Waters Technologies Corporation

Patent Trials and Appeals Board

Apr 15, 2021

2020003425 (P.T.A.B. Apr. 15, 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.
15/721,060 09/29/2017 Paul Rainville 8185.0151 4307
160377 7590 04/15/2021
Kacvinsky Daisak Bluni PLLC (8185)
2601 Weston Parkway
Suite 103
Cary, NC 27513
EXAMINER
XU, XIAOYUN
ART UNIT PAPER NUMBER
1797
NOTIFICATION DATE DELIVERY MODE
04/15/2021 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):
docketing@kdbfirm.com
ehysesani@kdbfirm.com
mbotnaru@kdbfirm.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte PAUL RAINVILLE, MATTHEW A. LAUBER,
LEE GETHINGS, ROBERT S. PLUMB, EOIN
COSGRAVE, and DARRYL W. BROUSMICHE
Appeal 2020-003425
Application 15/721,060
Technology Center 1700
Before JEFFREY T. SMITH, MONTÉ T. SQUIRE, and
SHELDON M. MCGEE, Administrative Patent Judges.
MCGEE, Administrative Patent Judge.
DECISION ON APPEAL
Pursuant to 35 U.S.C. § 134(a), Appellant1 appeals from the
Examiner’s decision to reject claims 1, 2, 8, 10–18, 20, 23–27, and 34–39.
We have jurisdiction. 35 U.S.C. § 6(b).
We affirm.

1 We use the word “Appellant” to refer to “applicant” as defined in 37
C.F.R. § 1.42. Appellant identifies the real party in interest as Waters
Technologies Corporation. Appeal Br. 3.
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Application 15/721,060

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CLAIMED SUBJECT MATTER
The claims are directed to methods of characterizing glycosylation of
a protein or peptide via a detection method such as mass spectrometry (MS).
See claims 1, 16, and 17 (Appeal Br. 13, 15, Claims App.).
Claim 1 is illustrative of the claimed subject matter and is reproduced
below with disputed limitations italicized for emphasis:
1. A method of characterizing glycosylation of protein or
peptide comprising the steps of:
providing a plurality of glycosylated proteins and/or
peptides;
denaturing the plurality [of] glycosylated proteins and/or
peptides with a denaturing solution to produce a denatured
mixture, wherein the denaturing solution comprises a MS
compatible surfactant, an organic solvent, urea and/or
guanidine;
combining the denatured mixture with a plurality of
proteases to produce a glycan amino acid complex, wherein the
plurality of proteases cleave the protein or the peptide;
purifying the glycan amino acid complex with HILIC SPE,
wherein the glycan amino acid complex is isolated; and
tagging the glycan amino acid complex with a tagging
reagent to produce a labeled glycan amino acid complex;
detecting the labeled glycan amino acid complex; and
characterizing glycosylation of the protein or peptide
through detection of the labeled glycan amino acid complex.
STATEMENT OF THE CASE
The Rejections
The Examiner rejects claims 1, 2, 8, 10–18, 20, 23–27, and 34–39
under 35 U.S.C. § 103 as unpatentable over the combined disclosures of
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Yu,2 Lauber,3 and Yu ̓ 20034 with or without additional prior art. Final Act.
2–6.
The Examiner finds that Yu discloses all the limitations recited in
claim 1 except for: 1) the step of “tagging the glycan amino acid complex
with a tagging reagent to produce a labeled glycan amino acid complex” and
2) the denaturing solution comprising “a MS compatible surfactant, an
organic solvent, urea and/or guanidine.” Id. at 2–3.
To address these differences between Yu and claim 1, the Examiner
first turns to Lauber, which the Examiner finds discloses the step of tagging
a glycan amino acid complex with the tagging reagent RapiFluor-MS, i.e.,
“RFMS.” Id. at 3. The Examiner also finds that Lauber teaches that RFMS
is predicted to provide at least a three-fold increase in MS sensitivity.
Appellant does not dispute any of these findings. See generally
Appeal Br., Reply Br. Based on the combined teachings of Yu and Lauber,
the Examiner determines that the skilled artisan would have been motivated
to tag Yu’s purified glycan amino acid complex “in order to increase gain in
MS sensitivity.” Final Act. 3.
The Examiner next turns to Yu ʼ2003, which the Examiner finds
teaches a denaturing solution which comprises a MS compatible surfactant,

2 Ying Qing Yu et al., Identification of N-linked Glycosylation Sites Using
Glycoprotein Digestion with Pronase Prior to MALDI Tandem Time-of-
Flight Mass Spectrometry, 79 Anal. Chem. 1731–38 (2007).
3 Matthew A. Lauber et al., Rapid Preparation of Released N-Glycans for
HILIC Analysis Using a Labeling Reagent that Facilitates Sensitive
Fluorescence and ESI-MS Detection, 87 Anal. Chem. 5401–09 (2015).
4 Ying-Qing Yu et al., Enzyme-Friendly, Mass Spectrometry-Compatible
Surfactant for In-Solution Enzymatic Digestion of Proteins, 75 Anal. Chem.
6023–28 (Nov. 2003) (“Yu ̓ 2003”).
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an organic solvent, urea and/or guanidine as recited in claim 1. Final Act. 3.
The Examiner also finds that Yu ̓ 2003 teaches that it was commonly known
to improve protein digestion with additives such as surfactants, organic
solvents, and urea, and using such agents “improve[s] the proteins’ solubility
and hence facilitate[s] a more complete peptide map.” Id.
Appellant does not contest the Examiner’s findings regarding Yu
ʼ2003. See generally Appeal Br., Reply Br. Based on these undisputed
findings, the Examiner determines that the skilled artisan would have
included “an organic solvent, urea and/or guanidine” in Yu’s denaturing
solution to realize this improved protein solubility. Final Act. 3.
Appellant’s Contentions
Appellant first argues that the skilled artisan would not have been
motivated to apply the teachings of Lauber to Yu’s method because Lauber
produces glycosylamines, while Yu produces glycopeptides. Appeal Br. 8;
Reply Br. 7. Specifically, Appellant urges that the rejection relies on
impermissible hindsight because “one would not have looked to a reference
[Lauber] in which glycans are released by glycosylation, in which proteins
remain intact, and in which glycosylamines are analyzed, in order to modify
a reference [Yu] in which proteins are cleaved and glycopeptide fragments
are analyzed.” Appeal Br. 8; Reply Br. 7; see also Appeal Br. 9 and Reply
Br. 9 (repeating the argument that glycosylamines are distinct from
glycopeptides).
Next, Appellant contends Yu ̓ 2003 discloses that sample preparation
methods such as hydrophilic interaction chromatography (HILIC) “are time-
consuming, only partially efficient, and often lead to a reduction in sample
recovery,” and when using Yu ʼ2003’s denaturing solution, “sample
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preparation prior to MS analysis requires only a simple acid degradation
step” which is optional. Appeal Br. 11. Thus, Appellant argues5 that if Yu
ʼ2003’s denaturing solution was used in Yu’s method, the skilled artisan
would have employed a simple acid degradation step, not the HILIC-based
sample preparation step absent impermissible hindsight. Id.
OPINION
We review the appealed rejections for reversible error based on the
arguments and evidence presented by Appellant. 37 C.F.R.
§ 41.37(c)(1)(iv); Ex parte Frye, 94 USPQ2d 1072, 1075 (BPAI 2010)
(precedential) cited with approval in In re Jung, 637 F.3d 1356, 1365 (Fed.
Cir. 2011) (explaining that even if the Examiner had failed to make a prima
facie case, “it has long been the Board’s practice to require an applicant to
identify the alleged error in the examiner’s rejections”).
Because Appellant focuses its arguments on independent claims 1 and
17, we select claim 1 and focus our discussion on this claim. 37 C.F.R.
§ 41.37(c)(1)(iv). Based on Appellant’s lack of substantive argument to the

5 We do not consider Appellant’s untimely “teaching away” arguments set
forth at page 12 of the Reply Brief based on Yu ʼ2003’s disclosure in the
paragraph bridging pages 6023–24. Appellant has not shown good cause
why these arguments could not have been raised in the Appeal Brief because
the Examiner’s findings regarding Yu ʼ2003’s disclosure in this very
paragraph were set forth in the Final Office Action. Final Act. 3. Appellant
thus had an opportunity to argue in the Appeal Brief that Yu ʼ2003 teaches
away from organic solvents, urea and/or guanidine, and the use of HILIC.
See 37 C.F.R. § 41.41(b)(2) (“Any argument raised in the reply brief which
was not raised in the appeal brief, or is not responsive to an argument raised
in the examiner’s answer, including any designated new ground of rejection,
will not be considered by the Board for purposes of the present appeal,
unless good cause is shown.”).
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subsidiary rejections of claims 8, 15, 20, and 36–39, all rejections stand or
fall with claim 1. Appeal Br. 7–11.
The issue presented by Appellant’s first argument is whether the
Examiner erroneously determined that the skilled artisan would have been
motivated to apply the teachings of Lauber to Yu’s method, and would have
had a reasonable expectation of success in doing so. We answer these
questions in the negative.
Appellant does not specifically dispute the Examiner’s finding that Yu
discloses the claimed purification of a “glycan amino acid complex” in the
form of a “glycopeptide.” Final Act. 2 (citing Yu, 1733, para. 3); Appeal Br.
7–11.6 Yu teaches that, after purification by HILIC solid-phase extraction,
“only glycans and glycopeptides” are recovered––each of which undergo a
mass spectrometry analysis. See, e.g., Yu, 1735, paras. 1–2. Yu also
teaches that glycopeptides may have “weak mass spectrometry ion signals.”
Id. at 1731, para. 1; see also id. at 1735, para. 2 (explaining that “pronase-
digested glycopeptides have the lowest ion intensity” but observing that
adding 10mM ammonium citrate to the 2,5-dihydroxybenzoic acid (DHB)
matrix yielded “at least a 10-fold increase of ion intensity.”). Thus, Yu
sought to improve the signals generated by the glycopeptides to be analyzed
by mass spectrometry.

6 Moreover, that finding is supported by the record. Compare Spec. ¶¶ 11,
26 (disclosing that “[t]he glycan amino acid complex can be a complex
having a short peptide combined with a glycan moiety,” and use of the
enzyme pronase to generate the glycan amino acid complex), with Yu, 1734,
para. 3 (referring to glycopeptides generated by pronase digestion as “part
peptide and part glycan”).
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Lauber discloses that the tagging reagent RFMS contains an “N-
hydroxysuccinimide (NHS) carbamate reactive group” which has “been used
for decades to derivatize free amino acids.” Lauber, 5402, col. 1, paragraph
3, 5403, col. 2, paragraph 1. Lauber also discloses that, in addition to rapid
tagging capabilities, RFMS “also supports . . . MS detection.” Id. (sentence
bridging pages 5403–5404). Also, Lauber discloses that the tagging reagent
RFMS is “predicted to provide, at a minimum, a 3-fold gain in MS
sensitivity.” Id., 5405, col. 1, paragraph 1.
Appellant also does not dispute the Examiner’s finding that Yu’s
glycopeptides––like Lauber’s glycosylamines––have terminal amine groups.
Ans. 8. Therefore, we agree with the Examiner that the skilled artisan would
have reasonably expected that the NHS-carbamate moiety in the tagging
reagent RFMS would have been capable of forming a bond with the terminal
amine of Yu’s glycopeptide, just as it does with the terminal amine of
Lauber’s glycosylamines. Ans. 8. The skilled artisan also would have
reasonably expected that tagging Yu’s glycopeptide with a tagging reagent
would have increased MS sensitivity to the presence of that glycopeptide as
desired by Yu. Yu, 1735, para. 3; Ans. 8.
Here, we express our disagreement with Appellant that the Examiner
is somehow suggesting that it would have been “obvious [to] use RFMS to
label any primary amine of any molecule.” Reply Br. 8 (emphasis added).
Yu’s glycopeptides have terminal amines (Ans. 8) and undergo analysis via
mass spectrometry (Yu, 1735, paras. 2–3). See Appeal Br. 8
(acknowledging that “in Yu, the species being analyzed are small
glycopeptide fragments”). Similarly, Lauber’s glycosylamines have
terminal amines. Ans. 8; Lauber 5403, Fig. 1. Once Lauber’s
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glycosylamines are “tagged” or derivatized with RFMS, an N-glycan with a
urea-linked RFMS label is produced, which is analyzed via mass
spectrometry. See, e.g., Lauber, Figs. 2, 3; see also Appeal Br. 8
(acknowledging that Lauber discloses that “N-glycans (i.e., glycosylamines)
are labeled and analyzed”). Thus, Yu and Lauber do not merely disclose
random molecules that happen to have terminal amine groups as Appellant’s
argument suggests. Rather, these references expressly disclose analyzing
certain molecules by mass spectrometry. And one reference (Lauber)
teaches that the tagging reagent RFMS is predicted to enhance MS
sensitivity by a minimum of “a 3-fold gain” (Lauber, 5405, para. 1), while
the other reference (Yu) seeks, inter alia, a way of improving glycopeptide
signals in MS analysis (Yu, 1735, paras. 2–3).
Based on these teachings, we fully agree with the Examiner’s well-
reasoned determination that the skilled artisan would have been motivated to
apply Lauber’s teachings regarding tagging a molecule with a terminal
amine group, to Yu’s specific glycopeptide via its terminal amine group, for
the purpose of “increase[d] gain in MS sensitivity.” Final Act. 3; see KSR
Int’l Co. v. Teleflex Inc., 550 U.S. 398, 417 (2007) (“[I]f a technique has
been used to improve one [method], and a person of ordinary skill in the art
would [have] recognize[d] that it would [have] improve[d] similar [methods]
in the same way, using the technique is obvious unless its actual application
is beyond his or her skill.”).
Appellant’s second argument also does not persuade us of reversible
error. Appeal Br. 10–11. In particular, Appellant’s argument is directed to
addition of Yu ̓ 2003’s acid labile surfactant (ALS), which is not the
modification proposed by the Examiner. Final Act. 3 (determining that the
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skilled artisan would have found it obvious “to include an organic solvent,
urea and/or guanidine in the denaturing solution”––not the acid labile
surfactant (ALS) also disclosed by Yu ʼ2003 (emphasis added)). Because
Appellant does not squarely address the substance of the Examiner’s
rejection, the argument does not identify reversible error.
Therefore, for the reasons well-expressed by the Examiner and above,
we sustain the obviousness rejections of claims 1, 2, 8, 10–18, 20, 23–27,
and 34–39.
CONCLUSION
The Examiner’s rejections are affirmed.
DECISION SUMMARY
Claims
Rejected
35 U.S.C. § Reference(s)/Basis Affirmed Reversed
1, 2, 10–
14, 16–18,
23–27, 34,
35
103 Yu, Lauber,
Yu ʼ2003
1, 2, 10–
14, 16–18,
23–27, 34,
35

8, 20 103 Yu, Lauber,
Yu ʼ2003, Zhang
8, 20
15, 36–39 103 Yu, Lauber,
Yu ʼ2003, Halim
15, 36–39
Overall
Outcome
1, 2, 8,
10–18, 20,
23–27,
34–39

No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a). See 37 C.F.R.
§ 1.136(a)(1)(iv).
AFFIRMED