A Nobel Laureate and former Yale professor must pay the University more than $1 million for stealing, licensing and unjustly profiting from his own prize-winning invention, a federal judge ruled Thursday.

Though John Fenn GRD ’40 argued that he had rights to his discovery under the Bayh-Dole Act, a federal patent law, U.S. District Judge Christopher Droney determined that Fenn knew Yale rightfully owned his invention — a method of mass spectrometry for analyzing large biological molecules — under the University’s official patenting policy.

“Dr. Fenn only obtained the patent through fraud, civil theft, and breach of fiduciary duty; he may not profit from his own wrongdoing,” Droney wrote in the decision. “A patent is property which, when wrongfully obtained, may be reassigned to its rightful owner.”

Droney ordered that Fenn, 87, pay Yale for penalties, royalties and legal bills and hand over the rights to his patented invention, which earned him a share of the 2002 Nobel Prize in chemistry.

The judge’s decision stated that Fenn misled the University about the value of his invention, while he secretly obtained a patent in 1992 and sold licensing rights to Analytica, a company he jointly owned.

“Clearly, Dr. Fenn’s motives included an intentional desire to ‘show up’ and embarrass Yale by depriving the institution of a valuable patent, but also included a desire to keep permanently the patent and the profits it generated,” Droney wrote.

Yale’s patenting policy states that the University collects a portion of faculty royalties to fund further research. But Yale does not claim any ownership of inventions unrelated to an employee’s designated activities or made without use of University facilities.

All University inventions must be reported to the Office of Cooperative Research, whether or not Yale will claim joint ownership. OCR Managing Director Jonathan Soderstrom said patenting policies like Yale’s are common in academia.

Fenn said he never intended to deceive the University and is considering an appeal, but he would not comment further on the case, as his attorneys are still examining the implications of the court decision.

“My side of story is a good one, which has not been heard very much in this case,” Fenn said. “That will be clear when more of the facts come out.”

Fenn said he completed development of electrospray ionization after Yale’s retirement policies forced him to forfeit laboratory space and graduate assistants when he turned 70.

The legal conflict began when Fenn and his Analytica business partner, graduate student Craig Whitehouse, entered litigation over patenting rights. Fenn sued Yale in 1996, after the University struck a licensing deal with Analytica without his involvement. Yale then filed counterclaims, seeking assignment of the patent and damages for charges ranging from breach of contract and fiduciary duty to theft.

Fenn said he believes Yale’s division of royalties is unfair. Under current policy, the first $100,000 of net royalties is split 50-50 between the inventor and University, with 40 percent of the second $100,000 and 30 percent of anything above $200,000 going to the inventor.

Fenn’s patent, No. 5,130,538, has already earned more than $5 million in royalties and will not expire for six years.

Yale spokeswoman Helaine Klasky said the University is glad to put the matter behind it.

“We are pleased by the result in this case and, in particular, by the court’s vindication of the Yale patent policy,” Klasky said. “Yale was unable to resolve this matter out of the courtroom, despite its repeated attempts to mediate with Dr. Fenn after he sued the University.”

Yale Provost Andrew Hamilton said Fenn’s work was revolutionary for the analysis of proteins and nucleic acids.

“None of these recent events detracts from the impact of John Fenn as a scientist or the importance of the work that he did at Yale during his career here,” Hamilton said. “Prior to Fenn’s work only small molecules … could be vaporized and measured by mass spectrometry, and so announcement of his new technique was greeted with the same awe as if elephants had been made to fly. His technique is widely used in the discovery of new drugs and by many research groups at Yale and around the world, including my own.”

Fenn, a professor emeritus at Virginia Commonwealth University, was represented by Hartford attorney Hubert Santos. Despite the ongoing conflict with Yale, he was awarded the University’s Wilbur Cross Medal in 2002.