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Applera Challenges Proteome Sciences’ European Patent for Isobaric Mass Tags

For the past several years, Proteome Sciences has been counting on in its isobaric mass-labeling technology to bring in some cash, and when the European Patent Office granted the UK-headquartered company a patent for the technology late last year, it appeared the channels to a steady stream of revenues had been opened.
But earlier this month, Applera posed a challenge to Proteome Sciences, filing an opposition to its European patent with the EPO and asking the organization to revoke the patent in its entirety. If Applera is successful in its opposition, it could have crippling consequences for Proteome Sciences.
In its opposition documents, Applera said the patent should be revoked for a number of reasons: it lacks novelty; does not involve any new inventive procedures; does not “disclose the invention in a manner sufficiently clear and complete for it to be carried out” by a knowledgeable person; and the subject matter of the patent reaches beyond “the content of the application/of the earlier application as filed.” 
Proteome Sciences, however, said that the substance of the opposition being raised now had been previously addressed and resolved during the patent process, and that the action taken by Applera does not have any effect on its own ongoing plans to out-license the Tandem Mass Tag technology.
The patent, number EP 1275004, was granted on June 13, 2007 and covers isobaric mass-tag technology, a method for labeling analytes in multiplex in a mass spectrometer. When it received its European patent, Proteome Sciences called it a “major milestone” and said it expected to be paid by other companies that were using the technology.
"The Grant of TMT1 in Europe puts Proteome Sciences in an outstanding position to generate substantial revenues from a combination of licence payments, back-license payments, [and] product sales and royalties,” CEO Christopher Pearce said in a statement issued last spring after being told by the EPO of the impending patent grant. “The market for isobaric tandem mass tags continues to grow disproportionately fast and earlier estimates over the patent lives appear to have considerably underestimated the scale and importance of quantitative mass spectrometry.”

Proteome Sciences said that it is reviewing Applera’s opposition and will be submitting a “full, robust, and thorough response to the opposition.”

While Proteome Sciences had declined to name other companies that may be using the TMT technology, among those that are already selling products using isobaric mass-tag technology is Applera company Applied Biosystems, with its iTRAQ reagent.
In its opposition filing with the EPO on March 11, Applera does not allege Proteome Sciences’ technology infringes other technologies or patents, and on face value, at least, appears to be a move taken to prevent Proteome Sciences from claiming any rights to licensing fees from Applera/ABI.
Officials from Applera could not be reached for comment in time for this publication. It is unknown if it plans to contest Proteome Sciences’ US patent for the same technology. The company also owns the patent rights to the technology in Australia, New Zealand, and Canada, and has pending applications in parts of Asia, including China and Japan, and elsewhere.
On its charge that Proteome Sciences’ technology lacks novelty, Applera said that TMT contains technology that mirrors technology developed by Yuriy Dunayevsky and colleagues in 1996 as well as technology developed by Hendrick Geysen in 1997.
On its claim that TMT lacks any inventive step, Applera cites earlier work by Guenter Schmidt and colleagues that Applera says is mirrored by the TMT technology.
Applera is requesting “oral proceedings” if its request for revocation of the patent is denied.
In a statement, Proteome Sciences said that it is reviewing Applera’s opposition and will be submitting a “full, robust, and thorough response to the opposition.”
Ian Pike, chief business officer for Proteome Sciences, told ProteoMonitor that the substance of Applera’s opposition had been raised during “third-party observations” as the EPO was evaluating the patent application. Because such observations are done anonymously, Proteome Sciences does not know who raised the earlier oppositions, but “you can guess who it is,” Pike said.
Proteome Sciences addressed them, the oppositions were dismissed, and the patent was subsequently granted.
Applera’s action does not change Proteome Sciences efforts to license the technology, Pike said.
“We’re in active discussions,” with interested parties, Pike said, reiterating earlier guidance that the company expects licensing agreements to be in place by “early 2008.” Pike declined to elaborate.
If Applera’s challenge is successful, the consequences to Proteome Sciences could be severe. Along with its ProteoShop platform for protein and peptide biomarker discovery and validation, the TMT technology is viewed as the main revenue generators for the company. Last year, in anticipation that it would finalize licensing deals for the technology, the company went into overdrive producing TMT reagents to have them available to licensees.
“This will provide two significant benefits to our cashflow, both from the early sale of TMT raw materials, and also from the accelerated timing of royalty payments,” R.S. Harris chairman of the company’s board said in interim 2007 report released last summer. “The completion of the TMT licenses will generate substantial revenue for our Company and these will be further enhanced by new and additional high value/high volume applications,” he added.

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