#WhyIScience Q&A: A research scientist uses mass spectrometry to discover how metabolites affect human health

Amy Deik remembers the day in fifth grade when she learned the water cycle. As she drew arrows connecting the evaporation, condensation, and precipitation phases, she thought, “This makes sense to me. This is how my brain works.” That interest in science led her to a weekend science course and a field trip to a plant research laboratory, where she saw scientists hybridizing roses and genetically modifying tomatoes. At 11 years old, she knew she wanted to be a botanist. 

Deik received her bachelor's degree in botany from Connecticut College and immediately went to work at International Paper, a paper manufacturing company, where she engineered trees to grow faster. She’d always had an interest in genetics research and moved to Boston in 2002 to work for a genetics-focused startup. 

In the mid-2000s, mass layoffs at the startup left only Deik and two other people to continue the company’s research. Deik had to quickly learn how to operate the firm’s mass spectrometers — machines that can measure tiny amounts of molecules such as metabolites and proteins. After the startup folded, Deik worked as an analytical chemist at a drug-repositioning company called Gene Logic, where she first met Clary Clish, who would later become the director of the Metabolomics Platform at the Broad Institute of MIT and Harvard. Deik moved to the Broad in 2009 and joined Clish as a biochemist in the Platform, where she also serves as lab manager. 

In this #WhyIScience, we spoke with Deik about metabolomics (the large-scale systematic study of metabolites) and the intersectionality of being a woman of faith and a scientist.

What do you do as a research scientist at Broad?

A lot of what we do at the Metabolomics Platform is look for early indicators of disease and use metabolomics to monitor disease progression. We do that with metabolite profiling — determining the levels of hundreds of metabolites in a sample and how that connects to human health. I run mass spectrometers daily to analyze thousands of small molecules that are present in a variety of samples, such as plasma, a mouse liver, or a cell culture. I run our lipid method, which annotates over 250 different lipids.

I also serve as our group's lab manager. For us, that means a lot of sample management. We are involved in dozens of collaborations each year inside and outside the Broad, so I'm always on call when samples are coming in and out. I also maintain the freezer inventory, know what samples are waiting to be aliquotted into smaller volumes for our four platform methods, and determine what methods we need to run on those samples. 

How do lipids relate to human health?

Lipids are a type of metabolite that are insoluble in water. They are diverse in size, polarity, absorption capability, and solubility. They serve essential functions in the body, such as making up all the membranes in our cells and transporting large molecules. A commonly known lipid species is triglycerides, which you get a blood test for at your annual physical, but there are also a lot most people have never heard of.

Different classes of metabolites change in different disease states. You might expect to see a change in lipids when a person has a metabolism-related disease like diabetes or cardiovascular disease. But you might not expect to see a change in various cancers. A few years ago, we discovered a lipid biomarker that helps diagnose a rare lung disease in women called lymphangioleiomyomatosis, which at the time had no known genetic cause and was previously very difficult to diagnose.

How is metabolomics evolving?

In the last decade, scientists have revolutionized mass spectrometers’ speed, precision, and specificity. I used to only be able to detect the difference of a full mass-unit. Now the resolution of these instruments is less than 1 part-per-million, which can correlate to the fourth decimal position.

A new technology we are adding to our platform is imaging mass spectrometry. With it, we can take slices of a specific tissue and ionize them with the spectrometer. The machine shows you specific molecule masses at different places within the slices. For example, you can see if molecules are in certain regions of a slice of a mouse brain and not others. It’s a brand new technology, so there are a lot of potential applications that we just don’t know yet. I'm curious to see how we use it and the insights it might give us.

How does your work intersect with other parts of your life?

I’m a woman of faith and it's interesting to be at the intersection of Christianity and science. Most people believe that you can only have one worldview or the other, but I've never had a problem with having both. I love the idea that, as a scientist, I’m allowed to want to understand the natural world around me. I believe that it’s a God-given right for us to figure out how things work and be fascinated by that. 

From conversations with people who share my faith, I think scientists can be viewed as scary people who do whatever they want just because they can. But I believe that scientists are, or try to be, very thoughtful, moral, and ethical in their work. And so I try to speak about science to people in a way that makes it understandable and therefore less scary.