Mass Spectrometry Method Not Patent Eligible in Ex Parte Appeal

The PTAB held that the claims in Ex parte Quimby, Appeal No. 2016-004681 (June 2, 2017) were directed toward unpatentable subject matter.  Of particular interest given the claim language, the Appellant was unsuccessful with arguments that 1) the claims do not disproportionately tie up the use of any underlying idea, 2) the claim provides an improvement in the technological field of mass spectrometry, and, 3) with respect to dependent claim 3, that the claims tied the mathematical formula with technological field of mass spectrometry analyte detection. (citing Research Corporation Technologies Inc. v. Microsoft Corp., 627 F.3d 859 (Fed. Cir. 2010)).

The independent claim is as follows:

  1. A method for selecting a target ion and a plurality of qualifier ions for identifying an analyte by mass spectrometry, the method comprising:

(a) obtaining a reference spectrum for the analyte;

(b) identifying a retention time window for the reference spectrum;

(c) extracting a matrix spectrum over the retention time window;

(d) measuring the abundance of each of a plurality of matrix ions in the matrix spectrum to produce a noise value at each matrix ion;

(e) calculating a signal-to-noise value for each of a plurality of analyte ions by dividing the abundance of each analyte ion by the noise value at a corresponding matrix ion;

(f) assigning the target ion as the analyte ion having the highest signal-to-noise value; and

(g) assigning a qualifier ion as the analyte ion with the next highest signal-to-noise value.

In the first step under the Alice framework, the PTAB agreed with the Examiner that claim 1 is directed to an abstract idea because the recited steps amount to nothing more than mere instructions for implementing the idea of selecting a target ion and a plurality of qualifier ions from mass spectra. In citing McRO, Inc. v. Bandai Namco Games Am. Inc., 837 F.3d 1299, the PTAB concludes that the claim does not recite an improvement to a particular computer technology.

In the first step, the Appellant argued that the claims “do not ‘risk disproportionately tying up’ the use of any underlying idea” and the claimed method is “limited to the calibration of a mass spectrometer for detection of a specific analyte.”  The PTAB was unpersuaded

“[B]ecause the fact that a claim may not completely preempt an entire underlying idea does not ipso facto render the claim patent-eligible. See Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1379 (Fed. Cir. 2015) (“[wjhile preemption may signal patent ineligible subject matter, the absence of complete preemption does not demonstrate patent eligibility.”).”

In the second step under the Alice framework, the PTAB agreed with the Examiner that each step in claim 1 is conventional and does not amount to significantly more than the implementation of the abstract idea of selecting the target and qualifying ions using a mathematical formula.

In the second step, with respect to the Appellant’s argument that “calculating a signal-to-noise value” step of claim 1 provides an improvement in the technological field of mass spectrometry, the PTAB concluded that this argument is conclusory and, without more, insufficient to “‘transform the nature of the claim’ into a patent-eligible application.” Alice, 134 S. Ct. at 2355.

Claim 3 depends from claim 1 and further recites:

wherein step (e) further comprises calculating a signal-to-noise value for each of a plurality of analyte ions by dividing the abundance of the analyte ion by the noise value at a corresponding matrix ion, and multiplying by a square root of the m/z of the analyte ion.

The Appellant argued that this step “clearly ties[s] a mathematical operation to the processing of the spectra which, in turn, transforms the spectra and improves the technological field of mass spectrometry analyte detection.” (citing Research Corporation Technologies Inc. v. Microsoft Corp., 627 F.3d 859 (Fed. Cir. 2010)).  In response, the PTAB held: 

“Appellants’ reliance on the Research Corporation Technologies decision is misplaced because the instant claims are distinguishable from the claims at issue in that case. In Research Corporation Technologies, the Court observed that the claimed methods…at issue incorporated algorithms and formulas that control the masks and half-toning. Research Corporation Technologies,627 F.3d at 869. “The invention presents functional and palpable applications in the field of computer technology.” Id. Here, the claimed subject matter is not in the field of computer technology. Rather, it involves the collection, compilation, and mathematical manipulation of mass spectral data from known databases.”

For another recent ex parte decision with the same outcome with respect to Research Corporation Technologies, see Ex parte Councill, Appeal No. 2015-003970 (May 11, 2017). 

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