Project goal

Dr. Ralser and his multidisciplinary team at the Francis Crick Institute are interested in cellular homeostasis and response to external stimuli. They aim to better understand metabolic processes and identify potential targets for drug development.

The challenges

The researchers at the Francis Crick Institute detect what are often very small changes in protein expression or post-translational modifications. Because their studies involve very large sample cohorts, they must work on a much larger scale than most other biological laboratories, something with which traditional proteomics approaches simply aren’t designed to cope. And while standard SWATH Acquisition produces high-quality data, covering the necessary mass range at a rate compatible with the team’s desired LC run time still presents a duty cycle challenge.

The solution

The team has a long history of working with SCIEX, and has been fortunate to have early access to a number of innovative and exciting technologies that have assisted with application development. The team’s most recent collaboration around Scanning SWATH® Acquisition has proven ideal for high throughput proteomics: since Scanning SWATH® Acquisition continuously scans the quadrupole, it supports much faster cycle times without losing selectivity. Additionally, each MS/MS iteration is directly correlated to the correct precursor which provides them a single, comprehensive and permanent digital record.

The outcome

By implementing Scanning SWATH® Acquisition, the team has been able to go down to cycle times of half a second, which complements their very short chromatography gradients. The increased throughput has enabled the team to run much larger scale experiments, allowing them to run up to 200 samples a day on a single instrument.