John Fenn, winner of the 2002 Nobel Prize in Chemistry, owes Yale University more than US$1 million in royalties and legal fees for secretly patenting his prize-winning electrospray ionization process (ESI), according to Connecticut District Court judge Christopher Droney.

Fenn invented the ESI in the late 1980s, which enables mass spectrometric analysis of large molecules, such as proteins, nucleic acids and carbohydrates. However, by not informing the university when he applied for a patent while a professor at Yale, Fenn violated the university's intellectual property policy.

The patent (US 5,130,538), which was issued to Fenn in 1992, has generated more than US$5 million in royalties, and will not expire for another 6 years. Yale's policy allows the first $100,000 royalties to be split equally between the inventor and the university; the inventor retains 40% of the second $100,000 and, if royalties exceed $200,000, the proportion retained by the inventor drops to 30%. Fenn's patent has already earned more than $5 million in royalties and will not expire for another 6 years.

When Yale found out about the patent, it claimed rights to it and asked Fenn to re-assign the patent to the university, but Fenn refused. Fenn sued Yale after the University struck a licensing deal with Analytica without his involvement, alleging theft, tortuous interference with business relations and violations of the Connecticut Unfair Trade Practices Act. Yale responded to Fenn's lawsuit by counterclaiming for breach of contract, fraud, negligent misrepresentation, theft, unjust enrichment and seeking assignment of the '538 patent.

The judge determined that [John] Fenn knew Yale rightfully owned his invention.

Although Fenn argued that he had rights to his discovery under the Bayh–Dole Act — which gives US universities the right to own inventions arising from federally funded research and license the technologies to companies for commercial development — the judge determined that Fenn knew Yale rightfully owned his invention under the University's official patenting policy. The judge also agreed with the university that Fenn had concealed material facts from Yale so that his actions, even after applying for the patent, would not be discovered. The court assigned the '538 patent to Yale, and awarded them treble damages of US$545,114 and punitive damages of US$492,435, in addition to any attorney fees incurred.