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Functional and Systems Biology

Access Advanced Tools for Metabolomics through EMSL User Program

Attend the EMSL LEARN webinar on Feb. 7 to learn about the variety of metabolomics capabilities available through EMSL

Maegan Murray |
Robert Young stands next to NMR

Nuclear magnetic resonance is a non-destructive resource that provides both quantitative and key molecular structure information. It is available use as part of several current and upcoming calls for proposals through the Environmental Molecular Sciences Laboratory. (Photo by Andrea Starr | Pacific Northwest National Laboratory) 


Metabolites are vital molecular components needed for sustaining everyday life. 

They serve as base materials for energy conversion in living systems and as key nutrients that feed those systems. They are important for signaling next steps in a process or pathway, and can reveal mechanisms of various human disease and diverse biological processes. 

Painting a full picture of metabolites together in a system—a field known as metabolomics—helps scientists to better understand the health and state of an organism and its response to different influences, such as nutrients, pollutants, and disease. 

Measuring and painting a complete picture of a metabolome, however, is challenging. Due to the vast number and classes of metabolites in a system, as well as their ubiquitous presence in different types of matrixes, a variety of methods and advanced tools are required for their analysis. 

Through the Environmental Molecular Sciences Laboratory, scientists can access a range of powerful instruments all in one location to acquire a full picture of what metabolites are present in a system of interest and gain insights into how they are created, used, and eliminated. EMSL also offers the computational tools to process data from these capabilities and model it in a constructive and useful way. 

As part of a free upcoming EMSL LEARN webinar, experts will speak about the variety of platforms available through the EMSL user program that allow scientists to dive deep into the field of metabolomics. The webinar takes place from noon – 1 p.m. on Wednesday, Feb. 7. Register to attend via Zoom. 

At a quick glance, the webinar will provide an overview about: 

  • Metabolomics, its challenges, and the needs for complementary approaches 

  • Pros and cons of available capabilities 

  • Expertise available for each platform and area of study at EMSL 

  • How scientists can access these tools through upcoming calls for proposals at EMSL 

The instruments to be discussed include: 

Each of these capabilities are available at no cost through several competitive calls for proposals through EMSL and partnering institutions. A handful of calls for proposals are open now, with letters of intent due in February and March. For more information and to submit a proposal, visit

Gas chromatography-mass spectrometry 

Presented by Nathalie Munoz | Chemist | EMSL 

In addition to providing a brief overview of metabolomics, its challenges, and the need for complementary approaches, chemist Nathalie Munoz will provide an overview of GC-MS. 

GC-MS instruments provide untargeted measurements of volatile and semi-volatile molecules.  

Attendees will learn the basics of how a GC-MS instrument works, how a sample is prepped before it is analyzed through instruments, the pros and cons of the technique, as well as the type of data generated after analysis is complete. 

“I hope attendees understand why different analytical platforms are needed to investigate the metabolome in-depth, as well as the strengths of GC-MS and some practical notes about using this type of instrumentation,” Munoz said. 

Real-time mass spectrometry 

Presented by Karl Weitz | Chemist | Pacific Northwest National Laboratory (PNNL)

Chemist Karl Weitz will showcase a newer technology called real-time mass spectrometry. It can be used as a non-invasive means to look for biomarkers in human breath, as well as in other applications such as monitoring dried soil as it is re-hydrated to examine microbes as they regenerate and start to respire after extended dormancy. It enables researchers to see how living systems interact with their environment in real time. 

“Real-time mass spectrometry is basically the monitoring of living systems at the speed of life,” Weitz said. 

The instrument even allows researchers to monitor terrestrial, or Earth-based, life as it lives in environments on other planets—or almost. 

“Since we know the atmospheric composition on Mars, we can recreate it in exposure bags and expose to dry soil to it,” Weitz said. “We then hydrate the soil and monitor respiration rates as the microbes come out of dormancy in a [simulated] Martian atmosphere. This gives us a new and unique insight on possible Mars terraforming strategies.” 

The technology was recently added as a new capability through the EMSL User Program. 

Liquid chromatography-mass spectrometry 

Presented by Priscila Lalli | Biomedical scientist | PNNL

Biomedical scientist Priscila Lalli will discuss basic principles of LC-MS. The platform provides identification of a wide range of small molecules involved in metabolic reactions. 

Lalli will talk about the advantages and challenges in the field of LC-MS metabolomics, the difference between targeted and untargeted metabolomics, and the different types of columns used for polar and non-polar metabolites and lipids with the platform. 

“LC-MS metabolomics and lipidomics is commonly used by the [EMSL] user community to understand the metabolic changes occurring in their soil and plant systems due to perturbation,” she said. 

Lalli said users can choose targeted or untargeted approaches. Untargeted approaches include both lipids and non-lipid species. 

Researcher work with a liquid chromatography-mass spectrometer
LC-MS allows users to detect a wide range of small molecules involved in metabolic reactions. Learn more about the resource as part of an EMSL LEARN Webinar on Feb. 7.  (Photo by Andrea Starr | Pacific Northwest National Laboratory)


Nuclear magnetic resonance 

Presented by Robert Young | Chemist | EMSL 

Chemist Robert Young will provide an overview of NMR instruments and their robust analytical capabilities suited for metabolomics research. 

NMR is non-destructive resource that provides quantitative and key molecular structure information. It has applications in a wide range of chemistry areas including biochemistry, materials science, and medicine. It requires minimal sample preparation and the measurements it produces are robust and highly reproducible. Although it has lower sensitivity relative to other techniques, it can often detect metabolites missed by other methods and is highly complementary to mass spectrometry in metabolomics research. 

Young will dive into typical workflows from sample prep to data analysis and will end with some practical considerations when sending samples to EMSL. 

“There will be some contrast with mass spectrometry capabilities to highlight how they are highly complementary techniques [in metabolomics],” Young said.