Ex Parte SUCKAU et al

Patent Trial and Appeal Board

Jun 28, 2018

13291159 (P.T.A.B. Jun. 28, 2018)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
13/291,159 11/08/2011
110047 7590
BENOIT & COTE
560 boul. Cremazie est
Suite 300
Montreal, QC H2P 1E8
CANADA
07/02/2018
FIRST NAMED INVENTOR
Detlev SUCKAU
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.
P3527USOO 3449
EXAMINER
LIU, SAMUEL W
ART UNIT PAPER NUMBER
1656
NOTIFICATION DATE DELIVERY MODE
07/02/2018 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 DETLEV SUCKAU, MARTIN SCHURENBERG,
RAINER PAAPE, and CHRISTINE LUBBERT
Appeal2017-006593
Application 13/291,159 1
Technology Center 1600
Before ELIZABETH A. LA VIER, RICHARD J. SMITH,
and JOHN E. SCHNEIDER, Administrative Patent Judges.
LA VIER, Administrative Patent Judge.
DECISION ON APPEAL
Pursuant to 35 U.S.C. § 134(a), Appellants seek review of the
Examiner's rejections of claims 1-15 and 18. We have jurisdiction under 35
U.S.C. § 6(b ). For the reasons set forth below, we REVERSE.
BACKGROUND
The Specification "relates to mass spectrometry imaging of histologic
thin tissue sections." Spec. ,r 1.
Claim 1 is illustrative, and recites:
1 Appellants state that the real party in interest is Bruker Daltonik GmbH.
Appeal Br. 1.
Appeal2017-006593
Application 13/291,159
1. A method for the identification and localization of proteins
in a first histologic thin tissue section taken from a tissue
sample, comprising:
(a) digesting enzymatically in situ the proteins in the first tissue
section and the proteins in a second tissue section that is taken
from the tissue sample and that has a composition similar to the
first tissue section;
(b) acquiring mass spectra for a mass spectrometric image of
the first tissue section;
( c) extracting the digest peptides of the second tissue section,
separating the digest peptides by a separation method, and
acquiring mass spectra and daughter ion mass spectra from the
digest peptides in separated fractions;
( d) identifying the proteins of the second tissue section by
comparing the mass spectra and the daughter ion mass spectra
acquired in step ( c) with protein databases and spectral libraries,
and creating a protein list with information on the digest
peptides of the proteins; and
( e) assigning the proteins in the protein list, on the basis of one
of measured and calculated masses of the digest peptides of the
proteins, to the digest peptides having a same mass in the mass
spectra of the mass spectrometric image of the first tissue
section.
Appeal Br. 15 (Claims Appendix).
REJECTIONS MAINTAINED ON APPEAL
1. Claims 1-15 and 18 stand rejected under 35 U.S.C. § 112, first
paragraph (pre-AIA) as failing to comply with the written
description requirement. Ans. 2.
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Appeal2017-006593
Application 13/291,159
2. Claims 1-8, 13, 15, and 18 stand rejected under 35 U.S.C. § I03(a)
as unpatentable overHerring,2 Crobu, 3 and Covey. 4 Ans. 3.
3. Claim 9 stands rejected under 35 U.S.C. § I03(a) as unpatentable
over Herring, Crobu, Covey, and Seshi. 5 Ans. 9.
4. Claim 10 stands rejected under 35 U.S.C. § I03(a) as unpatentable
over Herring, Crobu, Covey, and Christ. 6 Ans. 9.
5. Claims 11 and 12 stand rejected under 35 U.S.C. § 103(a) as
unpatentable over Herring, Crobu, Covey, Wong,7 and Whitney. 8
Ans. 10.
6. Claim 14 stands rejected under 35 U.S.C. § I03(a) as unpatentable
over Herring, Crobu, Covey, and Haase. 9 Ans. 12.
2 Herring et al., Direct Tissue Analysis by MALDI MS: Application to Kidney
Biology, 27 SEMIN. NEPHROL. 597 (2007). Page citations are to author
manuscript version available in PubMed Central (2008 January 9), PMCID:
PMC2180835.
3 Crobu, S., Analisi comparativa dei metaboliti presenti nelle urine di soggetti
sani ed affetti da carcinoma alla vescica mediante LC-MS/MS (2009)
(doctoral thesis, Universita' Delgi Studi di Verona).
4 Covey et al., US 2002/0192735 Al, published Dec. 19, 2002.
5 Seshi, US 2003/0203483 Al, published Oct. 30, 2003.
6 Christ et al., US 2009/0215069 Al, published Aug. 27, 2009.
7 Wong et al., Comparison of Different Signal Thresholds on Data Dependent
Sampling in Orbitrap and LTQ Mass Spectrometry for the Identification of
Peptides and Proteins in Complex Mistures, 20 J. AM Soc. MASS SPECTROM.
1405 (2009). Page citations are to author manuscript version available in
PubMed Central (2010 September 27), PMCID: PMC2946190.
8 Whitney et al., US 2007/0090285 Al, published Apr. 26, 2007.
9 Haase et al., US 2009/0039282 Al, published Feb. 12, 2009.
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Appeal2017-006593
Application 13/291,159
A. Rejection 1
DISCUSSION
The Examiner finds that the limitation "that has a composition similar
to the first tissue section" in claim 110 is not supported adequately by the
Specification as originally filed. Final Action 2. But, as Appellants point
out (see Appeal Br. 3), the Specification describes "[a] method for the
identification and localization of proteins or other biomolecules of a
histologic tissue section comprises enzymatically digesting the biomolecules
of two similar tissue sections while substantially preserving the biomolecule
positions in the tissue sections" (Spec. ,r 62 (emphasis added)).
Furthermore:
The second tissue sample, whose digest peptides are to be
measured in step ( c ), should be a tissue section which is as
comparable as possible, with the same proportions of all tissue
types. It is advantageous, if the second thin tissue section is
from a nearby cut, if possible even an adjacent thin section, and
it is essential that the enzymatic digestion is done in the same
way as that of the first thin tissue section. It is highly
advantageous, for example, to apply the same spray and
incubation processes to two adjacent thin tissue sections side by
side in order to achieve digest peptide distributions which are as
similar as possible.
Spec. ,r 40 ( emphases added).
The Examiner takes the view that these passages do not support
similarity of "composition" as claimed, so much as of "localization" or
"proportion." Ans. 13-14. The written description requirement, however,
10 The same language can also be found m claim 18, the only other
independent claim on appeal.
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Application 13/291,159
does not necessitate "in haec verba support," but rather a reasonably clear
demonstration that the inventor was in possession of the invention. Purdue
Pharma L.P. v. Paulding, Inc., 230 F.3d 1320, 1323 (Fed. Cir. 2000). Here,
we agree with Appellants that the originally-filed Specification satisfies this
standard with respect to the claim language in question. Two "adjacent thin
section[s]" of tissue that are "as comparable as possible" (Spec. ,r 40) would
be expected to share compositional similarities, in many cases, because of
their common location.
Accordingly, we reverse Rejection 1.
B. Rejections 2-6
Obviousness requires consideration of the claimed invention "as a
whole." 35 U.S.C. § 103(a). The Examiner relies on Herring as teaching
most of the steps of claim 1 (see Final Action 3---6), but must skip amongst
various disclosures in Herring to do so. This is problematic because the
method of claim 1, in essence, requires performing two different methods-
the first tissue section is subjected to one technique (steps (a) and (b)) and
the second tissue section to another (step (c)}-and then integrating the
resulting data (steps (d) and (e)). In other words, the combination of the
steps is a critical feature of claim 1. Herring offers a general overview of
several types of protein identification using MALDI MS 11 in the study of
kidney disease and toxicity, including an "[ o ]n tissue digestion" method
(Herring 4--5, Fig. 7) the Examiner finds corresponds to the in situ digestion
of step (a) of claim 1 (see Final Action 4). But we agree with Appellants
11 "MALDI MS" is an abbreviation for "matrix-assisted laser
desorption/ionization mass spectrometry." See Herring 7 n.1.
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Application 13/291,159
that the balance of Herring does not appear to utilize the on tissue digestion
method. See Appeal Br. 6-7; contra Final Action 5. Further, Appellants are
correct that Herring "does not mention the use of multiple tissue sections of
similar composition and never even remotely suggests using the extracted
peptides of one tissue section subjected to on-tissue digestion to aid in the
identification of proteins in another tissue section." Id. at 6. The Answer's
attempt to "connect[]" disparate portions of Herring (Ans. 16) is not
persuasive. Crobu and Covey, on which the Examiner relies for teaching the
"daughter ion mass spectra" acquisition in step ( c) (see Final Action 6-8),
cannot fill the gap.
Accordingly, we reverse the rejection of claim 1. As all of the
obviousness rejections rely similarly on Herring, we reverse Rejections 2---6
in their entirety.
CONCLUSION
The rejections of claims 1-15 and 18 are reversed.
REVERSED
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