Revolutionary technique for proteomics mass spectrometry

14 June 2011

Scientists at ETH Zurich and AB SCIEX, a global leader in life science analytical technologies, are working together to deliver a new mass spectrometry-based technique for quantitation for the first time ever on every peptide in a single proteomics sample analysis.

SWATH Acquisition is a breakthrough for proteomics mass spectrometry users to conduct comprehensive quantitation on the entire proteome. As a next step in its MRMAtlas collaboration with ETH Zurich’s Dr. Ruedi Aebersold, AB SCIEX is developing enhanced MS/MSALL functionality to enable SWATH Acquisition on the AB SCIEX TripleTOF 5600 System for scientists to utilize around the world. Details about SWATH Acquisition were presented last week at the American Society of Mass Spectrometry (ASMS) conference in Denver.

SWATH Acquisition is being developed in collaboration with Dr. Aebersold and his team at ETH Zurich to provide a new type of system for future proteomics research that is expected to generate new and exciting proteomics discoveries and overcome the diminishing scientific returns that iterations on current mass spectrometry platforms are delivering. A key advantage of the technique is that it provides a complete quantitative and qualitative archive of the sample that can be retrospectively interrogated in-silico, as new hypotheses are developed.

This new technique is a perfect complement to the MRMAtlas, which is a database that provides mass spectrometry-based assays to a large proportion of the human proteome. Scientists around the world can use this atlas to significantly advance biomarker research, protein-based drug development and fundamental biological and biomedical research. The MRMAtlas provides simple, validated assays expanding into never-before-seen areas of the proteome. With SWATH Acquisition on the TripleTOF 5600 System, the MRMAtlas will be more valuable to a greater number of scientists.

Existing high resolution and orbital trapping mass spectrometry systems can only qualitatively detect a subset of proteins in complex samples due to their relatively slow speed of MS/MS acquisition, and samples are often re-analyzed on additional instruments for better quantitation. To address these challenges, AB SCIEX is developing SWATH Acquisition for simultaneous quantitative and qualitative detection of all proteins and peptides in a single analysis.

The active collaboration with Dr. Aebersold and his team will continue to develop the software processing approach to interpret the data based on the MRMAtlas. SWATH Acquisition, which is an extension of AB SCIEX’s MS/MSALL technology, can only be done on the TripleTOF 5600 due to its unique combination of ultra-high acquisition speed with quantitative capabilities, accurate mass and high resolution. MS/MSALL has previously been used successfully in infusion methods for the quantitation and characterization of lipid species. Now, expanding on this capability, MS/MSALL using SWATH Acquisition gives a vast increase in duty cycle to enhance coupling with LC/MS – a significant advancement in mass spectrometry technology.

Ruedi Aebersold, Ph.D., Professor, Institute of Molecular Systems Biology at the Swiss Federal Institute of Technology (ETH-Zurich), said, “With SWATH and the MRMAtlas, we are able to rethink how we approach proteomics. We are able to interrogate samples in a way that was previously impossible and we expect this will yield new and exciting discoveries. Collaborating with AB SCIEX has allowed us to reach the levels of speed and quantitation that we needed to develop this technique, which we will make available to the entire scientific community around the world.”

Dave Hicks, Vice President and General Manager of the Pharmaceutical and Omics Business, AB SCIEX, said “Once again AB SCIEX has worked closely with a world-class scientist to advance mass spectrometry technology farther than anyone else thought possible. The power and speed provided by the TripleTOF 5600 System make this revolutionary SWATH Acquisition technique possible. We expect that this development will help reinvigorate proteomics research for years to come.”

Source: AB SCIEX