Ex Parte Satulovsky

Patent Trial and Appeal Board

Feb 16, 2017

12785705 (P.T.A.B. Feb. 16, 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.
12/785,705 05/24/2010 Javier E. SATULOVSKY 20090231-01 1472
7590
Agilent Technologies, Inc. in care of:
CPA Global
P. O. Box 52050
Minneapolis, MN 55402
EXAMINER
DEJONG, ERIC S
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
02/21/2017 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 JAVIER E. SATULOVSKY
Appeal 2015-008245
Application 12/785,705
Technology Center 1600
Before DEMETRA J. MILLS, JOHN E. SCHNEIDER, and
RYAN H. FLAX, Administrative Patent Judges.
MILLS, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35U.S.C. § 134. The Examiner has rejected
the claims for lack of patentable subject matter and anticipation. We have
jurisdiction under 35 U.S.C. § 6(b). We affirm.
Appeal 2015-008245
Application 12/785,705
STATEMENT OF CASE
The following claim is representative.
8. A method of analyzing a sample with tandem mass spectrometry
using a controller, the method comprising:
(a) providing an inclusion list of proteins of interest and expected
peptides corresponding to the proteins of interest, and providing for each
expected peptide in the inclusion list information pertaining to a
corresponding sequence and at least one property associated with that
sequence;
(b) performing mass spectrometry (MS) on the sample to acquire a
precursor ion spectrum;
(c) identifying a precursor ion, using the precursor ion spectrum,
having a mass that matches a mass of an expected peptide in the inclusion list
which belongs to a protein which has not already been identified in the
sample, wherein identifying the precursor ion comprises ranking for
subsequent processing precursor ions having masses that match masses of
expected peptides in the inclusion list in an order based at least in part on
maximizing the number of the proteins of interest identified by the analysis,
and identifying the precursor ion in the ranked order;
(d) performing tandem mass spectrometry (MS/MS) on the identified
precursor ion to acquire a product ion spectrum;
(e) calculating a match score between the product ion spectrum and at
least one expected peptide in the inclusion list, and comparing the match
score to a threshold;
(f) determining that the at least one expected peptide is present in the
sample when the match score exceeds the threshold, and flagging the at least
one expected peptide as identified in the sample;
(g) identifying a protein of interest to which the flagged at least one
expected peptide corresponds;
(h) determining that the identified protein of interest is present in the
sample when a sufficient number of peptides of the identified protein of
interest, including the flagged at least one expected peptide, are identified,
and when the identified protein of interest is determined to be present in the
sample, then flagging all remaining expected peptides in the inclusion list
that belong to the identified protein of interest as being identified in the
sample; and
(i) repeating steps ( c) through (h),
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Application 12/785,705
wherein the ranking comprises assigning a higher priority to precursor
ions having masses that only match masses of expected peptides belonging to
proteins of interest with unidentified peptides that have low likelihood of
being identified based on corresponding predicted or observed retention time
and proteotypic index, and assigning a lower priority to precursor ions having
masses that only match masses of expected peptides belonging to proteins of
interest with unidentified peptides that have high likelihood of being
identified based on corresponding predicted or observed retention
time and proteotypic index.
Grounds of Rejection
1. Claims 8—10 are rejected under 35 U.S.C. § 101 because the
claimed invention is not directed to patent eligible subject matter.
2. Claims 8—10 are rejected under pre-AIA 35 U.S.C. § 102(b) as
being anticipated by Graber.
Cited Reference
Graber US 6,940,065 B2 Sept. 6, 2005
FINDINGS OF FACT
The Examiner’s findings of fact are set forth in the Final Action at
pages 2—14.
PRINCIPLES OF LAW
In making our determination, we apply the preponderance of the
evidence standard. See, e.g., Ethicon, Inc. v. Quigg, 849 F.2d 1422, 1427
(Fed. Cir. 1988) (explaining the general evidentiary standard for proceedings
before the Office).
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Application 12/785,705
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
Banklnt’l, 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).
Rejection 1 Patent Eligibility
Taking up the first step of the patent-eligibility analysis, claim 1 is
directed to an abstract idea because it relates to data collection and to the
mathematical analysis of data in the field of mass spectrometry; 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., 841 F.3d
1288 (Fed. Cir. 2016).
Next, we look to the Specification to enlighten us as to the claimed
invention, as did the Federal Circuit in Enfish, LLC v. Microsoft Corp., 822
F.3d 1327 (Fed. Cir. 2016). The Specification explains the invention to be
directed to “data-dependent acquisition of mass spectrometry data,” and
“analysis ... or refining acquisition ... of mass spectrometry data,” which is
the abstract idea of the mathematical analysis of data. Spec. 136. Data
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Application 12/785,705
analysis and mathematical algorithms are abstract ideas. See, e.g., Alice 134
S. Ct. at 2355; Bilski v. Kappos, 561 U.S. 593, 611 (2010); Parker v. Flook,
437 U.S. 584, 59A-95 (1978); and Gottschalkv. Benson, 409 U.S. 63, 71-72
(1972). Put concisely, “[wjithout additional limitations, a process that
employs mathematical algorithms to manipulate existing information to
generate additional information is not patent eligible.” Digitech Image
Techs., LLCv. 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, 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 2355 (citing Mayo,
132 S. Ct at 1303). As in Amdocs, here, claim 1 may be directed to an
abstract idea of analyzing spectrometry related mathematical data.
However, in addition, claim 1 entails unconventional technical solutions
(i.e., a system and method of analyzing biological or chemical samples that
can provide improved coverage and sensitivity for detecting specific proteins
of interest, using spectrometry data) to a technological problem
(improvement in the coverage and sensitivity of the proteins of interest
determined by mass spectrometry. See Spec. 11 3—5; see also Amdocs, 841
F.3d at 1299. As in Amdocs, claim 1 ties the invention to a structure —a
computer controller for a mass-spectrometer(s). See claim 1, supra', see also
Amdocs, 841 F.3d at 1299. 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.
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Application 12/785,705
See claim 1, supra; see also Amdocs, 841 F.3d at 1299. 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.
Rejection 2 Anticipation
Separately argued claims are addressed separately herein. We agree
with and adopt herein the Examiner’s fact finding, statement of the rejection
and responses to Appellants’ arguments as set forth in the Answer. We find
that the Examiner has provided evidence and reasoning to support a prima
facie case of obviousness. We provide the following additional comment to
the Examiner’s argument set forth in the Final Rejection and Answer.
The Examiner finds that:
Graber et al. expressly teaches that the disclosed analysis
method employs the use of a sample comprising proteins, the
use of a predicted mass spectrum therefrom, and related
sequence information (see col. 8, lines 39-67). Graber et al.
sets forth the methods and related computer implemented-
systems for analyzing a sample wherein the sample is first
analyzed by MS to produce a first result and then further used
in a second MS/MS analysis to produce a second result (see
Abstract). This meets the claimed elements of steps b)
(performing mass spectroscopy on a sample to a acquire
precursor ion spectrum) and step d) (performing tandem mass
spectrometry (MS/MS) on the identified precursor to produce a
product ion spectrum). Graber et al. further teaches seeking
identification of minor components of a sample first using a
first MS experiment (see col. 6, lines 34-58). Graber further
teaches that the results of this first MS experiment is used to
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Application 12/785,705
prioritize signals with high intensity over those with lower
intensity for further investigation in the second MS/MS
performance step (a matching score compared to a threshold,
see also col. 6, line 59 through col. 8, line 28). Graber et al.
further teaches that the analysis of the disclosed MS-MS/MS
data employs a recursive compare and search procedure of mass
spectra data for the presence of peptide signals indicative of the
presence of particular protein of interest (further requiring the
use of a putative identification database (see col. 8, lines 45-
67).
Final Act. 8—9.
Appellants contend that:
GRABER et al. does not disclose a “ranking” scheme to
maximize the number of the proteins of interest identified in
which the ranking involves assigning a higher priority to
precursor ions having masses that only match masses of
expected peptides belonging to proteins of interest with
unidentified peptides that have low likelihood of being
identified. Indeed, the Final Office Action only asserts that
GRABER et al. discloses prioritizing signals with “high
intensity” over signals with “lower intensity.” See Final Office
Action, pp. 8-9.
App. Br. 13, italicized emphasis added. Appellants further argue that:
GRABER et al. does not disclose identifying a precursor ion,
which includes ranking by assigning a higher priority to
precursor ions having masses that only match masses of
expected peptides belonging to proteins of interest with
unidentified peptides that have low likelihood of being
identified (based on corresponding predicted or observed
retention time and proteotypic index), and assigning a lower
priority to precursor ions having masses that only match masses
of expected peptides belonging to proteins of interest with
unidentified peptides that have high likelihood of being
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identified (based on corresponding predicted or observed
retention time and proteotypic index), as recited in claim 8.
App. Br. 14.
ANALYSIS
We are not persuaded by Appellants’ arguments. With respect to
Appellants’ first argument, we find that claim 8 does not recite “a ‘ranking’
scheme to maximize the number of the proteins of interest.'1'’ On the other
hand, claim 8 does recite that:
[T]he ranking comprises assigning a higher priority to precursor
ions having masses that only match masses of expected
peptides belonging to proteins of interest with unidentified
peptides that have low likelihood of being identified based on
corresponding predicted or observed retention time and
proteotypic index, and assigning a lower priority to precursor
ions having masses that only match masses of expected
peptides belonging to proteins of interest with unidentified
peptides that have high likelihood of being identified based on
corresponding predicted or observed retention time and
proteotypic index.
Claim 8. Graber discloses:
In various embodiments of a search result based analysis, the
peak list of the mass spectra [inclusion list] can be stored in a
computer and the biomolecules corresponding to one or more
peaks can be identified by correlating the information contained
in the sample mass spectra with known or theo-retical mass
spectra. Based on the identification result, the biomolecules
associated with one or more peaks can be selected for further
MS/MS analysis and identification [performing MS].
Col. 11,11. 51—58. The results of the analysis can be refined. Col. 13,11. 40-
43. The biomolecules of Graber include peptides. Col. 4,1. 39. Tandem
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Application 12/785,705
mass spectrometry is contemplated by Graber. Col. 17,11. 9—10. This
disclosure of Graber corresponds with steps a), b), and d) of claim 8. Graber
also discloses that
In various embodiments, the isolated peptide fragments or reaction
products can be characteristic of the presence of a protein or the
presence of a protein function, e.g., an enzymatic activity,
respectively, in those mixtures. Isolated peptides, reaction products,
or both, can be characterized by mass spectrometric techniques to
provide for quantitative analysis of protein expression profiles in cells
and tissues.
Col. 17,11. 2—9. Further in Graber, “In various embodiments, fragmentation
spectra representing mass peak lists of fragment (daughter) ions are linked
with the spectra of the parent ions and stored in the database.” Col. 15,11.
28—31. “[T]he MS process can be exploited to produce one or more spectra
of mass peaks representing the relative abundance of those biomolecules
which can be selected for further MS/MS analysis and identification.” Col.
11,11. 60—64; col. 18,11. 54—64 (emphasis added). Therefore, just as in the
present specification, Graber can identify a protein of interest and fragments
associated with that protein of interest, and amounts of a protein of interest,
through spectrometry refinements (repeated subsequent processing, claim 8
step (i)).
For example, in Graber:
[T]he initial one or more mass spectrums can be spectrums
generated by a single laser pulse and additional mass spectra
can be added to the one or more initial mass spectrums until a
certain quality metric for the resultant mass spectrums is
reached. A quality metric can be generated for each mass
spectrum based on criteria such as, for example, the number of
peaks over a given signal to noise ratio, or the fraction of the
spectrum exceeding a given total ion count.
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Application 12/785,705
Col. 13,11. 56—64. Also in Graber,
In various embodiments, one or more mass signals associated
with a match (within a certain confidence interval) to a mass
spectrum in the database are selected for further MS/MS or MS"
analysis. For example, matched peaks can be selected and
further analyzed by MS/MS or MS" to confirm the putative
identification determined by the database. In various
embodiments, if the initial search results are inconclusive, for
example, the higher intensity mass signals corresponding to the
inconclusive match, the lower intensity mass signals
corresponding to the inconclusive match, or combinations of
both, are selected for further analysis by MS/MS or MS".
Col. 8,11. 39—60, italicized emphasis added. Thus, Graber discloses
calculating a match score based on a peptide inclusion list (peptide data
base) in comparison to a threshold (confidence interval), as in claim 8 step
(e), (f), (g), and (h), as claimed. We find that identifying signals associated
with a match is a form of flagging peptide of interest (step f). See also
Graber, col. 36,1. 28. As to the ranking limitation in claim 8, step (c) and
the “wherein” clause of claim 8, as identified by the Examiner, Graber
discloses:
that the results of this first MS experiment is used to prioritize
signals with high intensity over those with lower intensity for
further investigation in the second MS/MS performance step (a
matching score compared to a threshold, see also col. 6, line 59
through col. 8, line 28). Graber et al. further teaches that the
analysis of the disclosed MS-MS/MS data employs a recursive
compare and search procedure of mass spectra data for the
presence of peptide signals indicative of the presence of
particular protein of interest (further requiring the use of a
putative identification database (see col. 8, lines 45-67)).
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Ans. 7—8, Final Act. 8—9. Thus, Graber performs ranking of high and
lower intensity precursor ions (MS) associated with peptides when
compared to a proteotypic index (putative identification database for
proteins). Col. 36,11. 40-45. The comparison is based on retention
time dependent precursor selection. Graber, Figs. 9, 11, Col. 33,11.
20-35.
We find that the Examiner has provided evidence in the prior art of
each element claimed. Claims 9 and 10 share similar issues with claim 8.
Claim 9 recites, “assigning a lower priority to precursor ions having masses
that only match masses of expected peptides belonging to proteins of interest
expected to have a large number of peptides.” Graber discloses calculating a
match score based on a peptide inclusion list (peptide data base) in
comparison to a threshold (confidence interval), and prioritizing signals with
high intensity over those with lower intensity for further investigation in the
second MS/MS performance step. Ans. 7—8, Final Act. 8—9. Thus, Graber
reasonably discloses assigning higher and lower priority signals based upon
a confidence interval. We agree with the Examiner that an “expectation” or
property of the peptides is not further limiting of the tandem mass
spectrometry method steps recited in claim 9. Ans. 20.
Claim 10 recites, “the ranking comprises ranking the precursor ions
based at least in part on two or more of the following criteria: .... (3) a
match between the observed isotopic envelope of the precursor ion and a
predicted isotopic envelope of an expected peptide having a mass that
matches the precursor ion mass.” App. Br.__(Claim App’x, Claim 10).
Two or more of the indicated criteria of the “wherein clause” are recited in
claims 9 and 10 discussion above, thus the limitation is met by Graber.
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The rejection of claims 8—10 is affirmed for the reasons above.
CONCLUSION OF LAW
The 35 U.S.C. § 101 rejection is reversed.
The cited references support the Examiner’s anticipation rejection,
which is affirmed. All pending, claims fall under this rejection.
No time for taking any action connected with this appeal may be
extended under 37 C.F.R. § 1.136(a)(1). See 37 C.F.R. § 41.50(f).
AFFIRMED
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