Ex Parte Krause et al

Patent Trial and Appeal Board

May 22, 2013

10518727 (P.T.A.B. May. 22, 2013)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte MARTIN KRAUSE, CHRISTIAN SCHELER,
ULRIKE BOTTGER, HARDY WEISSHOFF, and
MICHAEL LINSCHEID
__________

Appeal 2011-009254
Application 10/518,727
Technology Center 1600
__________

Before DEMETRA J. MILLS, ERIC GRIMES, and JOHN A. EVANS,
Administrative Patent Judges.

GRIMES, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a method
relating to “proteome characterization by means of non-isotope metal coded
markers and . . . mass spectrometry” (Spec. 1). The Examiner has rejected
the claims as obvious. We have jurisdiction under 35 U.S.C. § 6(b). We
reverse.
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Application 10/518,727

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STATEMENT OF THE CASE
Claims 1-6, 8, 22, and 24-40 are on appeal. Claim 1 is representative
and reads as follows (emphasis added):
1. A method for the identification and/or quantification of one or
more proteins derived from the proteome of a cell in a sample containing a
mixture of such proteins, wherein said method comprises the steps of:
a) providing a sample which contains a mixture of proteins;
b) providing a reagent for the analysis of peptides which comprises A,
Y and PRG in which
A constitutes at least one functional group for the reversible, covalent
or non-covalent binding to a support material,
Y is a group comprising at least one chelate function for metals, and
comprising a metal ion bound thereto wherein the metal is selected from the
group consisting of Ag, Al, As, Au, Be, Cd, Ce, Co, Cr, Cu, Dy, Er, Eu, Fe,
Gd, Hg, Ho, In, La, Li, Lu, Mn, Na, Nd, Ni, Pb, Pr, Rb, Rd, Sb, Sm, Sn, Tb,
Tl, Tm, V, W, Y, Yb and Zn;
PRG is a reactive group for the selective binding to peptides or other
biomolecules to be analyzed; and wherein the arrangement of A, Y, and
PRG is interchangeable and said reagent is not isotopically labeled;
c) chemically or proteolytically cleaving the proteins in the sample in
order to produce peptides;
d) coupling the peptides to the reagent of step b) wherein the peptides
are labeled by the reagent;
e) selecting the peptides labeled in step d) using a functional group for
the reversible, covalent or non-covalent binding to a support material and
removal of unbound peptides;
f) releasing the bound peptides from the support material and elution
from the matrix; and
g) detecting and identifying the labeled peptides by means of mass
spectrometry.

Appeal 2011-009254
Application 10/518,727

3
The Examiner has rejected all of the claims on appeal under 35 U.S.C.
§ 103(a) based on Aebersold,1 Moutiez,2 and Li3 (Answer 4). The Examiner
finds that Aebersold discloses a method very similar to that of claim 1,
except that Aebersold’s A-L-PRG reagent (corresponding to the A-Y-PRG
reagent of claim 1) is isotopically labeled, and “Aebersold . . . does not use
metal ion as a standard in mass spectrometric analysis” (id. at 5).
The Examiner finds that Li discloses the use of a silver ion as a
standard in mass spectrometry (id.) and that Moutiez discloses that a Gd3+
ion chelated by the compound DOTA can be separated using affinity
chromatography and detected based on luminescence (id. at 6). The
Examiner concludes that it would have been obvious
to modify the A-L-PRG of Aebersold et al with Gd3+ DOTA
chelate not being modified by isotope label and use the metal
ion as standard (as taught by Li et al) in the method of
Aebersold et al, because a peptide sample attached to L-PRG
with Gd3+ DOTA can be separated by metal ion chelate affinity
column by HPLC, and optionally can be detected by
luminescence before passing into the mass spectrometer.
(Id.)
Appellants argue that “Aebersold et al. specifically teach the use of
isotopically labeled reagents . . . to identify and/or quantify one or more

1 Aebersold et al., WO 00/11208, March 2, 2000.
2 E. Moutiez et al., Time-resolved Luminescence as a Novel Detection Mode
for the Simultaneous High-performance Liquid Chromatographic
Determination of Gadolinium-DOTA and Gd3+,122 ANALYST 1347-1352,
(1997),
3 Hongbo Li et al., Complexes of Silver (I) With Peptides and Proteins as
Produced in Electrospray Mass Spectrometry, 8 J. AM. SOC. MASS
SPECTROM. 781-792 (1997).
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proteins” (Appeal Br. 9-10). Appellants argue that the Examiner “fail[s] to
articulate any rationale or scientific reasoning for removing isotopic labels
from the reagents of Aebersold et al. in order to arrive at the presently
claimed invention” (id. at 7).
We agree with Appellants that the Examiner has not provided an
adequate reason for concluding that, based on the cited references, a skilled
worker would have considered it obvious to eliminate the isotope label from
Aebersold’s A-L-PRG reagent. Aebersold discloses “reagents and mass
spectrometry-based methods. . . to screen for and identify proteins . . . in
cells, tissue or biological fluids” (Aebersold 4). The reagents “provide for
differential isotopic labeling of the isolated peptides or reaction products
which facilitates quantitative determination by mass spectrometry” (id. at 5).
Aebersold’s reagents have the general structure A-L-PRG, where the
linker L “may be differentially isotopically labeled, e.g., by substitution of
one or more atoms in the linker with a stable isotope thereof. For example,
hydrogens can be substituted with deuteriums or C12 with C13.” (Id.)
Aebersold discloses that the isotopic labeling of the linker results in sets of
reagents that are distinguishable by mass (id. at 11). Aebersold also
discloses that “[t]o promote ionization, the linker may contain acidic or basic
groups. . . . The linker may also contain groups having a permanent charge,
e.g., phosphonium groups . . . , chelated metal ions,” etc. (Id. at 14.)
Thus, as Appellants have pointed out (Appeal Br. 9-10), Aebersold’s
emphasis is on isotopically labeling the linker group to allow distinguishing
via mass spectrometry between proteins coupled to different A-L-PRG
reagents. Aebersold also suggests that including a chelated metal ion in the
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linker could provide an additional benefit – apparently, promoting
ionization – but it does not suggest that the chelated metal ion would serve
the same function as the isotopic labeling that is the focus of its method.
The Examiner points out that Moutiez discloses that a chelated Gd3+
ion can allow separation by metal ion chelate affinity chromatography and
detection using luminescence (Answer 6), but does not point to evidence
showing that those skilled in the art would have recognized that a chelated
metal ion would serve the same function, as part of the linker in Aebersold’s
A-L-PRG reagent, as isotopic labeling. The Examiner therefore has not
provided an adequate basis to support the conclusion that a skilled artisan
would have considered it obvious to eliminate the isotopic label from
Aebersold’s A-L-PRG reagent, even if a chelated metal ion was included as
part of the linker.
SUMMARY
We reverse the rejection of claims 1-6, 8, 22, and 24-40 as obvious
based on Aebersold, Moutiez, and Li.

REVERSED

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