry-based technique capable of measuring samples containing thousands of proteins within just a few minutes. To demonstrate the technique's potential, the researchers used blood plasma collected from COVID-19 patients and identified eleven previously unknown proteins which are markers of disease severity. The work was published in Nature Biotechnology.

In order to obtain fingerprints of proteins, researchers typically use mass spectrometry. Scanning SWATH, a new mass-spectrometry-based technology, was developed under the leadership of Markus Ralser. The team says that this technology is much faster and cost-effective than previous methods, enabling researchers to measure several hundred samples per day.

"In order to speed up this technology, we changed the mass spectrometer's electric fields. The data produced are of such extreme complexity that humans can no longer analyze them," explains Ralser. "We therefore developed computer algorithms that are based on neural networks and which use these data to extract the relevant biological information. This enables us to identify thousands of proteins in parallel and greatly reduces measuring timescales. Fortunately, this method is also more precise."

As part of this research, the team analyzed blood plasma samples from 30 Charité inpatients with COVID-19 of varying degrees of disease severity, comparing the protein patterns obtained with those of 15 healthy individuals. The actual measurements conducted on individual samples only took a few minutes. The researchers were able to identify a total of 54 proteins whose serum levels varied according to the severity of COVID-19. While 43 of these proteins had already been linked to disease severity during earlier studies, no such relationship had been established for 11 of the proteins identified. Several of the previously unknown proteins associated with COVID-19 are involved in the body's immune response to pathogens which increases clotting tendency.