Advancing Omics Research and Reducing Bias with New MS Technology for Data-Independent Acquisition Experiments

By December 20, 2016

Targeted LC-MS based assays are increasingly applied in the post-discovery Omics area with an emphasis on validation, the first of many phases in translational research; and in studies that are aimed at gaining the understanding of biological systems in terms of drug development and treatment.

Understanding the context of analytical results is driving current research, and therefore driving the development of LC-MS acquisition methods that can provide both qualitative and quantitative information in a single experiment.


Data independent acquisition (DIA) is a critical technique for laboratories that need to qualitatively identify metabolites, lipids and proteins in complex samples and extract high resolution quantitative information.

In a DIA experiment, the behavior of the mass spectrometer doesn’t change based on the data being generated. This means the results are not biased and no data is lost by the MS system switching between acquisition modes or experimental threshold limits, which is a concern for Data Dependent Acquisition (DDA) approaches.

A new acquisition mode, 2D MS/MS, was first presented by Richardson, et al., at ASMS in 2015, and was recently introduced commercially as SONAR from Waters.

“As proteomics research has matured, scientists are already collecting the majority of the information available from proteins. What they want to be able to do is approach a protein or specific peptides with a hypothesis, and use targeted MS/MS quantification to investigate their ideas without setting up additional methods or experiments.

“Now, with SONAR data acquisition, they can perform a more selective all-in-one analysis. Compatible with high-speed UPLC separations, it’s a more efficient workflow for more accurate qualitative and quantitative analysis within a single injection.” (from World HUPO 2016)

In SONAR mode, the quadrupole is rapidly scanned across the m/z range of interest, alternating scans of low energy and high energy and collecting qualitative and quantitative data for all precursors and all products. The rapid scanning electronics samples 200 quadrupole positions per scan with typical scan times 0.1 to 0.5 sec (each energy level). The quadrupole can scan at >10,000 amu/sec, >2000 spectra/sec and is compatible with high speed chromatographic and electrophoretic separations.

Enabling researchers to perform advanced data manipulation, SONAR data is compatible with analytical workflows that utilize Waters Progenesis QI and Symphony software, and with third-party software packages such as Skyline. SONAR is available on the Waters Xevo G2-XS QTof Mass Spectrometer under MassLynx Software control.

This method offers advantages by providing quantitative MS/MS data at UPLC speeds from a data independent acquisition (DIA) method for use in highly complex samples. A recent poster note titled Advances in Targeted Omics Quantitation Using a Novel Scanning Quadrupole DIA Method provides more information.

In a recent webinar titled Qualitative and Quantitative Proteomics – Novel DIA and Processing Strategies for Complex Profiling, from the Journal of Proteomics, Dr. James Langridge from Waters reviews how SONAR works, and Dr. Paul Skipp, Associate Professor/Centre Director, Centre for Proteomic Research at University of Southampton, discusses how it is enabling the global profiling and targeted quantitation of the human skin proteome.


More resources: