U-M Bioinformatics Startup, Fragmatics, Celebrates Licensing with Startup Bell Celebration

5/20/2025

On May 20, the team from Fragmatics joined Innovation Partnerships at the North Campus Research Complex to honor their official launch as a University of Michigan (U-M) startup with a bell ringing celebration. In attendance was U-M’s Dr. Alexey I. Nesvizhskii, the Godfrey Dorr Stobbe Professor of Bioinformatics, professor of computational medicine and bioinformatics, professor of pathology and founder and CEO of Fragmatics. Family, colleagues and supporters of the Fragmatics team joined the celebration, which included glowing remarks from Drew Bennett, director of software, content licensing and research partnerships as well as Jeff Kittendorf and David Olson, mentors-in-residence at Innovation Partnerships.

Fragmatics is a bioinformatics company developing tools for mass spectrometry-based proteomics, or the study of proteins and their cellular activities. Fragmatics’ flagship product, MSFragger, has been called the “Gold Standard” of proteomic search engine optimization and related tools. With MSFragger, researchers and clinicians have the ability to identify peptides with increased speed and accuracy compared to competitor systems. The data collected using MSFragger can be used to inform applications ranging from oncology to drug discovery.

“The technology Fragmatics is bringing to market is world-changing, providing outputs several times faster than their competitors,” said Bennett on the impact of Nesvizhskii’s work.

“I knew going into this project that Fragmatics was providing a powerful tool, but it’s been truly amazing to see the scale of impact that the company is having so early on. It’s not often you have a product with an existing client base and interest from companies abroad before you’ve even spun out into a startup.”

While Fragmatics recently celebrated their official startup launch, their technology has been in development for more than a decade. The Nesvizhskii Lab disclosed the application for what would become MSFragger in 2016. The tool was originally built for an academic user base, as Nesvizhskii—an academic himself—believes strongly in the power of supporting university researchers and providing no-cost solutions to advance their work. However, with the creation of a cost structure and additional mentorship from the team at Innovation Partnerships, the MSFragger technology was eventually brought to a commercial audience. MSFragger has seen incredible success in both academic and commercial applications, with many top life science and pharma companies utilizing this novel technology including Pfizer, Novartis and Moderna. Today, Fragmatic’s proteomics technology has signed thousands of academic licences for university use and has grown their commercial customer base to more than 40 licensees. 

“The support this work has received from Innovation Partnerships and the University of Michigan has been nothing short of astounding,” said Nesvizhskii on the experience of bringing Fragmatics to market.

“I am incredibly grateful to Drew Bennett, David Olson, Jeff Kittendorf and the rest of the Innovation Partnerships team, as well as my department chairs, for their tireless support of my research. Communicating the practical significance of your research is vital, now more than ever, and it’s been such a privilege to work with an organization that not only understands the significance, but can push your research to places you never thought possible.”