Xin Wang

Patent Trials and Appeals Board

Feb 12, 2021

2020001102 (P.T.A.B. Feb. 12, 2021)

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.
13/822,922 03/13/2013 Xin Wang 37936-0002US1 8764
26211 7590 02/12/2021
FISH & RICHARDSON P.C. (NY)
P.O. BOX 1022
MINNEAPOLIS, MN 55440-1022
EXAMINER
DALBO, MICHAEL J
ART UNIT PAPER NUMBER
2865
NOTIFICATION DATE DELIVERY MODE
02/12/2021 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):
PATDOCTC@fr.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte XIN WANG
Appeal 2020-001102
Application 13/822,922
Technology Center 2800
Before TERRY J. OWENS, N. WHITNEY WILSON, and
JANE E. INGLESE, Administrative Patent Judges.
OWENS, Administrative Patent Judge.
DECISION ON APPEAL
STATEMENT OF THE CASE
Pursuant to 35 U.S.C. § 134(a), the Appellant1 appeals from the
Examiner’s decision to reject claims 55, 56, and 59–86. We have jurisdiction
under 35 U.S.C. § 6(b).
We REVERSE.

1 We use the term “Appellant” to refer to “applicant” as defined in
37 C.F.R. § 1.42. The Appellant identifies the real party in interest as
MassDefect Technologies, LLC (Appeal Br. 1).
Appeal 2020-001102
Application 13/822,922

2
CLAIMED SUBJECT MATTER
The claims are directed to background subtraction-mediated data-
dependent acquisition. Claim 55, reproduced below, is illustrative of the
claimed subject matter:
55. A method of analyzing mass spectrum of a sample
containing at least one component of interest, comprising the
steps of:
obtaining a background data set from a background sample
different from the sample containing at least one component of
interest, the background sample being a biological sample
and comprising a plurality of biological background
components, and the sample containing at least one component
of interest being a biological sample and further comprising the
plurality of biological background components;
after obtaining the background data set, performing a
continuous chromatographic measurement of the sample
containing at least one component of interest;
acquiring an original mass spectrum of the sample
containing at least one component of interest with a first mass
spectrometric acquisition function at a first chromatographic
time point by using a mass spectrometer, wherein the original
mass spectrum comprises m/z and intensity information of ion
signals detected at the first chromatographic time point;
defining sections of data in the background data set at the
first chromatographic time point specified in the acquiring step
to form defined sections of the background data set, the
defining comprises applying a chromatographic fluctuation
time window and a mass precision window around ion signals
in the background data set at the first chromatographic time
point;
conducting background subtraction for ions in the original
mass spectrum using ion information in the defined sections of
the background data set, resulting in a current background
subtracted mass spectrum; and
conducting an event of a data-dependent acquisition
function of ion signals detected at a second subsequent
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Application 13/822,922

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chromatographic time point based on the current background-
subtracted mass spectrum;
wherein the background subtraction occurs in real time
before conducting the event of the data-dependent acquisition
function at the second subsequent chromatographic time point,
the first and second chromatographic time points are two time
points in the continuous chromatographic measurement, and the
data-dependent acquisition function is a subsequent mass
spectrometric measurement or diversion of the sample
containing at least one component of interest.
REFERENCES
The prior art relied upon by the Examiner is:
Name Reference Date
McLafferty US 4,008,388 Feb. 15, 1977
Zhao US 2005/0048547 A1 Mar. 3, 2005
Overney US 2006/0243900 A1 Nov. 2, 2006
Senko US 2006/0284067 A1 Dec. 21, 2006
Le Blanc US 2006/0284069 A1 Dec. 21, 2006
Wang US 2013/0297226 A1 Nov. 7, 2013
Zhang 43 J. Mass. Spectrom.
1181–90
2008

REJECTIONS
Claim(s) Rejected 35 U.S.C. § Reference(s)/Basis
55, 56, 60–63, 65, 67–
72, 74–85
103(a) Zhang, McLafferty,
Le Blanc
59, 64 103(a) Zhang, McLafferty,
Le Blanc, Wang
66 103(a) Zhang, McLafferty,
Le Blanc, Zhao
73, 86 103(a) Zhang, McLafferty,
Le Blanc, Senko

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Application 13/822,922

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OPINION
We need address only the broadest independent claim, i.e., claim 55.
That claim requires obtaining a background data set from a background
sample comprising biological background components, then performing a
continuous chromatographic measurement of a sample containing at least
one component of interest and the background biological components,
acquiring an original mass spectrum of the sample containing at least one
component of interest with a first mass spectrometric acquisition function at
a first chromatographic time point in the continuous chromatographic
measurement, conducting in real time background subtraction for ions in the
original mass spectrum, then conducting an event of a data-dependent
acquisition function of ion signals detected at a second subsequent
chromatographic time point in the continuous chromatographic measurement
based on the current background-subtracted mass spectrum.
Zhang discloses “a background subtraction algorithm using accurate
mass data in control scans of a specified time window around an analyte
scan to cope with possible LC [(liquid chromatography)] fluctuations
between the control and analyte samples” (p. 1189).
McLafferty discloses “an automated mass spectrometric system
comprising (i) a mass spectrometer, including its electronics and vacuum
system; (ii) a sample inlet device; and (iii) electronic analysis means for
analyzing the mass spectra obtained from samples; and (iv) electronic
control means for controlling the operation of the mass spectrometer and
certain of its operating parameters” (col. 5, ll. 43–50). “The electronic
analysis means provide the unique capability of searching for and
identifying the presence of specific target compounds in a sample by
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analyzing the mass spectral data output by the spectrometer in real time,
despite the presence of a great many confusing mass peaks attributable to
residual background and sample impurities” (col. 6, ll. 31–37).
LeBlanc discloses “automatic MS/MS acquisition using data-
dependent acquisition techniques for identifying eluting compounds in a
chromatography/mass spectrum system” (¶ 2). “Ions associated with fast-
rising mass signals may be identified by, for example, subtracting one, or an
average of, previously acquired mass spectrums from the current mass
spectrum” (¶ 11). Le Blanc’s system “improves the efficiency in collection
of useful information while minimizing the quantity of data collected”
(¶ 70), thereby “minimizing the amount of information that has to be sifted
through, and improving the real-time analysis capabilities for such data”
(id.).
Setting forth a prima facie case of obviousness requires establishing
that the applied prior art would have provided one of ordinary skill in the art
with an apparent reason to modify the prior art to arrive at the claimed
invention. See KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 418 (2007).
The Examiner finds (Non-Final 5–6):
Zhang does not expressly indicate that the chromatogram
of the sample is a continuous chromatographic measurement of
the sample;
wherein the chromatogram of the sample is obtained after
obtaining the background data set; and
wherein the background subtraction occurs in real time
and the first and second chromatographic time points are two
time points in the continuous chromatographic measurement,
i.e. the data-dependent acquisition function is trigged [sic]
during the continuous chromatographic measurement.

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The Examiner finds that McLafferty discloses “the background
subtraction occurs in real time (see column 4 lines 25-68 and column 11
lines 2-9 and column 6 lines 31-38: real time analysis, analysis includes
background subtraction)” (Non-Final 6).
Those portions of McLafferty disclose:
This invention enables the identification of any one of a
number of a preselected "target" compounds in unknown
mixtures of compounds with little or no sample purification.
Thus, for one thing, it enables the elimination of a gas
chromatograph or, at the least, a substantial reduction in its
complexity. As a result, this invention provides a system which
is less complex and less expensive than the corresponding
systems of the prior art. In addition to the elimination or
simplification of the gas chromatograph, the present invention
further reduces the cost and complexity of compound
identification by eliminating bulk data storage means. This is
the result of its incorporation of means capable of real time
analysis [(col. 4, ll. 62–68)].
. . .
The invented system, while not requiring purification of
the sample by means such as a gas chromatograph, is
nevertheless adapted to operate with a gas chromatograph;
thereby, users of the present invention have a choice between a
direct analysis mode and a gas chromatograph/mass
spectrometer (GC/MS) analysis mode. In the latter mode any
suitable adapter known in the art enables the continuous real
time analysis of the effluent from the gas chromatograph [(col.
11, ll. 1–4)].

The Examiner does not establish that McLafferty’s disclosure of
means capable of real time analysis when identifying a compound in an
unknown mixture of compounds with little or no sample purification with a
gas chromatograph or disclosure of using an adapter to enable real time
analysis of gas chromatograph effluent would have provided one of ordinary
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skill in the art with an apparent reason to conduct real time background
subtraction for ions in an original mass spectrum in Zhang in the above-
stated sequence of steps required by the Appellant’s claim 55.
The Examiner finds (Non-Final 7) that Le Blanc discloses
“conducting an event of a data-dependent acquisition function of ion signals
detected at a second subsequent chromatographic time point based on the
current real time background subtracted mass spectrum (see paragraph 0002,
0011, 0041, 0034, 0045-0046, and 0070: uses an algorithm that triggers
DDA based upon a real time dynamic background subtraction).”
The Examiner does not establish that disclosure of an algorithm that
triggers DDA based upon a real time dynamic background subtraction is a
disclosure of conducting an event of a data-dependent acquisition function
of ion signals detected at a second subsequent chromatographic time point
based on the current real time background subtracted mass spectrum.
The Examiner finds (Non-Final 7) that Le Blanc discloses
wherein the first and second chromatographic time points are
two time points in the continuous chromatographic
measurement, i.e. wherein the data-dependent acquisition
function is trigged [sic] during the continuous chromatographic
measurement based on a background subtraction in real time
(see Title and paragraphs 0026, 0031, 0041, 0043, 0045, 0046,
0063, and 0070: uses a dynamic background subtraction
algorithm to allow for real-time automated adjustments of a MS
to MS/MS data acquisition from a single LC/MS analysis).

The Examiner does not establish that a disclosure of using a dynamic
background subtraction algorithm to allow for real-time automated
adjustments of an MS to MS/MS data acquisition from a single LC/MS
analysis is a disclosure of first and second chromatographic time points that
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are two time points in a continuous chromatographic measurement wherein
the data-dependent acquisition function is triggered during the continuous
chromatographic measurement based on a background subtraction in real
time.
Thus, the Examiner has not set forth a factual basis that is sufficient to
support a conclusion of obviousness of the Appellant’s claimed invention.
See In re Warner, 379 F.2d 1011, 1017 (CCPA 1967) (“A rejection based on
section 103 clearly must rest on a factual basis, and these facts must be
interpreted without hindsight reconstruction of the invention from the prior
art”). Accordingly, we reverse the rejections.
CONCLUSION
The Examiner’s decision to reject claims 55, 56, and 59–86 is
REVERSED.
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Application 13/822,922

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DECISION SUMMARY
Claim(s)
Rejected
35 U.S.C. § Reference(s)/Basis Affirmed Reversed
55, 56, 60–
63, 65, 67–
72, 74–85
103(a) Zhang,
McLafferty,
Le Blanc
55, 56, 60–
63, 65, 67–
72, 74–85
59, 64 103(a) Zhang,
McLafferty,
Le Blanc, Wang
59, 64
66 103(a) Zhang,
McLafferty,
Le Blanc, Zhao
66
73, 86 103(a) Zhang,
McLafferty,
Le Blanc, Senko
73, 86
Overall
Outcome
55, 56, 59–
86

REVERSED