Ever since Gregor Mendel began experimenting with pea plants in the mid-19th century, scientists have explored genes as the sources of desirable and undesirable traits in fruits and vegetables.  More recently, the direct manipulation of genes has led to a growing number of genetically-modified foods developed for better taste, longer shelf life, or pest resistance.

However, as Dr. Jessica Prenni and her team at Colorado State University's (CSU) Proteomics and Metabolomics Facility have discovered, not all quality traits have a genetic marker.  Their research suggests that the next big wave in food science may come from the field of metabolomics.

"One of our more recent papers appeared in a plant technology journal," said Dr. Prenni.  "We utilized non-targeted metabolite profiling to discover novel markers of quality traits in a breeding population of malting barley."

The research, funded by the malting barley and brewing industry, explored the idea of using metabolites to guide breeding beyond genomic markers.

"We were able to show that we could correlate small-molecule metabolites with malting quality traits that were measured on these breeding lines, and build a model that showed how these metabolites were predictive of certain malting quality traits, which could be very informative in the breeding process," Dr. Prenni noted.  "It was significant because there were not necessarily genetic markers for all of these quality traits."

The barley research involved 72 different lines in a breeding population grown in two locations.

"We were able to see differences in the metabolome in the same exact barley line, just based on where it was grown," said Dr. Prenni.  "This particular paper has generated quite a lot of interest in the agricultural community, which is now recognizing the value of looking at the metabolites, because they’re so much closer to phenotype than the genes are.  We’ve been getting a lot of feedback from people who want to explore this approach in other crops."

Identifying metabolites that could lead to better-tasting beer is just one of the many projects being explored by Dr. Prenni and her staff of 10 at the Colorado State University facility she has led since 2006.

"We do everything from very routine types of analysis to collaborative research projects," she explained.  "There are two arms to the lab; one is focused on protein analysis and proteomics, and the other is on metabolomics, small molecules.  We really work with a lot of different disciplines."

Mass spectrometry has become increasingly vital to the Facility's operations in recent years.

"When I came here to CSU, we got some funding to establish a metabolomics program, and we did a thorough investigation of all the instruments available and ended up buying the Waters QToF Micro," said Dr. Prenni.

The Proteomics and Metabolomics Facility has since added a Xevo G2-S QToF, Xevo G2-S ToF, and Xevo TQ-S systems -- all paired with Waters ACQUITY UPLC systems -- to their instrument resources.

"The ability to do MS^E data acquisition has been a big driver in our decision to stay with Waters," noted Dr. Prenni.  "It's invaluable for the application of non-targeted metabolite profiling.  Over the last few years, we have developed a new data analysis workflow that allows us to de-convolute the MS^E data that we get from a non-targeted metabolite profiling experiment, and recreate spectra for the metabolites that we’re seeing at both low - and high collision energy.  We then use those spectra to help with the process of metabolite annotation."

Prenni's team has focused much of its own research on metabolite identification.

"The more that we can annotate, the more that we can identify, the more biological insight we can get from the data sets," said Dr. Prenni.  "So for example, if we do a non-targeted profiling experiment, we might have 100 samples, half of which are controls and half of which are from a disease state.  An investigator will want to know the differences in the metabolome between these two groups.  And so we will profile them using our non-targeted workflow, and then we’ll perform statistical analysis on the data.  And we might come up with maybe 200 metabolites that are significantly different between the two groups.  But usually, we can only annotate or identify maybe 20-50% of those.  That’s significant, but it's still limiting.  And so our big goal is to push that more and more towards 100%."

The Proteomics and Metabolomics Facility has recently added  a new tool; Dr. Prenni and her team collaborated with Waters on the development and testing of the recently-launched Waters ionKey/MS system.

"The micro-flow regime is hugely beneficial in many ways.  For one, we use a lot less solvent," she commented.  "We calculated it at about 150 times less solvent than you would use if you were at a typical standard-flow assay.  Another big advantage is that it allows us to go back and forth between micro-scale and nano-scale on the same instrument by taking one tile or iKey out and putting the other one in, essentially enabling small molecule and peptide work on the same system.  Finally, we are also seeing huge boosts in sensitivity in the microflow regime.  In one of our recent papers describing a multiplexed steroid assay in serum, we show a 100 to 400-fold increase in on-column sensitivity as compared to a standard flow assay."

Dr. Prenni’s team intends to accelerate their metabolite identification work by building spectral libraries.  She sees ion mobility and the use of collisional cross-sections as additional, measurable physical parameters that can aid the effort.

An analytical chemist, Dr. Prenni is supported by five Ph.D.-level scientists -- a microbiologist, a chemist, a biochemist, a plant scientist, and a biologist.  She is quick to point out that everything done in the laboratory is a team effort.

"Corey Broeckling, my associate director, has played a huge role in our success, particularly in the development of the algorithms for the MS^E data for non-targeted metabolite profiling," she noted.

In addition to the Facility staff and the students she teaches, Dr. Prenni guides another important team -- her family.

"The thing that occupies most of my time is my children," she said.  "I have three.  So I spend a lot of time with them and their various activities."  Like many people in her adopted state, she and her family are skiers who visit Winter Park regularly.

The Portland, Oregon native began her scientific journey as an undergraduate at Southern Oregon University, where she earned a B.S. degree in Chemistry.

"I just always had a love of science, and it was something that came easily to me," said Dr. Prenni.  "I had some great lab experiences as an undergraduate, and then I had a very, very good mentor as a graduate student at the University of Colorado where I obtained my Ph.D.  I learned a lot of intangible leadership skills from her, and I’ve been able to apply them."

For Dr. Prenni and her team, unlocking the mysteries of molecules is a quest that makes every day interesting.

"One of the beautiful things about mass spectrometry is that a molecule’s a molecule," she said with a laugh, "whether it’s a molecule being studied in a plant or a human or a dog.  To us, they’re all molecules.  And so being able to think broadly and think about how you could use this amazing technology to answer all these broad questions -- I think that’s really what has been a big part of our success.  We’ve recognized that and we’ve been able to communicate that to the research community at CSU."