Bruker Daltonik GmbH

Patent Trials and Appeals Board

Dec 30, 2020

2020002619 (P.T.A.B. Dec. 30, 2020)

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.
15/107,133 06/22/2016 Gabriele BIERBAUM P3810US00 2643
110047 7590 12/30/2020
BENOIT & COTE
560 boul. Cremazie est
Suite 300
Montreal, QUEBEC H2P 1E8
CANADA
EXAMINER
FERNANDEZ, SUSAN EMILY
ART UNIT PAPER NUMBER
1651
NOTIFICATION DATE DELIVERY MODE
12/30/2020 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):
docket@benoit-cote.com
phil@benoit-cote.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte GABRIELE BIERBAUM, CHRISTIANE SZEKAT,
NAHED ALSABTI, MICHAELE JOSTEN, and MARION REIF1
Appeal 2020-002619
Application 15/107,133
Technology Center 1600
Before ERIC B. GRIMES, FRANCISCO C. PRATS, and
DEBRA L. DENNETT, Administrative Patent Judges.
GRIMES, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134(a) involving claims to a
method for identifying methicillin resistant Staphylococcus aureus (MRSA),
which have been rejected as patent ineligible. We have jurisdiction under
35 U.S.C. § 6(b).
We REVERSE.

1 Appellant identifies the real party in interest as Bruker Daltonik GmbH.
Appeal Br. 1. We use the word “Appellant” to refer to “applicant” as defined
in 37 C.F.R. § 1.42.
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STATEMENT OF THE CASE
“Methicillin resistant S. aureus (MRSA) started to spread in the
hospitals in the late 1980s . . . . Today MRSA pose[s] a problem for hospital
hygiene in most countries of the world.” Spec. ¶ 2.
The invention provides a method for identifying methicillin
resistant Staphylococcus aureus (MRSA) in a bacterial sample
comprising the steps: classifying bacteria in the sample as
Staphylococcus aureus (SA) and determining the presence or
absence of the phenol soluble modulin peptide or a variant
thereof wherein the presence of the PSM-mec peptide or variant
thereof indicates methicillin resistant Staphylococcus aureus.
The variant is preferably the formylated version of the PSM-
mec peptide having a mass to charge ratio of 2415.
Id. ¶ 6.
“The method according to the present invention may further comprise
the step of determining the status of the agr (accessory gene regulator)
system.” Spec. ¶ 9. “The presence of the agr system and the presence of the
PSM-mec peptide or variant thereof indicate a methicillin resistant
Staphylococcus aureus.” Id. “The status of the agr system can be determined
by the presence or absence of delta-toxin wherein the presence of the delta-
toxin indicates the presence of the agr system.” Id. “[T]he presence of a
mass signal . . . centered at m/z 3007 or m/z 3037 indicates the presence of
the delta toxin.” Id.
Claims 1, 14, 16, and 24–27 are on appeal. Claim 1, reproduced
below, is illustrative:
1. A method for identifying methicillin resistant Staphylococcus
aureus (MRSA) in a bacterial sample comprising the steps:
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directly depositing whole bacteria cells on a MALDI
time of flight (MALDI-TOF) mass spectrometer target plate
without prior extraction,
acquiring a MALDI-TOF mass spectrum of the whole
bacteria,
classifying bacteria in the sample as Staphylococcus
aureus (SA) by comparing the MALDI-TOF mass spectrum
with reference mass spectra of a library comprising at least one
reference mass spectrum of Staphylococcus aureus,
determining the presence or absence of a first mass signal
in the MALDI-TOF mass spectrum centered at m/z 3007 or m/z
3037;
determining the presence or absence of a second mass
signal in the MALDI-TOF mass spectrum centered at m/z 2415,
wherein the presence or absence of a formylated version of the
phenol soluble modulin peptide (PSM-mec) is determined by
the presence or absence of the second mass signal, and
indicating the bacteria of the bacterial sample to be
methicillin resistant if the first and the second mass signals are
present, and to be undetermined with regard to methicillin
resistance and with regard to methicillin susceptibility if the
first mass signal is absent.
OPINION
Claims 1, 14, 16, and 24–27 stand rejected under 35 U.S.C. § 101 as
being directed to an abstract idea without significantly more. Ans. 3. The
Examiner finds that “[t]he four final steps of claim 1 could be performed by
a human using mental steps or basic critical thinking . . . . They fall within
the ‘Mental Processes’ grouping of abstract ideas.” Id.
The Examiner also finds that “[t]his judicial exception is not
integrated into a practical application.” Ans. 4. Specifically, “[t]he additional
elements of claim 1 are the first two steps of the claim . . . . These additional
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elements are data gathering steps that do not add a meaningful limitation to
the method as they are insignificant pre-solution activity.” Id.
The Examiner cites Wunschel2 and Josten3 as evidence that “the first
two steps of claim 1 are well-understood, routine, and conventional activities
for those in the field of bacterial analysis.” Ans. 4–5. Specifically, Wunschel
“indicates that bacterial analysis by MALDI-TOF mass spectrometry ‘. . . has
been demonstrated in numerous laboratories’ (abstract).” Id. at 4 (alteration
in original). The Examiner finds that Josten “further provides evidence that
these steps were well-understood, routine, conventional activities performed
on Staphylococcus aureus.” Id. at 5.
The Examiner concludes that “simply appending well-understood,
routine, conventional activities previously known in the industry were found
not to be enough to qualify as ‘significantly more’ when recited in a claim
with a judicial exception.” Ans. 5. “As such, claim 1 is not eligible subject
matter under 35 U.S.C. 101.” Id.
Appellant argues that the claims are restricted to the field of mass
spectrometry, so no danger of tying up a judicial exception exists. Appeal
Br. 3–4. Appellant argues that
[t]he first two steps of the claim involve the acquisition of a
mass spectrum of the sample material. That is, they require the
use of a specific machine (a mass spectrometer) and a specific

2 Sharon C. Wunschel et al., “Bacterial Analysis by MALDI-TOF Mass
Spectrometry: An Inter-Laboratory Comparison,” J. Am. Soc. Mass
Spectrom. 16: 456–462 (2005).
3 Michaele Josten et al., “Analysis of the Matrix-Assisted Laser Desorption
Ionization–Time of Flight Mass Spectrum of Staphylococcus aureus
Identifies Mutations That Allow Differentiation of the Main Clonal
Lineages,” J. Clin. Microbiol. 51(6): 1809–1817 (2013).
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transformation (of a cellular material to a discrete
representation of mass signals indicative of the molecular
components of the cells).
Id. at 5. Appellant argues that “the subsequent four steps of Claim 1, which
were viewed as ‘mental steps’ by the examiner, are unperformable without
the first two steps, because they involve an analysis of the acquired mass
spectrum.” Id. “Thus, far from being insignificant [pre-solution activity], the
first two steps are absolutely essential.” Id.
Appellant also argues that any judicial exception in claim 1 is
integrated into a practical application, according to the USPTO’s current
guidelines, because the claimed method implements any judicial exception
in conjunction with a particular machine—a mass spectrometer—that is
inherent to the claim. Appeal Br. 7–8. Finally, Appellant argues that the
claimed method “effects a transformation of the bacterial sample from a
cellular material to a discrete representation of mass signals indicative of the
molecular composition of the cells.” Id. at 8–9. Appellant concludes that,
“[w]hen viewed as a whole, the claims define a practical application of mass
spectrometry to the determination of methicillin resistance/susceptibility,
and any judicial exception in the claims is integrated into this practical
application.” Id. at 10.
Principles of Law
A. Section 101
An invention is patent-eligible if it claims a “new and useful process,
machine, manufacture, or composition of matter.” 35 U.S.C. § 101.
However, the U.S. Supreme Court has long interpreted 35 U.S.C. § 101 to
include implicit exceptions: “[l]aws of nature, natural phenomena, and
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abstract ideas” are not patentable. E.g., Alice Corp. v. CLS Bank Int’l, 573
U.S. 208, 216 (2014).
In determining whether a claim falls within an excluded category, we
are guided by the Court’s two-part framework, described in Mayo and Alice.
Alice, 573 U.S. at 217–18 (citing Mayo Collaborative Servs. v. Prometheus
Labs., Inc., 566 U.S. 66, 75–77 (2012)). In accordance with that framework,
we first determine what concept the claim is “directed to.” See Alice, 573
U.S. at 219 (“On their face, the claims before us are drawn to the concept of
intermediated settlement, i.e., the use of a third party to mitigate settlement
risk.”); see also Bilski v. Kappos, 561 U.S. 593, 611 (2010) (“Claims 1 and 4
in petitioners’ application explain the basic concept of hedging, or protecting
against risk.”).
Concepts determined to be abstract ideas, and thus patent ineligible,
include certain methods of organizing human activity, such as fundamental
economic practices (Alice, 573 U.S. at 219–20; Bilski, 561 U.S. at 611);
mathematical formulas (Parker v. Flook, 437 U.S. 584, 594–95 (1978)); and
mental processes (Gottschalk v. Benson, 409 U.S. 63, 67 (1972)). Concepts
determined to be patent eligible include physical and chemical processes,
such as “molding rubber products” (Diamond v. Diehr, 450 U.S. 175, 191
(1981)); “tanning, dyeing, making water-proof cloth, vulcanizing India
rubber, smelting ores” (id. at 182 n.7 (quoting Corning v. Burden, 56 U.S.
252, 267–68 (1853))); and manufacturing flour (Benson, 409 U.S. at 69
(citing Cochrane v. Deener, 94 U.S. 780, 785 (1876))).
In Diehr, the claim at issue recited a mathematical formula, but the
Court held that “a claim drawn to subject matter otherwise statutory does not
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become nonstatutory simply because it uses a mathematical formula.” Diehr,
450 U.S. at 187; see also id. at 191 (“We view respondents’ claims as
nothing more than a process for molding rubber products and not as an
attempt to patent a mathematical formula.”). Having said that, the Court also
indicated that a claim “seeking patent protection for that formula in the
abstract . . . is not accorded the protection of our patent laws, and this
principle cannot be circumvented by attempting to limit the use of the
formula to a particular technological environment.” Id. (citing Benson and
Flook); see, e.g., id. at 187 (“It is now commonplace that an application of a
law of nature or mathematical formula to a known structure or process may
well be deserving of patent protection.”).
If the claim is “directed to” an abstract idea, we turn to the second
step of the Alice and Mayo framework, where “we must examine the
elements of the claim to determine whether it contains an ‘inventive
concept’ sufficient to ‘transform’ the claimed abstract idea into a patent-
eligible application.” Alice, 573 U.S. at 221 (internal quotation marks
omitted). “A claim that recites an abstract idea must include ‘additional
features’ to ensure ‘that the [claim] is more than a drafting effort designed to
monopolize the [abstract idea].’” Id. (alterations in original) (quoting Mayo,
566 U.S. at 77). “[M]erely requir[ing] generic computer implementation[]
fail[s] to transform that abstract idea into a patent-eligible invention.” Id.
B. USPTO Section 101 Guidance
In January 2019, the U.S. Patent and Trademark Office (USPTO)
published revised guidance on the application of § 101. See 2019 Revised
Patent Subject Matter Eligibility Guidance, 84 Fed. Reg. 50 (Jan. 7, 2019)
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(“Revised Guidance”).4 “All USPTO personnel are, as a matter of internal
agency management, expected to follow the guidance.” Id. at 51; see also
October 2019 Update at 1.
Under the Revised Guidance and the October 2019 Update, we first
look to whether the claim recites:
(1) any judicial exceptions, including certain groupings of
abstract ideas (i.e., mathematical concepts, certain methods of
organizing human activity such as a fundamental economic
practice, or mental processes) (“Step 2A, Prong One”); and
(2) additional elements that integrate the judicial exception into
a practical application (see MPEP §§ 2106.05(a)–(c), (e)–(h)
(9th ed. Rev. 08.2017, Jan. 2018)) (“Step 2A, Prong Two”).5
Revised Guidance, 84 Fed. Reg. at 52–55.
Only if a claim (1) recites a judicial exception and (2) does not
integrate that exception into a practical application, do we then look, under
Step 2B, to whether the claim:

4 In response to received public comments, the Office issued further
guidance on October 17, 2019, clarifying the Revised Guidance. USPTO,
October 2019 Update: Subject Matter Eligibility (the “October 2019
Update”) (available at https://www.uspto.gov/sites/default/files/
documents/peg_oct_2019_update.pdf).
5 This evaluation is performed by (a) identifying whether there are any
additional elements recited in the claim beyond the judicial exception, and
(b) evaluating those additional elements individually and in combination to
determine whether the claim as a whole integrates the exception into a
practical application. See Revised Guidance - Section III(A)(2), 84 Fed. Reg.
54–55.
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(3) adds a specific limitation beyond the judicial exception that
is not “well-understood, routine, conventional” in the field (see
MPEP § 2106.05(d)); or
(4) simply appends well-understood, routine, conventional
activities previously known to the industry, specified at a high
level of generality, to the judicial exception.
Revised Guidance, 84 Fed. Reg. at 52–56.
Revised Guidance Step 2A, Prong 1
Following the Revised Guidance, we first consider whether the claims
recite a judicial exception. The Revised Guidance identifies three groupings
of subject matter included in the abstract idea exception, including “[m]ental
processes—concepts performed in the human mind (including an
observation, evaluation, judgment, opinion).” 84 Fed. Reg. at 52.
Claim 1 recites the steps of:
classifying bacteria in the sample as Staphylococcus
aureus (SA) by comparing the MALDI-TOF mass spectrum
with reference mass spectra of a library comprising at least one
reference mass spectrum of Staphylococcus aureus,
determining the presence or absence of a first mass signal
in the MALDI-TOF mass spectrum centered at m/z 3007 or m/z
3037;
determining the presence or absence of a second mass
signal in the MALDI-TOF mass spectrum centered at m/z 2415,
wherein the presence or absence of a formylated version of the
phenol soluble modulin peptide (PSM-mec) is determined by
the presence or absence of the second mass signal, and
indicating the bacteria of the bacterial sample to be
methicillin resistant if the first and the second mass signals are
present, and to be undetermined with regard to methicillin
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resistance and with regard to methicillin susceptibility if the
first mass signal is absent.
We agree with the Examiner that these steps represent abstract ideas
in the category of mental processes. The “classifying” step of claim 1
requires comparing an obtained mass spectrum with reference mass spectra
in a library. Comparison is a mental process. See Genetic Technologies, Ltd.
v. Merial L.L.C., 818 F.3d 1369, 1378 (Fed. Cir. 2016) (“The term ‘to detect
the allele’ . . . is a mental process step, one that . . . merely sets forth a
routine comparison that can be performed by the human mind.”).
Both “determining” steps are likewise mental processes, because they
merely require observing a mass spectrum to identify whether or not certain
signals are present at certain positions. The Specification’s Figure 1 shows
that visual inspection is adequate to determine the presence or absence of the
specified signals. See Spec. ¶ 23 (“Figure 1 shows a measured spectra of the
strain USA100 . . . . The mass signal at m/z 3007 is caused by the delta
toxin, and the mass signal at m/z 2415 . . . corresponds to the PSM-mec
peptide.”)
Finally, the “indicating” step of claim 1 is also a mental process step,
because it only requires mentally assigning a meaning to the results of the
“determining” steps: if both mass signals are present, the bacteria in the
sample are methicillin resistant but if the first mass signal (i.e., the one at
m/z 3007 or m/z 3037) is absent, the results are inconclusive.
In summary, the last four steps of claim 1 can practically be
performed in the human mind, and therefore recite an abstract idea in the
category of mental processes.
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Revised Guidance Step 2A, Prong 2
Although claim 1 recites an abstract idea, it would still be patent-
eligible if “the claim as a whole integrates the recited judicial exception into
a practical application of the exception.” Revised Guidance, 84 Fed. Reg. at
54. “A claim that integrates a judicial exception into a practical application
will apply, rely on, or use the judicial exception in a manner that imposes a
meaningful limit on the judicial exception.” Id. The analysis of whether a
claim integrates a judicial exception into a practical application includes
“[i]dentifying whether there are any additional elements recited in the claim
beyond the judicial exception(s)” and “evaluating those additional elements
individually and in combination to determine whether they integrate the
exception into a practical application.” Id. at 54–55.
One of the exemplary considerations indicating that an additional
element may integrate an exception into a practical application is “an
additional element [that] implements a judicial exception with, or uses a
judicial exception in conjunction with, a particular machine or manufacture
that is integral to the claim.” Revised Guidance, 84 Fed. Reg. at 55.
Here, we agree with Appellant that claim 1 as a whole integrates the
recited abstract idea (mental processes) into a practical application. As
discussed above, in addition to the four steps that can be performed in the
human mind, claim 1 recites steps of
directly depositing whole bacteria cells on a MALDI time of
flight (MALDI-TOF) mass spectrometer target plate without prior
extraction, [and]
acquiring a MALDI-TOF mass spectrum of the whole bacteria.
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The Examiner concludes that these steps
do not meaningfully limit the claim since they do not add a
meaningful limitation to specifically the last four steps of
claim 1 that are drawn to the judicial exception. They are drawn
to steps that are performed to obtain the data needed for the
judicial exception, wherein data gathering is considered by the
courts to be insignificant extra-solution activity.
Ans. 10.
However, we agree with Appellant that these steps meaningfully limit
the claim, because “they require the use of a specific machine (a mass
spectrometer) and a specific transformation (of a cellular material to a
discrete representation of mass signals indicative of the molecular
components of the cells).” Appeal Br. 5. “Thus, far from being insignificant,
these additional limitations necessarily tie the method directly to the analysis
of a bacterial sample using a mass spectrometer.” Id. at 6. Appellant cites
SiRF Technology, Inc. v. International Trade Comm’n, 601 F.3d 1319, 1332
(Fed. Cir. 2010), and argues that, “[a]s in SIRF, the appellant’s mass
spectrometer is essential to the claimed method, and does not represent a
technologically non-specific component, i.e., a computer, that is used simply
for performing calculations more quickly.” Reply Br. 3.
We agree with Appellant that the requirement for a MALDI-TOF
mass spectrometer integrates the mental process steps recited in claim 1 into
a practical application, because the mass spectrometer is “a particular
machine or manufacture that is integral to the claim.” Revised Guidance,
84 Fed. Reg. at 55. As Appellant points out, the mass spectrometer is
integral to the claim because “the analysis of the sample is completely
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dependent on the acquisition of a mass spectrum of the sample, and would
be impossible without it.” Appeal Br. 5.
And a MALDI-TOF mass spectrometer is a “particular machine,”
distinct from, for example, a general-purpose computer. Clark6 provides a
schematic illustration of a mass spectrometer, shown below:

Clark’s Figure 2 shows a “[g]eneral schematic for MS analysis of
ionized microbiological isolates and clinical material.” Clark 551, legend to
Fig. 2. Clark explains that
[o]nce appropriately processed samples are added to the
MALDI plate, overlaid with matrix, and dried, the sample is
bombarded by the laser. This bombardment results in the
sublimation and ionization of both the sample and matrix.
These generated ions are separated based on their mass-to-
charge ratio via a TOF tube, and a spectral representation of

6 Andrew E. Clark et al., “Matrix-Assisted Laser Desorption Ionization–
Time of Flight Mass Spectrometry: a Fundamental Shift in the Routine
Practice of Clinical Microbiology,” Clin. Microbiol. Rev. 26: 547–603
(2013). Clark was cited by the Examiner with respect to claims 24–27.
Ans. 6.
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these ions is generated and analyzed by the MS software,
generating an MS profile.
Id.
We therefore conclude that claim 1 includes “an additional element
[that] implements a judicial exception with . . . a particular machine or
manufacture that is integral to the claim.” Revised Guidance, 84 Fed. Reg.
at 55. Claim 1 therefore “integrates [its] judicial exception into a practical
application [because it] appl[ies] . . . the judicial exception in a manner that
imposes a meaningful limit on the judicial exception.” Id. at 54. “When the
exception is so integrated, then the claim is not directed to a judicial
exception . . . and is eligible. This concludes the eligibility analysis.” Id.
The Examiner reasons that
the machine recited in the claimed invention (mass
spectrometer) is not used to perform the judicial exception, and
instead is used to obtain the data for the judicial exception.
Therefore, the machine (mass spectrometer) does not play a
significant part in permitting the claimed method to be
performed as it is not used for performing the steps of
classifying the bacteria, determining the presence or absence of
the first mass signal and the second mass signal, and indicating
the bacteria of the bacterial sample to be methicillin resistant.
Ans. 8–9.
We do not agree with this analysis. The Revised Guidelines do not
require a particular machine recited in a claim to be used to perform the
judicial exception, only that “an additional element implements a judicial
exception with, or uses a judicial exception in conjunction with, a particular
machine.” Revised Guidance, 84 Fed. Reg. at 55. Here, as Appellant points
out, the mass spectrometer recited in the claim is essential to the analysis
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recited in the claim steps that represent the judicial exception. The fact that
the mass spectrometer is not used to perform those steps is of no moment.
In summary, the rejection of claims 1, 14, 16, and 24–27 under 35
U.S.C. § 101 is reversed.
DECISION SUMMARY
In summary:
Claims
Rejected
35 U.S.C. § Reference(s)/Basis Affirmed Reversed
1, 14, 16,
24–27
101 Eligibility 1, 14, 16,
24–27

REVERSED