DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 07/30/2026 has been entered.
Status of Claims
Claims 13-16, 18-19, 21 and 26-29 are pending following the Reply filed 07/30/2026. Claims 1, 4-5, 7-8, 17, 20, 22 and 24-25 have been cancelled. Claims 13-15, 18-19 and 26-29 have been amended without introducing new matter. Claims 13-16, 18-19, 21 and 26-29 have been examined on the merits.
Withdrawn
The objection to the drawings is withdrawn in light of the replacement drawings filed 07/30/2026.
Any objection or rejection regarding claims 1, 4-5, 7-8, 17, 20, 22 and 24-25 is moot, because the claims have been cancelled.
The objection to claim 21 is withdrawn in view of the new grounds of rejection. See 35 U.S.C. 103 for further discussion.
The rejection of claim 29 under 35 U.S.C. 112(b) is withdrawn in light of the amendments.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 27 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 27 recites the limitation "the trypsin" in line 1. There is insufficient antecedent basis for this limitation in the claim.
Suggestion to obviate the rejection: Applicant may, for example, amend the claim to depend from claim 28.
In the interest of compact prosecution, the claim is interpreted as depending from claim 28.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claim(s) 14, 18-19, 21, 26 and 28-29 is/are rejected under 35 U.S.C. 103 as being unpatentable over Shimada, et al. (US 2021/0215690 A1; effectively filed 02/08/2018; cited on Form 892), hereafter, “Shimada”, and in further view of Movius (US 2007/0021591 A1; previously cited).
Regarding claim 21, which is the independent claim, Shimada teaches a method for improving a detection sensitivity in a detection method for a monoclonal antibody (i.e., a polypeptide) in a sample, the detection method comprising:
(a) a step of capturing the monoclonal antibody in the sample and immobilizing the monoclonal antibody in pores of a porous body;
(b) a step of bringing the porous body in which the monoclonal antibody is immobilized with nanoparticles on which protease is immobilized to conduct selective protease digestion of the monoclonal antibody; and
(c) a step of detecting, by a liquid chromatography mass spectrometry (LC-MS), peptide fragments obtained by the selective protease digestion, wherein the selective protease digestion of step (b) is conducted in the presence of a chaotropic reagent and a reducing agent (see claim 1).
Shimada deduces that the presence of both the chaotropic reagent and the reducing agent facilitates the bringing the antibody to be substrate into contact with the protease on the nanoparticle surface, improves the stability of the peptides cleaved and released, and probably prevents the peptides from being adsorbed onto the vessel or being oxidized by contact with air, thereby contributing to the improvement of detection sensitivity (see pg. 5, para. [0087]).
The examiner notes that in the detailed protocol disclosed by Shimada, after the addition of the chaotropic reagent (contained in Tris-HCl) and addition of nanoparticles comprising immobilized trypsin (i.e., digesting step), there is no step of removing the chaotropic reagent before LC-MS analysis (see pg. 6, paras. [0107]-[0114]). Therefore, it is understood that the chaotrope is present in the solution when injected into an LC-MS system for analysis.
In view of Shimada’s examples, the reliable detection lower limit was 1.95 µg/mL when detection was conducted without the reducing agent and the chaotropic reagent, whereas the detection lower limit according to the method above was 0.061 µg/mL, demonstrating that the present method could not only increase the sensitivity but also detect a significantly low concentration of antibodies (see pg. 9, para. [0179]). Shimada teaches that this method can detect a much lower antibody concentration with high reliability (see pg. 9, para. [0180]), and this improved protocol improves the versatility of the detecting antibodies using mass spectrometry, which has industrial applicability for pharmacokinetic studies and therapeutic drug monitoring studies (see pg. 9, para. [0181]).
Shimada does not explicitly teach incubating the digested sample in the presence of a chaotrope at a mildly acidic pH.
Movius teaches methods for achieving the deaggregation of binding proteins and compositions suitable for the deaggregation of highly concentrated solutions of binding proteins containing one or more chaotrope and formulated at an acidic pH (see Abstract). Movius teaches that protein aggregation is of major importance to the biotechnology industry because of the importance of in vitro production of recombinant proteins (see pg. 1, para. [0007]). Movius teaches that proteins in solution, even highly purified proteins, can form aggregates upon storage, or during production processes, and in vitro aggregation limits protein stability, solubility, and production yields of recombinant proteins (see pg. 1, para. [0007]). Movius teaches that existing methodologies for achieving protein deaggregation commonly employ the step of solubilizing the protein in high concentrations of strong chaotropes, such as guanidine hydrochloride, which results in nearly complete protein unfolding (see pg. 1, para. [0011]). Movius teaches that compositions for deaggregating binding proteins comprise one or more chaotropic agent, including guanidine hydrochloride (see pg. 6, para. [0066]), and are buffered to about pH 5 (see pg. 6, para. [0068]). Movius teaches that the binding proteins include antibody fragments and variable fragment single-chain antibodies (see pg. 1, para. [0002]).
In view of the instant specification, “a mildly acidic pH” refers to an acidic pH of about 4 or higher and below 7 (see pg. 3, para. [0008]), which includes pH 5.
Therefore, Shimada teaches a method for the digestion of monoclonal antibodies in the presence of a chaotrope to produce peptide fragments for detection using LC-MS analysis, and Movius teaches that such antibody fragments are prone to aggregation during production processes, which can be prevented by the presence of a chaotrope at a mildly acidic pH.
It would have been obvious at the time of filing for a person of ordinary skill in the art to have arrived at the claimed invention by combining the teachings of Shimada and Movius, because each reference relates to production processes involving fragmented proteins which are prone to aggregation during storage and production processes. Therefore, one would have been motivated to combine the teachings of Movius with that of Shimada when processing antibody polypeptides (binding proteins), because Movius teaches that in vitro aggregation of binding proteins, including antibody fragments, limits protein stability and solubility which can be detrimental to the digested peptides during storage and to their further use in production processes. Hence, one would have expected that incubating the digested samples in the presence of a chaotrope at a mildly acidic pH would be an effective means to ensure the stability and solubility of the peptides for downstream processes (e.g., LC-MS). Hence, the combination would have been readily apparent and deemed to be a mere (A) combining of prior art elements according to known methods to yield predictable results (see MPEP 2143(I): Rationales to support rejections under 35 U.S.C. 103).
Regarding claim 18, which depends from claim 21, Shimada teaches the method wherein the chaotropic reagent is guanidium hydrochloride (see claim 2) which is the same as guanidine hydrochloride (see Movius at pg. 6, para. [0060]). Movius teaches the method wherein the chaotropic agent is guanidine hydrochloride, as discussed above
Regarding claim 19, which depends from claim 21, Movius teaches the mildly acidic pH is about 5, as discussed above.
Regarding claim 26, which depends from claim 21, the polypeptides of Shimada and Movius include antibodies, as discussed above, which meets the limitation of an “antigen binding protein”.
Regarding claim 28, which depends from claim 21, Shimada teaches that a single protease can be “used alone” and trypsin is particularly preferred (see pg. 4, para. [0073]).
Regarding claim 29, which depends from claim 21, Movius teaches that existing methodologies for achieving protein deaggregation commonly employ the step of solubilizing the protein in high concentrations of strong chaotropes, as discussed above.
Regarding claim 14, which depends from claim 28, Shimada teaches that the reaction solution comprising Tris-HCl is added to the sample solution (see pg. 6, para. [0107]) before digesting the polypeptide (i.e., adding trypsin) (see pg. 6, para. [0108]), wherein the Tris-HCl contains a chaotropic reagent and a “reducing” agent (see pg. 6, par. [0114]). It is understood that the reducing agent has the effect of “reducing” the polypeptide, and Movius teaches that chaotropes have the effect of “denaturing” (see pg. 2, para. [0018] and [0023]).
Claim(s) 13 is/are rejected under 35 U.S.C. 103 as being unpatentable over Shimada and Movius, as applied to claims 14, 18-19, 21, 26 and 28-29 above, in further view of Sato, et al. (WO 2019143636 A1; previously cited), hereafter, “Sato”, and Edgeland (previously cited). See also the “Supplemental Data” associated with Egeland’s disclosure (previously cited).
Regarding claim 13, which depends from claim 21 above, it should be noted that the further limitation of the claim does not require any further active steps in the claimed method and is directed to a result that is expected to be achieved by the processing of a polypeptide according to the method. As set forth under Claim interpretation in the Office Action filed 08/19/2025, the claimed results are understood to be the effect of digesting any polypeptide that contains the recited sequences.
In view of Applicant’s Examples, the claimed peptides are the result of the tryptic digestion of a BiTE® molecule (see instant specification at “Example 8”, pg. 67, paras. [00157]-[00158]) which is further disclosed as a “bispecific T-cell engager” molecule (see instant specification at pg. 5, para. [0008]). Therefore, it is understood that polypeptides that do not contain the same subsequences as BiTE® (e.g., HGNFGNSY) will not be expected to produce peptides with the same sequence identity when digested, because these results are dependent on the amino acid sequence of the polypeptide selected for processing.
Sato teaches methods of treating cell proliferative disorders, such as cancer, by administering to a subject an effective amount of a bispecific antibody, such as an anti-CD3 antibody (see pg. 7, para. [0020]; pg. 8, para. [0023]). Sato provides a bispecific antibody that binds CD3 and another antigen, wherein the bispecific antibody comprises a first heavy chain binding domain and a second heavy chain binding domain, wherein a polypeptide comprising a CDR-H3 comprises the amino acid sequence of SEQ ID NO: 25. Sato teaches that antibody fragments can be made by various techniques, including but not limited to proteolytic digestion of an intact antibody (see pg. 30, para. [00108]). Sato teaches that bispecific antibodies of the invention may be identified, screened for, or characterized for their physical/chemical properties and/or biological activities by various assays known in the art (see pg. 52, para. [00154]) and anti-CD3 epitopes may be determined by mass spectrometry (see pg. 29, para. [00101]). As shown in the following alignment, Sato’s SEQ ID NO: 25 (bottom) comprises instant SEQ ID NO: 108 (top):
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It should be noted that this same motif is present in numerous sequences Sato teaches to be useful for constructing bi-specific antibodies, including SEQ ID NOs 1-4, 7, 17, 19, 31, 34-35, 37 and 39-40 (see Table 1, pgs. 63-68).
Egeland evaluates the effect of increasing the amount of trypsin in bottom-up based targeted protein analysis (see Abstract). Egeland teaches that the peptides used contained varying amounts of “chymotryptic” cleavage sites, including sites that are carboxyl terminal to tyrosine, the idea being that if the increased trypsin amounts result in increased chymotryptic activity, this effect would be apparent when studying the peptides’ digestion profiles (see pg. 156, col. 2, para. 3). Egeland discloses that a follow-up experiment was performed to prove the presence of chymotryptic activity during digestion (see pg. 156, col. 2, para. 4).
Figure S4 of Egeland’s “Supplemental Data” shows that peptides observed and confirmed by MS/MS (denoted with a checkmark below) in samples digested for up to twenty hours included peptides comprising a tyrosine (Y) at the C-terminus. For clarity, see the annotated version of the figure below:
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25
1043
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25
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As seen in the figure above, the digestion of hCGβ-T5 using trypsin at an E:S ratio of 1:1 produced a peptide with a tyrosine at the C-terminus using unmodified trypsin (VLQGVLPALPQVVCNY) and also using modified trypsin (QGVLPALPQVVCNY), and the digestion of hCGβ-T9 produced a peptide with a tyrosine at the C-terminus under all conditions (GVNPVVSY).
Therefore, Egeland discloses the processing of a polypeptide comprising digesting the polypeptide with a protease (i.e., trypsin) to produce a digested sample comprising at least two peptides, wherein at least one of the digested peptides comprises a tyrosine (Y) at the C-terminus. Egeland demonstrates that digesting polypeptides with predicted chymotryptic cleavage sites with trypsin will produce peptides with a C-terminal tyrosine when digested by certain types of trypsin at certain E:S ratios.
It would have been obvious at the time of filing for a person of ordinary skill in the art to have arrived at the claimed method resulting in the generation of the claimed peptide fragment, because Sato teaches this fragment to comprise a common motif present in bi-specific antibodies that are useful for treating cancer. One would have recognized from Egeland that the use of certain proteases at certain E:S ratios during protein digestion will result in peptide fragments comprising a C-terminal tyrosine, which would be useful for the analyses and construction of the bi-specific antibodies taught by Sato. One of ordinary skill would have recognized from Egeland that the results of any digestion using trypsin would be dependent on the polypeptide selected for said digestion, and that these portions of the protein can be predicted based on the presence of art-recognized cleavage sites in the sequence. Furthermore, one would have expected that the results of the tryptic digestions disclosed by Egeland would be predictable when applying the same techniques to the tryptic digestion of a bi-specific antibody. One would have been motivated to have combined these teachings with Shimada and Movius, because these references teach the advantages of further incubating and analyzing antibody fragments in the presence of a chaotrope. Hence, the combination would have been readily apparent and deemed to be a mere (A) combining of prior art elements according to known methods to yield predictable results (see MPEP 2143(I): Rationales to support rejections under 35 U.S.C. 103).
Claim(s) 15-16 is/are rejected under 35 U.S.C. 103 as being unpatentable over Shimada and Movius, as applied to claims 14, 18-19, 21, 26 and 28-29 above, in further view of Agilent (previously cited).
Regarding claim 15, which depends from claim 28 above, Shimada teaches that the reaction solution comprising Tris-HCl is added to the sample solution (see pg. 6, para. [0107]) before digesting the polypeptide (i.e., adding trypsin) (see pg. 6, para. [0108]), wherein Tris-HCl acts as a buffer agent (see pg. 6, para. [0114]). Therefore, Shimada teaches a buffer exchange before digesting the polypeptide with trypsin. However, this exchange appears to be conducted during the same step as adding the chaotrope and the reducing agent, which are both present in the Tris-HCl.
Agilent teaches that peptide mapping, an invaluable tool for biopharmaceuticals, is the most widely used identity test for proteins, particularly those produced by recombinant means, and most commonly involves enzymatic digestion (usually using trypsin) of a protein to produce peptide fragments, followed by separation and identification of the fragments in a reproducible manner (see pg. 2, col. 1, para. 1). Agilent teaches that the five steps for protein digestion include (1) sample preparation, (2) selection of cleavage agent, (3) reduction and alkylation, (4) digestion process, and (5) enrichment/cleanup (preparing sample for LC/MS analysis) (see pg. 3, Table 1). Agilent teaches that to provide an optimal pH for the enzymatic cleavage, a buffer is added prior to the addition of trypsin (see pg. 7, col. 1, para. 2), which Agilent describes in the step-by-step process as taking place after the reduction and alkylation step (see Step 3 on pg. 7 and Step 4 on pg. 8). Agilent teaches that pH of the reaction is among several factors that are critical to the effectiveness of the digestion (see pg. 7, col. 1, para. 3) and is empirically determined to ensure the optimization of the performance of a given cleavage agent (see pg. 7, col. 2, para. 1).
It would have been obvious at the time of filing for a person of ordinary skill to have arrived at the claimed invention by combining the teachings of the aforementioned references to have arrived at the claimed invention, because Agilent teaches the step of buffer exchange prior to trypsin digestion is an effective means to control the pH during digestion, which is a critical factor during said digestion. One would have recognized from these combined teachings that buffer exchange could be performed after the reducing and/or alkylating step prior to the digestion step, and it was well within the ordinary skill in the art to have modified or added to the method taught by Shimada. One would have recognized that each reference is directed to methods of digesting proteins using trypsin for the identification and analysis of said proteins, and one would have been motivated to combine these teachings in order to optimize the conditions of the protein sample during enzymatic digestion. As each reference teaches enzymatic digestions using the same protease (i.e., trypsin) to produce peptide fragments for further analysis, one would have recognized the results of the combination would have been predictable. Hence, the combination would have been readily apparent and deemed to be a mere (A) combining of prior art elements according to known methods to yield predictable results (see MPEP 2143(I): Rationales to support rejections under 35 U.S.C. 103).
Regarding claim 16, which depends from claim 15, Agilent teaches that gel filtration can be used to remove low molecular weight components, while buffer exchange replaces the sample buffer with a new buffer (see pg. 4, col. 2, para. 4). Agilent teaches that gel filtration is one of the easiest chromatography methods to perform because samples are processed using an isocratic elution (see pg. 5, col. 1). In its analytical form, gel filtration (also known as size exclusion chromatography) can distinguish between molecules (e.g. proteins) with a molecular weight difference of less than a factor of 2 times (see pg. 5, col. 1).
In view of the instant specification, “the buffer exchange comprises using a size exclusion cartridge, optionally a NAPTM-5 column with the Sephadex® gel filtration material” (see pg. 7, para. [0009]).
Agilent teaches the use of Agilent Bio SEC columns for size exclusion chromatography (see pg. 5, top figure). Hence, the “column” of Agilent’s disclosure meets the limitation of a “cartridge”.
Claim(s) 27 is/are rejected under 35 U.S.C. 103 as being unpatentable over Shimada and Movius, as applied to claims 14, 18-19, 21, 26 and 28-29 above, in further view of Wu (previously cited).
Regarding claim 27, which depends from claim 28, Shimada does not explicitly teach that the trypsin is a recombinant protein.
Wu teaches trypsin is an important digestive enzyme in peptide sample preparation for proteomics, and the majority of commercial products are obtained from animal sources (see pg. 1059, “Rationale”). In Wu’s study, the researchers evaluated whether recombinant trypsin (r-trypsin) and recombinant acetylated trypsin (r-Ac-trypsin) are suitable for proteomics research (see pg. 1059, “Rationale”). Wu discloses that the r-trypsin and r-Ac-trypsin had better efficiency than the commercial products at high protein/enzyme ratios, and both demonstrated similar specificity and efficiency compared to commercial products in typical in-solution digestion of HSA (see pg. 1064, col. 1). While the activity and specificity of the r-Ac-trypsin were similar to that of commercial trypsins, it also demonstrated superior activity and specificity on complicated samples and, more interestingly, was more resistant to autolysis, which enabled more complete digestion of proteomic samples (see pg. 1059, “Results”). Wu concludes that the r-Ac-trypsin studied is a recombinant product, showing similar or superior properties such as stability activity and specificity compared to commercial products, and can be used in peptide sample preparation in proteomics studies (see pg. 1059, “Conclusions”).
It would have been obvious at the time of filing for a person of ordinary skill in the art to have arrived at the claimed invention by substituting the trypsin used by Shimada with the recombinant trypsin taught by Wu, because Wu teaches recombinant trypsin proteins having better efficiency than animal-derived products. One would have been motivated to do so, because Wu teaches recombinant trypsin proteins to have similar or superior properties compared to non-recombinant products. Furthermore, Wu teaches that both recombinant trypsins had better efficiency than the commercial products at high protein/enzyme ratios. Therefore, a person of skill would have recognized that the substituted component and its functions were known in the art and one could have substituted one known element for another to obtain predictable results. Furthermore, both Shimada and Wu relate to methods for studying proteins comprising proteolytic trypsin digestion, and a person of skill would have recognized that many different types of trypsin may be used to perform such studies. Therefore, as the substituted component was known in the art and has been demonstrated in the art to be suitable for such processes, there would have been a reasonable expectation of success. Hence, the combination would have been readily apparent and deemed to be a mere (B) simple substitution of one known element for another to obtain predictable results (see MPEP 2143(I): Rationales to support rejections under 35 U.S.C. 103).
Response to Arguments
Regarding the rejections under 35 U.S.C. 103, Applicant argues that these rejections are moot by way of the amendments to the claims. In particular, claims 1, 4, 5, 7, 8, 17, 20, 22, 24, and 25 have been canceled herein, and claims 13-16, 18, 19 and 26-29 depend, directly or indirectly, from allowable claim 21.
Applicant also states, “Applicant acknowledges the Office Action’s conclusion (at page 30) that independent claim 21 is free of the prior art and allowable”, that the accompanying amendment “leaves each claim dependent, directly or indirectly, from allowable claim 21”, and “cancellation of claim 25 resolves the sole issue identified in the Advisory Action” (see Remarks at pg. 5, para. 1).
Applicant’s arguments with respect to claim(s) 21 and its dependents have been considered but are moot because the new ground of rejection does not rely on any reference applied in the prior rejection of record for any teaching or matter specifically challenged in the argument.
It should be noted that claim 21 was expressly objected to in the previous Office Action, and therefore did not carry the status of being “allowable”.
Nonetheless, upon further consideration, as set forth in the present rejections under 35 U.S.C. 103, new prior art has been found teaching the limitations of claim 21. See the rejections under 35 U.S.C. 103 for further discussion.
It should also be noted that even when amending a claim to be dependent from an allowable claim, this does not automatically render the amended claim to be allowable without further consideration, particularly when the amended claim previously depended from a claim that recited different limitations. Such amendments require further examination to determine the patentability of the claim as a whole.
Regarding the Advisory Actions, filed 07/15/2026 and 08/07/2026, it should be noted that the Advisory Action filed 08/07/2026 stated that “no previous claim has depended from claim 21. Therefore, the claims in their amended form require further search and consideration.” Therefore, Applicant’s statement that the cancellation of claim 25 was the “sole issue” raised by the Examiner lacks sufficient grounds, because the claims which were amended After-Final had not yet been treated on the merits which would be required for the examiner to raise every potential issue. Applicant is reminded that the amendment of any finally rejected claim is not entered as a matter of right. See 37 CFR 1.116. In each of the Advisory Actions above, the examiner set forth reasons at least as to why the After-Final amendments required further consideration on the merits, and more than a cursory review, to determine patentability. See also MPEP 714.13(II-III).
In light of the cancelled claims above, the examiner notes that while prosecution is open, Applicant reserves the right, in accordance with 37 CFR 1.121, to reinstate previously cancelled subject matter, if desired, so long as it does not introduce new matter into the disclosure of the application. See 37 CFR 1.121(c, f) and MPEP 714.
Conclusion
No claims are allowed.
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/DENNIS IGNATIUS ARMATO JR/Examiner, Art Unit 1651
/MELENIE L GORDON/Supervisory Patent Examiner, Art Unit 1651
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