Ex Parte Horn et al

Patent Trial and Appeal Board

Oct 30, 2017

12773659 (P.T.A.B. Oct. 30, 2017)

United States Patent and Trademark Office
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
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
12/773,659 05/04/2010 David Maron Horn 20090294-02 6439
22878 7590
Agilent Technologies, Inc.
Global IP Operations
5301 Stevens Creek Blvd
Santa Clara, CA 95051
EXAMINER
DEJONG, ERIC S
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
11/01/2017 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):
IPOPS .LEGAL @ agilent.com
Agilentdocketing@cpaglobal.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte DAVID MARON HORN and
JAVIER EDUARDO SATULOVSKY
Appeal 2016-006984
Application 12/773,6591
Technology Center 1600
Before DONALD E. ADAMS, FRANCISCO C. PRATS, and
ULRIKH W. JENKS, Administrative Patent Judges.
ADAMS, Administrative Patent Judge.
DECISION ON APPEAL
This appeal under 35 U.S.C. § 134(a) involves claims 1—15 (Final
Act.2 1). Examiner entered rejections under 35 U.S.C. § 101 and 35 U.S.C.
§ 102(b). We have jurisdiction under 35 U.S.C. § 6(b).
We AFFIRM.
1 Appellants identify the real party in interest as “Agilent Technologies,
Inc.” (Appellants’ October 13, 2015 Supplemental Appeal Brief (Br.) 3.)
2 Examiner’s June 18, 2015 Office Action.
Appeal 2016-006984
Application 12/773,659
STATEMENT OF THE CASE
Appellants disclose, inter alia, “[a] method of analyzing data from a
mass spectrometer for a data dependent acquisition” (Spec. 1 8). Claim 1 is
representative and reproduced below:
1. A method of selecting an isotopic cluster for analysis, said
method comprising:
obtaining a mass spectrum of a sample, wherein the mass
spectrum comprises isotopic clusters;
isolating a portion of the mass spectrum for a plurality of
isotopic clusters of interest using an isolation window of
predefined width along an m/z axis of the mass spectrum, using
a computer configured for data dependent acquisition;
for each isotopic cluster of interest, calculating, using the
computer configured for data dependent acquisition, a purity
value for each isotopic cluster of interest located within the
isolation window;
calculating a selection score for each isotopic cluster of
interest, based on the calculated purity values; and
selecting one or more of the isotopic clusters of interest
having the highest selection scores for further analysis thereof.
(Br. 13.)
The claims stand rejected as follows:
Claims 1—15 stand rejected under 35 U.S.C. § 102(b) as anticipated by
Sachs.3
Claims 1—15 stand rejected under 35 U.S.C. § 101 as directed to non-
statutory subject matter.
3 Sachs et al., US 6,906,320 B2, issued June 14, 2005.
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Anticipation'.
ISSUE
Does the preponderance of evidence on this record support
Examiner’s finding that Sachs teaches Appellants’ claimed invention?
FACTUAL FINDINGS (FF)
FF 1. Sachs:
[FJeatures mass spectrometry data analysis techniques that can
be employed to selectively identify analytes differing in
abundance between different sample sets. The employed
techniques determine the statistical significance of changes to
signals associated with mass-to-charge ratios (“m/z-intensity
pairs”) between individual samples and sample sets. Based on
the statistical significance, changes likely to indicate analyte
level differences are identified. Based on intensities of the
signals, ratios of analyte abundances can be determined.
(Sachs, Abstract; see also id. at 2:53—54 (“Intensity is any measure reflecting
the number of ions detected”); id. at 2:11—14 (Sachs’ method “features a
computer program for analyzing spectra to identify differences in the level
of one or more analytes between two or more sample sets”); Ans. 5 (Sachs
discloses “the use [of] mass spectroscopic techniques relying on isotopic
analysis and the identification of analytes differing in abundance in samples
of interest. . . (isotopic analysis, selection based on purity and purity
values)”).)
FF 2. Sachs discloses:
[A] mass spectrometry-based method for identifying differences
in the level of one or more analytes between two or more
sample sets. The method comprises the steps of:
a) obtaining spectra for individual samples for two or more
sample sets, wherein a spectrum comprises m/z intensity
pairs, wherein an m/z intensity pair comprises an m/z
identifier and a signal associated with the m/z identifier,
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b) for each m/z identifier of one or more m/z identifiers from
the m/z intensity pairs, determining a relationship between
the corresponding signals in those spectra, and
c) assigning each relationship a rank or value based on both
within-sample-set and between-sample-set signal
distributions, wherein the rank or value is a measure of a
likelihood that the signal arises from an analyte having a
different level between the sample sets. Step (c) evaluates
the statistical significance of the relationship.
(Sachs 1:59-2:10; see Ans. 5 (Sachs “teaches the determination of [a]
relationship amongst identified clusters of interest and the assignment of
such relationships based on rank or value”).)
FF 3. Sachs’ ‘“rank or value’ provides a statistical measure of the
significance of a signal that varies between spectra sets” (Sachs 3:13—14).
FF 4. Sachs’
data analysis techniques . . . can be employed to selectively
identify analytes differing in abundance between different
sample sets. The employed techniques determine the statistical
significance of changes in m/z-intensity pairs in spectra
between individual samples and sample sets. Based on the
statistical significance, changes likely to indicate analyte level
differences are identified.
(Sachs 5:10-17; id. at 5:18—20 (Sachs’ “mass spectrometry analysis
techniques can be employed to accurately detect analyte changes in different
samples, even analytes present in small amounts”); see Ans. 5 (Sachs
discloses “the use of [] monotic functions to [the] analysis of clusters of
interest for ‘rank or value’”).)
FF 5. Sachs discloses that “[ijncreasing the number of spectra taken on a
sample set facilitates accurate detection of analyte level differences” (Sachs
8:6-7).
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FF 6. Sachs discloses that
additional techniques can be performed to further characterize
analytes of interest. Further characterization can be performed,
for example, to determine the identity or chemical structure of a
particular analyte whose expression level changes between
sample sets.
Analytes, such as polypeptides, can be further
characterized using techniques such as tandem mass
spectrometry. Tandem mass spectrometry involves the use of
multiple stages of mass spectrometry to further analyze a
particular ion or ions at a particular m/z. It is common practice
to record an initial mass spectrum to permit the identification of
a parent ion(s) of interest. Further analysis involves converting
the parent ion into products and analyzing the resulting product
ions by mass spectrometry.
Results generated from mass spectrometry can be used
for analyte identification. For example, the results can be
compared to a database containing predicted mass spectra for
smaller components. Techniques for performing tandem mass
spectrometry, including the optional use of isotope tagging are
well known in the art. . . . A database of identified analytes and
their index and m/z values can be created and employed, so that
future analytes can be putatively identified by searching against
the database for previously identified analytes with similar
patterns of index values or m/z values.
(Sachs 32:28—54; see also id. at 8:65—9:8.)
FF 7. Sachs discloses that the selective identification of analytes “having
different abundances between two samples has a variety of different uses in
different fields[,wherein] [t]wo general field classifications, which to some
extent overlap, are (1) biological and (2) qualitative” and Sachs provides
examples of each (Sachs 32:56—33:47).
ANALYSIS
Appellants’ method of selecting an isotopic cluster for analysis
comprises the following steps: (a) “obtaining a mass spectrum of a sample,
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wherein the mass spectrum comprises isotopic clusters;” (b) “isolating a
portion of the mass spectrum for a plurality of isotopic clusters of interest
using an isolation window of predefined width along an m/z axis of the mass
spectrum;” (c) “calculating ... a purity value for each isotopic cluster of
interest located within the isolation window;” (d) “calculating a selection
score for each isotopic cluster of interest, based on the calculated purity
values; and” (e) “selecting one or more of the isotopic clusters of interest
having the highest selection scores for further analysis” (Br. 13).
Appellants’ claimed method further requires that a “computer configured for
data dependent acquisition” is used to perform steps (b) and (c) (id.).
Sachs teaches a method, wherein mass spectrum of a sample is
obtained, wherein the mass spectrum comprises isotopic clusters (see e.g.,
FF 1-2).
Examiner reasons that “[o]ne of ordinary skill in the art would
recognize that analysis of data [] from any portion of a mass spectrum would
inherently involve reviewing [] data in an isolated region of [the] spectra”
and, “[a]s such, an ‘isolation window’ as recited in [Appellants] claims
merely tells a practitioner to review the regions of a mass spectrum where
useful data exists” (Ans. 8). We find no error in Examiner’s rationale. In
this regard, absent evidence to the contrary, we find that a practitioner would
analyze mass spectrum data using an isolation window of predefined width
along an m/z axis of the mass spectrum with a computer configured for data
dependent acquisition (see FF 1 (Sachs’ method “features a computer
program for analyzing spectra to identify differences in the level of one or
more analytes between two or more sample sets”)).
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Sachs teaches the calculation of: (i) a purity value for each isotopic
cluster of interest and (ii) a selection score for each isotopic cluster of
interest, based on the calculated purity values (see FF 1 4). In this regard,
we recognize Appellants’ contention that “Sachs is drawn to ‘mass
spectrometry data analysis techniques that can be employed to selectively
identify analytes differing in abundance between different sample sets” (Br.
11). Stated differently, Sachs’ techniques are employed to identity
differences in analyte purity among different sample sets (see e.g., FF 1).
Further, in the absence of evidence to the contrary, we find that Sachs’s
calculation steps are inherently performed on a computer configured for data
dependent acquisition (see id.).
Sachs teaches the selection of isotopic clusters of interest for further
analysis, which inherently includes the selection of isotopic clusters having
the highest selection score (see FF 6—7).
Therefore, we find no error in Examiner’s finding that Sachs teaches
Appellants’ claimed invention (Ans. 4—5).
For the foregoing reasons, we are not persuaded by Appellants’
contention that “Sachs fails to discuss a purity value, much less ‘a purity
value for the respective isotopic cluster of interest located within the
isolation window’” and “Examiner makes no attempt to point to where a
discussion of a ‘purity value’ can be found in Sachs” (Br. 11).
Although Sachs teaches that by “[ijncreasing the number of spectra
taken on a sample set facilitates accurate detection of analyte level
differences” (see FF 5); Appellants’ claim 1 is not limited “to a modification
of the precursor ion selection rules that decrease the chance of precursor ion
contamination prior to an MS/MS scan [to achieve] more interpretable
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MS/MS spectra can be generated when analyzing a complex sample with a
tandem mass spectrometer” as Appellants assert is disclosed in paragraph 7
of their Specification (Br. 11—12; cf. Br. 13 (Appellants’ claim 1)).
Therefore, we are not persuaded by Appellants’ contention that Examiner
failed to read limitations from Appellants’ Specification into Appellants’
claim 1 “when asserting that certain passages of Sachs teach aspects of
[Appellants’] claimed invention” (Br. 12).
CONCLUSION OF LAW
The preponderance of evidence on this record supports Examiner’s
finding that Sachs teaches Appellants’ claimed invention. The rejection of
claim 1 under 35 U.S.C. § 102(b) as being anticipated by Sachs is affirmed.
Claims 2—15 are not separately argued and fall with claim 1.
Statutory Subject Matter.
ISSUE
Does the evidence of record support Examiner’s finding that
Appellants’ claimed invention is directed to non-statutory subject matter?
FACTUAL FINDINGS (FF)
FF 8. Examiner finds that “[t]he only physical step recited in [Appellants’]
claimed [method] is ‘obtaining a mass spectrum of a sample’,” which, as
discussed in the anticipation rejection above, is routine in this art (Ans. 2).
FF 9. Examiner finds that, but for the obtaining step of Appellants’
claimed method, “[t]he remaining steps recited in [Appellants’] [] claims are
directed only to the computational and algorithmic operations applied to data
obtained from a mass spectrum,” which, as discussed in the anticipation
rejection above, are routine in this art (Ans. 2—3).
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ANALYSIS
Examiner finds that Appellants’ claimed method is directed to non-
statutory subject matter (Ans. 2—3).
The scope of 35 U.S.C. § 101 “is subject to an implicit exception for
Taws of nature, natural phenomena, and abstract ideas,’ which are not
patentable.” Intellectual Ventures ILLC v. Capital One Financial Corp.,
850 F.3d 1332, 1338 (Fed. Cir. 2017), citing Alice Corp. Pty. Ltd. v. CLS
BankInt’l., 134 S. Ct. 2347, 2355 (2014).
To determine whether the exception applies ... a court must
determine: (1) whether the claim is directed to a patent-
ineligible concept, i.e., a law of nature, a natural phenomenon,
or an abstract idea [(the “abstract idea” step)]; and if so, (2)
whether the elements of the claim, considered “both
individually and ‘as an ordered combination,”’ add enough to
“‘transform the nature of the claim’ into a patent-eligible
application [(the ‘inventive concept’ step)].”
(Intellectual Ventures, 850 F.3d at 1338, citing Alice Corp., 134 S. Ct. at
2355).
Appellants’ claimed method comprises the steps of: (I) obtaining a
mass spectrum and (II) mathematically manipulating the data obtained from
the mass spectrum (see FF 8—9).
Mathematically manipulating mass spectrum data is an abstract
process. See Intellectual Ventures, 850 F.3d at 1340 (“an invention directed
to collection, manipulation, and display of data was an abstract process”). In
addition, “simply implementing a mathematical principle on a physical
machine, namely a computer, [is] not a patentable application of that
principle.” Mayo Collaborative Services v. Prometheus Laboratories, Inc.,
132 S. Ct. 1289, 1301 (2012). Therefore, we find that Appellants’ claims
are “directed to a patent-ineligible concept,” specifically an abstract idea.
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Without additional limitations, a process that employs
mathematical algorithms to manipulate existing information to
generate additional information is not patent eligible. “If a
claim is directed essentially to a method of calculating, using a
mathematical formula, even if the solution is for a specific
purpose, the claimed method is nonstatutory.” Parker v. Flook,
437 U.S. 584, 595[] (1978) (internal quotations omitted).
Digitech Image Techs., LLC v. Elecs. For Imaging, Inc., 758 F.3d 1344,
1351 (Fed. Cir. 2014).
Obtaining a mass spectrum and mathematically manipulating mass
spectrum data, as required by Appellants’ claimed invention, are “well-
understood, routine, conventional activities] already engaged in by the
scientific community.” Rapid Litigation Mgmt. Ltd. V. CellzDirect, Inc.,
827 F.3d 1042, 1047 (Fed. Cir. 2016). See FF 1-7.
Thus, when the elements of Appellants’ claims are considered “both
individually and ‘as an ordered combination,”’ the claim elements fail to add
enough to “‘transform the nature of the claim’ into a patent-eligible
application.” Intellectual Ventures, 850 F.3d at 1338; see id. at 1341^42.
In applying the first step of the Supreme Court’s two-part test for
distinguishing between claims to patent-ineligible exceptions, and claims to
patent-eligible applications of those exceptions, we find no error in
Examiner’s finding that Appellant’s “claimed invention is directed to non­
statutory subject matter” (Ans. 2). See Rapid Litigation Mgmt. Ltd. v.
CellzDirect, Inc., 827 F.3d at 1047.
For the reasons set forth above, wherein Appellant’s inventive concept
makes use of “‘well-understood, routine, conventional activity already
engaged in by the scientific community,”’ we find that Appellant’s claimed
invention fails the second step of the Supreme Court’s test: The “search for
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an ‘inventive concept’.” Id. “At step two, more is required than ‘well-
understood, routine, conventional activity already engaged in by the
scientific community,’ which fails to transform the claim into ‘significantly
more than a patent upon the’ ineligible concept itself’ {id. (citations
omitted)).
As discussed above, Appellants’ claim 1 is not limited to
“minimiz[ing] the chance of precursor ion contamination prior to an MS/MS
scan” or “provid[ing] more readily interpretable MS/MS spectra,” therefore,
we are not persuaded by Appellants’ contentions regarding unclaimed
features of Appellants’ disclosure or that Appellants’ claim 1 “allows for the
[] improvement in the technological process of mass spectrometry (Br. 5—6;
see also id. at 10). To the contrary, Appellants’ claim 1 does not require that
mass spectrometry be performed, but instead requires only that a mass
spectrum of a sample be obtained, by any manner, and that “further
[unspecified] analysis” may be performed {see Br. 13). Thus, although it is
true that “the use of mass spectrum data [] inherently necessitates a mass
spectrometer to produce the data,” Appellants’ claim 1 does not require the
use of a mass spectrometer, but instead requires only that a mass spectrum of
a sample be obtained, by any means (Br. 9; cf. id. at 13).
We are not persuaded by Appellants’ contention that Appellants’
claim 1 requires “that the original sample is transformed to a different state,
i.e., transformed into a selected isotopic cluster sample that can be further
analyzed” (Br. 7). To the contrary, rather than “transform” an original
sample into a different state, Appellants’ claim 1 manipulates data associated
with a sample’s mass spectrum to identify portions of the entire spectrum
that may be of interest {see Br. 13). In this regard, we note again that
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Appellants’ claim 1 does not recite, as a positive method step, the
performance of mass spectroscopy. Instead, Appellants’ claim 1 only
requires that a mass spectrum of a sample be obtained, by any means (see
Br. 13).
We recognize Appellants’ contentions regarding the requirement in
Appellants’ claim 1 relating to “a computer configured for data dependent
acquisition” (Br. 8). Appellants, however, fail to establish that a computer
configured for data depend acquisition differs, in any significant manner,
from a generic computer; or that such a computer is not well-know, routine,
and convention in the field of mass spectra analysis (see FF 1). Thus, we are
not persuaded that the use of such a computer renders the claimed subject
matter patent eligible.
The fact that a computer “necessarily exist[s] in the
physical, rather than purely conceptual, realm,” ... is beside the
point. There is no dispute that a computer is a tangible system
. . ., or that many computer-implemented claims are formally
addressed to patent-eligible subject matter. But if that were the
end of the § 101 inquiry, an applicant could claim any principle
of the physical or social sciences by reciting a computer system
configured to implement the relevant concept. Such a result
would make the determination of patent eligibility “depend
simply on the draftsman’s art,” . . . thereby eviscerating the rule
that ‘“[ljaws of nature, natural phenomena, and abstract ideas
are not patentable.’”
Alice, 134 S. Ct. at 2358—59 (internal citations omitted). On this record, we
find that the computer recited in Appellants’ claim 1 “amount[s] to ‘nothing
significantly more’ than an instruction to apply the abstract idea . . . using
some unspecified, generic computer.” (Id. at 2359).
We find that data manipulation steps of Appellants’ claim 1 is
analogous to claim 2 of Example 23 of the July 2015 Update on Subject
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Matter Eligibility, published July 30, 2015 (80 Fed. Reg. 45429) (which is
“directed to a series of steps for calculating a scaling factor,” where, as here,
“the claim is directed to an abstract idea”). Thus, we are not persuaded by
Appellants’ contentions regarding claim 1, of Example 23 of the July 2015
Update on Subject Matter Eligibility (“recit[ing] a series of steps for
relocating textual information in an underlying window to an unobscured
portion of the underlying window” and “does not recite a basic concept that
is similar to any abstract idea previously identified by the courts”). Cf. Br.
8-9.
We are not persuaded by Appellants’ contention that their
mathematical algorithms are not abstract ideas, because Appellants’ claims
refer to the “selection] [of] an isotopic cluster for analysis” (Br. 9). See
Digitech, 758 F.3d at 1351.
CONCLUSION OF LAW
The evidence of record supports Examiner’s finding that Appellants’
claimed invention is directed to non-statutory subject matter.
The rejection of claim 1 under 35 U.S.C. § 101, as directed to non-
statutory subject matter is affirmed. Claims 2—15 are not separately argued
and fall with claim 1.
TIME PERIOD FOR RESPONSE
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a).
AFFIRMED
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