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Verne M. Willaman Gateway to the Sciences.

Metabolomics Core Facility continues to expand while pushing scientific bounds

7 September 2022
Ashley Shay, Sergei Koshkin, and Andrew Patterson wearing lab coats
Ashley Shay, director of the Metabolomics Core Facility; Sergei Koshkin, assistant research professor; and Andrew Patterson, John T. and Paige S. Smith Professor, professor of molecular toxicology, professor of biochemistry and molecular biology, and scientific director of metabolomics at Penn State. 

Established nearly a decade ago, Penn State’s Metabolomics Core Facility is housed in the Huck Institutes of the Life Sciences on the University Park campus. The primary goal of the facility is to identify and quantify the small molecules (or metabolites) in plant and animal biofluids, cells and tissues. Additionally, the research scientists at the facility perform proton nuclear magnetic resonance (1H NMR) spectroscopy to determine the structure of organic compounds and to analyze samples containing protons.

Metabolites can be defined as endogenous compounds such as amino acids, lipids, sugars, and organic acids, among others. This could include compounds found in foods, the microbiome, and those in the environment (the exposome). In the study of metabolomics, mass spectrometry is often employed, in order to detect and quantify many thousands of metabolites simultaneously.  Measuring and comparing large numbers of metabolites present in biological samples can offer insights into the underlying biological processes involved in their production.

“Creation of the Metabolomics Facility at Penn State was the vision of Drs. Gary Perdew, Jeff Peters, Steve Benkovic, Vivek Kapur, and Peter Hudson,” said Andrew Patterson, John T. and Paige S. Smith Professor, professor of molecular toxicology, professor of biochemistry and molecular biology, and scientific director of metabolomics at Penn State.

“Substantial investment from Penn State — the Huck Institutes, Eberly College of Science, College of Agricultural Sciences, and Penn State Cancer Institute — along with the dedication and hard work of past facility director Dr. Philip Smith, helped to create a truly impressive and unique environment to conduct trans-disciplinary metabolomics research,” said Patterson, adding, “Growth of metabolomics at Penn State has been fostered by amazing graduate students and postdoctoral fellows, along with supportive and engaged faculty.”

In May of 2022, Ashley Shay came aboard as the new director of the Metabolomics Core Facility. She said she hopes to expand the facility's capacity and bring in more collaborations from within Penn State and beyond. Shay earned her doctorate in molecular medicine at Penn State in 2017, and returned to work at the University partly because it was a supportive environment, she said, and partly because her diverse scientific background, fostered at Penn State, is a great match for the facility.

Shay's research interests lie in the implementation and expansion of liquid chromatography-tandem mass spectrometry to determine the chemical structure of novel lipid mediators (secreted by multiple cell types involved in inflammatory processes) and metabolites in inflammatory diseases. She also utilizes "in vitro" and "in vivo" approaches to determine their functions. 

"Mass spectrometry is a very versatile and powerful tool that can be implemented across multiple scientific disciplines," said Shay. "The facility is currently working on numerous projects that include testing samples from fungus to human tissues and everything in between."

Currently, there are two full-time research faculty at the Metabolomics Core Facility. The machines can run 24/7, and Shay, along with Sergei Koshkin, assistant research professor, are responsible for the health and safety of the lab and its equipment 24 hours a day.  

Koshkin brought his enthusiasm for doing great science to the facility in early 2022 after relocating from Russia. He specializes in developing and applying mass spectrometry methods to analyze biomolecules in living systems. He is also interested in identifying prognostic, diagnostic, and predictive biomarkers and researching mechanisms and regulations of normal and disease-causing processes in these systems.

"Modern mass spectrometry is very fast and sensitive. It can help provide answers to complex problems by providing large and diverse data sets," said Koshkin. "Sometimes researchers have very broad questions at first and giving them all this data can sometimes help them narrow the scope of their work." 

Koshkin completed both his master of science and doctoral degrees in chemistry from Kazan Federal University, Russia, in 2010 and 2015, respectively. After completing his doctorate, he continued at Kazan Federal University working as a technician, chief engineering officer for research and development, research fellow, and senior research fellow. He also worked as the head of the center for mass spectrometry analysis at the Federal Service for Surveillance in Healthcare, the Russian equivalent of the FDA [U.S. Food and Drug Administration], from 2020 through 2022. His work has been published in more than 22 academic journals. 

"I am excited to be at Penn State and looking forward to expanding the breadth of mass spectrometry work at the University," Koshkin said. 

Shay, who worked as a research fellow, instructor, and mass spectrometry core director for the Center of Experimental Therapeutics and Reperfusion Injury at Harvard Medical School, has been published in more than 15 academic journals and has filed a provisional patent application along with collaborators. She said that, in the future, she would like to increase the visibility of the facility and foster interests in learning about mass spectrometry.

“We are receiving two state-of-the-art LC-MS instruments. One is the Thermo TSQ Quantis Plus Triple Quadrupole mass spectrometer and the other is the Thermo Orbitrap Exploris 120 mass spectrometer, both of which are coupled with Vanquish HPLC systems. The addition of these instruments will increase the facilities productivity and versatility,” said Shay.

The Vanquish HPLC system are currently the most advanced liquid chromatography instruments available. These new instruments, along with the others that are currently at the core facility can be utilized by Penn State faculty, staff, and students — even if they are already engaged in a project at another core facility. A cornerstone of the research community at Penn State is collaboration and that extends to include the core facilities, but research groups may not know that multiple facilities can be used to further explore their samples.

“Something I think research groups under-utilize is the potential for interactions between the core facilities.” said Shay. “For example, you can have cell lines grown by the Sartorius Cell Culture Facility and then sent to the Proteomics and Genomics cores to obtain rich datasets that provide a more complete picture to your scientific question.”   

About the Huck Institutes’ Core Facilities at Penn State

The directors and staff at the Huck Institutes’ Core Facilities are world-class research faculty with outstanding academic credentials, expert mastery of instrumentation, and up-to-date knowledge on the scholarship in their fields. Huck facilities provide services to over 300 research groups annually, and are available for researchers at Penn State and outside the University. To learn more about the core facilities and view a video tour, visit the website.