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Last year, Technology Networks hosted two webinars that featured groundbreaking research utilizing SWATH DIA (data-independent acquisition) for exposomics and metabolomics. Researchers Dr. Vinicius Verri Hernandes from the University of Vienna and Dr. Cristina Balcells from Imperial College London (ICL) demonstrated how a DIA approach can be successfully implemented in small molecule analysis using the ZenoTOF 7600 system. Their innovative approaches highlight the potential of SWATH DIA to enhance the detection and analysis of chemical exposures and metabolites, paving the way for new insights into environmental health and disease mechanisms.

Understanding the exposome

The exposome encompasses all environmental factors the human body is exposed to throughout life, from air pollution and synthetic chemicals to noise and physical activity. Vinicius and Cristina emphasized the importance of studying the exposome to understand the full spectrum of compounds we are exposed to and their impact on health.

“An exposome is every factor the human body is exposed to throughout life. This can include air pollution, synthetic chemicals, noise, and even physical activity.” – Dr. Cristina Balcells.

The concept of the exposome is recent, first introduced in 2005. It aims to measure environmental influences and associated biological responses comprehensively. By studying the exposome, researchers can understand how various environmental factors contribute to health and disease, leading to better prevention and intervention strategies.

The role of metabolomics

Metabolomics, the study of metabolites within a biological system, plays a crucial role in exposome research. Positioned at the end of the biochemical cascade, environmental factors significantly influence metabolomics. Both researchers highlighted the challenges in analyzing metabolites due to their wide range of concentrations and the need to consider both endogenous and exogenous metabolites.

“Metabolomics is the part of the biochemical cascade that is mostly influenced by environmental aspects and is probably the most complex to deal with analytically.” – Dr. Vinicius Verri Hernandes.

Metabolomics provides a snapshot of an organism’s biochemical activity, reflecting the interactions between genetic and environmental factors. This makes it a powerful tool for understanding the impact of the exposome on health. However, the complexity of metabolomics data, with its vast range of metabolite concentrations and chemical diversity, poses significant analytical challenges.

Combining targeted and untargeted approaches

Vinicius and Cristina discussed the advantages and disadvantages of targeted and untargeted metabolomics. Targeted approaches offer lower limits of detection and quantitative data but are limited to a predefined set of compounds. Untargeted approaches provide broader chemical space coverage and are helpful for discovery but struggle with low-concentration compounds and quantitation.

“Targeted approaches can reach lower detection limits and provide quantitative data, but the chemical space we can analyze is very limited. Untargeted approaches offer broad coverage but underperform with low concentration compounds.” – Dr. Vinicius Verri Hernandes.

Combining targeted and untargeted approaches allows researchers to leverage the strengths of both methods. Targeted metabolomics focuses on specific metabolites of interest, providing precise and quantitative data. In contrast, untargeted metabolomics casts a wider net, capturing a broad spectrum of metabolites without prior knowledge of their identities. This dual approach enhances the ability to detect and quantify a wide range of metabolites, including those at low concentrations.

Optimizing SWATH DIA for exposomics and metabolomics

To overcome these challenges, both researchers have developed methods that leverage SWATH DIA to measure both the metabolome and the chemical exposome simultaneously. Vinicius’s method combines targeted MRM (Multiple Reaction Monitoring) and untargeted SWATH in a single LCMS run, while Cristina’s approach involves optimizing collision energies for SWATH DIA to maximize feature detection.

“We believe that SWATH can be fit for measuring the metabolome and the chemical exposome simultaneously.” – Dr. Cristina Balcells.

SWATH DIA is a powerful technique that allows for the comprehensive and simultaneous analysis of multiple compounds. By dividing the mass range into variable windows and fragmenting all precursors within each window, SWATH DIA ensures that no information is lost, providing a complete picture of the sample’s chemical composition. This makes it particularly well-suited for exposomics and metabolomics, where the goal is to capture a wide range of compounds, including those at low concentrations.

Workflow and method development

Cristina shared a detailed workflow for optimizing SWATH DIA, including using a custom R package to optimize declustering potentials (DP) and collision energies (CE) for each SWATH window. This workflow involves injecting samples multiple times with different DP and CE settings to build a comprehensive data catalog.

“We designed an R package that helps us optimize the DP and CE for each SWATH window, aligning with our goals of maximizing new and identified features.” – Dr. Cristina Balcells.

The optimization process involves several key steps:

1. Sample preparation: Samples are prepared using a standardized protocol to ensure consistency and reproducibility.
2. Injection and data acquisition: Samples are injected multiple times with different DP and CE settings to capture a wide range of fragmentation patterns.
3. Data processing: The acquired data is processed using the custom R package, which identifies the optimal DP and CE settings for each SWATH window.
4. Validation: The optimized method is validated using various samples to ensure its effectiveness and reproducibility.

Key findings and results

Both researchers validated their optimized methods using various samples, demonstrating significant improvements in detection limits, sensitivity, and the number of MS2 matches and quantifiable features. These advancements highlight the potential of SWATH DIA for comprehensive exposome and metabolomics studies.

“We achieved higher numbers of MS2 hits and quantifiable features with our optimized method, validating its effectiveness across different serum samples.” – Dr. Cristina Balcells.

The optimized SWATH DIA methods developed by Vinicius and Cristina have shown promising results in various applications. For example, Vinicius’s method significantly improved the detection and quantitation of compounds in non-spiked samples. At the same time, Cristina’s approach increased the number of identified features and discoveries in serum samples. These findings highlight the potential of SWATH DIA to enhance our understanding of the exposome and its impact on health.

Conclusion and future directions

The webinars concluded with a discussion of SWATH DIA’s benefits for exposomics and metabolomics, particularly in preserving structural information and improving data deconvolution. Both researchers highlighted plans to make their tools publicly accessible and develop graphical user interfaces to facilitate broader adoption.

“SWATH DIA can help us preserve structural information on unknown chemicals, and as deconvolution algorithms improve, the benefits will only increase.” – Dr. Cristina Balcells.

The future of SWATH DIA in exposomics and metabolomics looks promising, with ongoing advancements in data processing and deconvolution algorithms. By making their tools publicly accessible and developing user-friendly interfaces, Vinicius and Cristina aim to facilitate broader adoption of SWATH DIA, enabling more researchers to leverage its powerful capabilities for comprehensive chemical analysis.

Watch the webinars

Bridging Exposomics and Metabolomics in a Single LC-MS Run

Optimizing SWATH-DIA for Exposomics and Metabolomics

Meet the presenters

If you are interested in learning more about the techniques discussed, you can contact the presenters using the contact details below. Cristina’s work has not yet been published, but you can read Vinicius’s publication on this topic for more detailed insights here.

Dr. Hernandes – Connect on LinkedIn

Dr. Balcells – Connect on LinkedIn

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