New Technique to Revolutionise Proteomics Mass Spectrometry

Scientists at ETH Zurich and AB Sciex are working together to deliver the first mass spectrometry-based technique that will allow quantitation of every peptide in a single proteomics sample analysis. SWATH™ Acquisition is a breakthrough for proteomics mass spectrometry users to conduct simultaneous quantitative and qualitative detection of all proteins and peptides in a single analysis. AB Sciex is developing enhanced MS/MSALL functionality to enable SWATH™ Acquisition on the Ab Sciex TripleTOF™ 5600 System as part of the MRMAtlas collaboration with Dr Ruedi Aebersold and his team at ETH Zurich. 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-analysed on additional instruments for better quantitation. The technique is expected to generate exciting proteomics discoveries and overcome the diminishing scientific returns of iterations on current mass spectrometry platforms.

SWATH™ Acquisition provides a complete quantitative and qualitative archive of the sample, which 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. 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 characterisation 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.