Ex Parte Bern

Patent Trial and Appeal Board

Nov 21, 2016

12272973 (P.T.A.B. Nov. 21, 2016)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR
12/272,973 11/18/2008 Marshall W. Bern
124903 7590 11/23/2016
Park, Vaughan, Fleming & Dowler LLP -- Yao Group
2800 Fifth Street, Suite 110
Davis, CA 95618
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www .uspto.gov
ATTORNEY DOCKET NO. CONFIRMATION NO.
PROT-20080360-US-NP 7337
EXAMINER
BORIN, MICHAEL L
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
11/23/2016 ELECTRONIC
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the
following e-mail address( es):
syadmin@parklegal.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte MARSHALL W. BERN1
Appeal2015-006279
Application 12/272,973
Technology Center 1600
Before RYAN H. FLAX, TIMOTHY G. MAJORS, and
DEVON ZASTROW NEWMAN, and, Administrative Patent Judges.
FLAX, Administrative Patent Judge.
DECISION ON APPEAL
This is a decision on appeal under 35 U.S.C. § 134(a) involving
claims directed to a method for identifying potential modifications to
peptides. Claims 1-20 are on appeal as rejected under 35 U.S.C. § 101. We
have jurisdiction under 35 U.S.C. § 6(b). We reverse.
STATEMENT OF THE CASE
The appealed claims can be found in the Claims Appendix of the
Appeal Brief. Claims 1, 15, and 20 are the independent claims. Claim 1 is
representative and reads as follows:
1 The Real Party in Interest is Protein Metrics Inc. App. Br. 1.
Appeal2015-006279
Application 12/272,973
1. A method for identifying potential modifications to peptides
associated with a precursor peptide, comprising:
receiving a set of tandem-mass-spectrometry data associated
with the precursor peptide, wherein the received spectral data
indicates a measured mass for the precursor peptide and a
number of peak locations;
accessing, by one or more computers, a peptide or protein
database to obtain spectral information for candidate peptides;
generating, by one or more computers, multiple theoretical
spectra for the candidate peptides using the spectral information,
wherein generating multiple theoretical spectra for a respective
candidate peptide involves:
identifying one or more known mass modifications for the
candidate peptide;
determining at least one variable mass modification to at
least one amino acid within the candidate peptide;
varying the variable mass modification within a
predetermined range to produce a set of varied mass
modifications; and
for each varied mass modification, generating a modified
theoretical spectrum for the candidate peptide by
combining the known mass modifications and the variable
mass modification; and
identifying the potential modifications by comparing the
peak locations of the received spectral data with peak
locations of each modified theoretical spectrum in the
generated theoretical spectra.
App. Br. 25 (Claims App'x).
2
Appeal2015-006279
Application 12/272,973
The following rejection is on appeal:
Claims 1-20 stand rejected under 35 U.S.C. § 101 as directed to non-
statutory subject matter, i.e., an abstract idea. Non-final Action 2-3.2
DISCUSSION
The Examiner determined all pending/ appealed claims are directed to
an abstract idea, i.e., computational analysis, or, converting one form of
numerical representation into another (in analyzing protein mass-
spectrometry data) (claims 1-14). Non-final Action 4--5; Ans. 2. The
Examiner further determined the claims do not add limitations that transform
the abstract idea into something more than a patent-ineligible abstract idea,
as they simply require generic computer implementation (they do not
purport to improve the functioning of the computer or effect an improvement
in any other technology or technical field). Non-final Action 5.
In analyzing patent eligibility questions under 35 U.S.C. § 101, the
Supreme Court instructs us to "first determine whether the claims at issue
are directed to a patent-ineligible concept." Alice Corp. Pty Ltd. v. CLS
Bank Int'!, 134 S. Ct. 2347, 2355 (2014). If this threshold is met, we move
to a second step of the inquiry and "consider the elements of each claim both
individually and 'as an ordered combination' to determine whether the
additional elements 'transform the nature of the claim' into a patent-eligible
application." Id. (quoting Mayo Collaborative Servs. v. Prometheus Labs.,
Inc., 132 S. Ct. 1289, 1297 (2012)).
2 Appeal is taken from the Non-final Action dated Aug. 14, 2014.
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Appeal2015-006279
Application 12/272,973
Taking up the first step of the patent-eligibility analysis, claim 1 is
reasonably directed to an abstract idea because it relates to the mathematical
analysis of data; however, we note, "[a]t some level, 'all inventions ...
embody, use, reflect, rest upon, or apply laws of nature, natural phenomena,
or abstract ideas,'" and whether one takes a macroscopic or microscopic
view of a claim may be determinative on the issue. Alice, 134 S. Ct. at 2354
(quoting Mayo, 132 S. Ct. at 1293); and see Amdocs (Israel) Ltd. v. Openet
Telecom, Inc., --- F.3d --- , 2016 WL 6440387 *9 (Fed. Cir. Nov. 1, 2016).
Looking to the Specification to enlighten us as to the claimed invention, as
did the Federal Circuit in Enfzsh, LLC v. Microsoft Corp., 822 F.3d 1327
(Fed. Cir. 2016), we find it expressly explains the invention to be directed to
"techniques for analyzing mass-spectrometry data," which is the abstract
idea of the mathematical analysis of data. Spec. i-f 1. Data analysis and
algorithms are abstract ideas. See, e.g., Alice 134 S. Ct. at 2355; Bilski v.
Kappas, 561 U.S. 593, 611 (2010); Parker v. Flook, 437 U.S. 584, 594--95
(1978); and Gottschalkv. Benson, 409 U.S. 63, 71-72 (1972). Put
concisely, "[ w ]ithout additional limitations, a process that employs
mathematical algorithms to manipulate existing information to generate
additional information is not patent eligible." Digitech Image Techs., LLC v.
Elecs.for Imaging, Inc., 758 F.3d 1344, 1351 (Fed. Cir. 2014).
Turning to the second step under Alice, the facts and claimed subject
matter here are analogous to those of the recent Federal Circuit decision in
Amdocs, 2016 WL 6440387, which leads us to determine that the claims
recite the "something more" required by the Supreme Court to transform an
abstract idea into a patent-eligible invention. See also Alice, 134 S. Ct. at
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Appeal2015-006279
Application 12/272,973
2355 (citing Mayo, 132 S. Ct at 1303). As in Amdocs, here, claim 1 may be
directed to an abstract idea of analyzing data using mathematical algorithms,
but it entails unconventional technical solutions (i.e., creating theoretical
spectra including known and variable mass modifications of peptide amino
acids) to a technological problem (i.e., the difficulty in identifying peptides
that are prone to chemical modifications, both expected and unknown, using
spectral data). See Spec. i-fi-1 4, 5, 6, 8, 25, 32, 33, and 38; see also Amdocs,
2016 WL 6440387 at *10. As in Amdocs, claim 1 ties the invention to a
structure - "one or more computers" and, indirectly, to mass-
spectrometer(s). See claim 1, supra; see also Amdocs, 2016 WL 6440387 at
*10. As in Amdocs, claim 1 is not drawn to preempt the generic
enhancement of data in a similar system, but is directed to a technological
solution needed in peptide analysis using mass-spectroscopy. See claim 1,
supra; see also Amdocs, 2016 WL 6440387 at *10. Considered as an
ordered combination, we are not persuaded that claim 1 recites an invention
that is merely the routine or conventional use of technology previously
known to skilled persons.
For the reasons above, we reverse the rejection of claim 1 and its
dependent claims under 35 U.S.C. § 101.
SUMMARY
The rejection of claims 1-20 under 35 U.S.C. § 101 is reversed.
REVERSED
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