Breakthrough Proteomics Technique SWATH™ Acquisition Is Made Available for Molecular and Cellular Proteomics

Scientists at ETH Zurich, along with AB SCIEX, a global leader in life science analytical technologies, have completed their development of MS/MSALL with SWATHTM Acquisition, a groundbreaking mass spectrometry-based proteomics technique that quantifies nearly all peptides and proteins in a sample from a single analysis. The method was published this year in Molecular and Cellular Proteomics.

Liquid chromatography coupled to tandem mass spectrometry (LC/MS/MS) is widely used by proteomics researchers, but current methods do not provide the speed, quantitative accuracy, specificity, sensitivity and reproducibility that are needed to produce complete and quantitative proteome maps of biological systems. For the first time, SWATHTM Acquisition uses a data-independent MS/MS acquisition method to systematically generate complete, high-specificity fragment ion maps that can be queried for the presence and quantity of any protein of interest using a targeted data analysis strategy.

The new method depends on an advanced hybrid quadrupole-time of flight mass spectrometer, the AB SCIEX TripleTOFTM 5600 System. The unique combination of high resolution, mass accuracy and ultra-high MS/MS spectral acquisition rates mean it is the only mass spectrometer on which the method can be performed efficiently. SWATHTM Acquisition with the TripleTOF 5600 System, an extension of the AB SCIEX MS/MSALL functionality, will soon be commercially available and has been developed as part of a collaboration between AB SCIEX and Dr. Ruedi Aebersold and his team at ETH Zurich.

"SWATHTM Acquisition allows us to explore multiplexed MS/MS datasets to a level that was not possible with traditional clustering or database approaches," said Ruedi Aebersold, Ph.D., Professor, Institute of Molecular Systems Biology at the Swiss Federal Institute of Technology (ETH Zurich) "By collaborating with AB SCIEX to develop the technique on the TripleTOFTM 5600, we have made this breakthrough method available for proteomics researchers to conduct comprehensive quantitation on the entire proteome."

The technique generates highly specific fragment ion data for all precursors within the monitored range. Unlike traditional acquisition approaches, this technique does not rely on precursor ion mass detection to trigger MS/MS acquisition. Instead, it systematically fragments all components of a sample through a rapidly moving selection window.

From the resulting data, several high resolution fragment ion chromatograms for each peptide of interest can be extracted to collectively identify the targeted peptide, as in selected or multiple reaction monitoring (SRM/MRM). Working with ion libraries from public sources such as MRMAtlas, or generated in-house through database search software such as ProteinPilotTM Software, researchers can interrogate the dataset over and over again for quantitative data on peptides/proteins of interest. The technique provides a complete qualitative and quantitative archive of the sample and can be retrospectively interrogated in silico as new hypotheses are developed.