DETAILED CORRESPONDENCE
Status of the Application
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims 1-7, 12-14, 19 and 21 are pending in this application.
Applicant’s amendment to the claims filed 01/16/2026 is acknowledged. This listing of the claims replaces all prior versions and listings of the claims.
Applicant’s remarks filed on 01/16/2026 in response to the non-final rejection mailed on 07/18/2025 are acknowledged and have been fully considered.
Applicant’s Declaration under 37 CFR 1.132 filed 01/16/2026 is acknowledged and has been fully considered.
Rejections previously applied to claims 15-17 and 20 are withdrawn in view of applicant’s amendment to cancel claims 15-17 and 20.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Election
The elected subject matter is
Species A1) the A2-type beta-casein variants comprise A2 beta-casein, and
Species B1) the A1-type beta-casein variants comprise A1 beta-casein,
elected without traverse in the reply filed on 03/06/2024.
Claims 1-7, 12-14, 19 and 21 are being examined on the merits only to the extent the claims read on the elected subject matter.
Claim Rejections - 35 USC § 112(b)
The rejection of claims 1-7, 12-17 and 19-20 under 35 U.S.C. 112(b) as being indefinite for lack of antecedent basis is withdrawn in view of
the amendment to claim 1 to no longer recite “position 67” without a reference,
the amendment to claim 1 to no longer require a specific accuracy without establishing a method or metric for determination of said accuracy,
the amendment to claim 19 to depend from claim 1,
and the cancelation of claims 15-17 and 20.
Claims 7, 14 and 21 are newly rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
The instant rejection is necessitated by claim amendment.
Claim 7 is indefinite for the phrase “The method as claimed in claim 1, wherein the concentrations of three or four bovine A2 beta-casein digestion peptides are determined”. The specification discloses A2-type beta-casein variants have proline at position 67 [page 3, lns 27-28], and discloses the determination of beta-casein digestion peptides having proline at position 67 that correspond to VYFPFPGPIPN and SLVYFPFPGPIPN [page 4, lns 23-27], which correspond to SEQ ID NOs: 5-6 recited in claim 1 step (iv). As claim 1 step (iv) recites adding isotopically labelled peptides corresponding to SEQ ID NOs: 5-6, one of skill in the art would reason the isotopically labeled peptides corresponding to SEQ ID NOs: 5-6 in claim 1 step (iv) correspond to A2-type beta casein fragments. However, as claim 1 step (v) recites “performing liquid chromatography-mass spectrometry on the solution to determine the concentrations of the peptides from (iii) present in the solution and the peptides from (iv) present in the solution”, it is unclear how the two isotopically labeled peptides corresponding to A2-type beta casein fragments of SEQ ID NOs: 5-6 in claim 1 step (iv) would be used to determine the concentrations of the three or four A2 beta-casein digestion peptides required by claim 7, as claim 7 does not recite three or four isotopically labeled peptides corresponding to A2-type beta-casein fragments.
Claims 12-13 are indefinite for the limitations “the digestion peptide VYPFPGPIHNSLPQ (SEQ ID NO: 3)” in claim 12, “the digestion peptide SLVYPFPGPIHNSLPQ (SEQ ID NO: 4) in claim 12, “the digestion peptide VYPFPGPIPNSLPQ (SEQ ID NO: 7)” in claim 13, and “the digestion peptide SLVYPFPGPIPNSLPQ (SEQ ID NO: 8) in claim 13. There is insufficient antecedent basis for these limitations in the claims, as claim 1 from which claims 12-13 depend only recites the corresponding peptides of SEQ ID NOs: 1-2 and 5-6.
Claim 14 is indefinite for the recitation of “wherein the concentrations of the following peptides are determined in step (v)”, wherein the required peptides correspond to SEQ ID NOs: 1-8. As the method of claim 1 recites the determination of concentration of two isotopically labeled peptides each from (iii)-(iv) via LC-MS, it is unclear how the two isotopically labeled peptides corresponding to SEQ ID NOs: 1-2 will be used to determine the concentration of the peptides corresponding to SEQ ID NOs: 1-4, and how the two isotopically labeled peptides corresponding to SEQ ID NOs: 3-4 will be used to determine the concentration of the peptides corresponding to SEQ ID NOs: 5-8.
Claim 21 is indefinite for the phrase “the method as claimed in claim 1, wherein the method further comprises” followed by the recitation of a step (iii) and step (iv). As claim 1 already recites a step (iii) and step (iv), it is unclear whether steps recited by the phrase are intended to replace steps (iii) and (iv) of claim 1, or whether the claim is intending to include the isotopically labeled peptides recited in claim 21 along with the peptides recited in steps (iii) and (iv) of claim 1.
Response to Remarks: Beginning page 6 of Applicant’s response to the rejections under 35 USC 112(b); Applicant in summary contends the rejections should be withdrawn in view of the instant amendments to the claims.
Applicant’s remarks are considered and found not convincing, as the instant claim amendments necessitate new rejections.
Claim Rejections - 35 USC § 103
Claims 1-7, 14 and 21 are rejected under 35 U.S.C. 103 as being unpatentable over Chinese Application No. CN 108519485 (cited on the IDS submitted 08/03/2021; reference is made to a machine translation cited on the Form PTO-892 mailed 01/09/2024; herein referred to as CN485) in view of Giansanti et al. (Nat Protocols, 2016, 11:993; cited on the Form PTO-892 mailed 01/09/2024; herein referred to as Giansanti) and evidentiary references ExPasy PeptideCutter Digest of A1 (3 pages, 03/26/2024; cited on the Form PTO-892 mailed 04/03/2024; herein referred to as CHYM-A1) and ExPasy PeptideCutter Digest of A2 (3 pages, 03/26/2024; cited on the Form PTO-892 mailed 04/03/2024; herein referred to as CHYM-A2).
The instant rejection is maintained from the previous Office Action and any newly recited portions are necessitated by claim amendment.
Claim 1 as amended is drawn to a method for determining the amounts of bovine A1-type beta-casein variants or bovine A2-type beta-casein variants in a composition where the composition is bovine milk, comprising the steps:
(i) contacting the composition with chymotrypsin under conditions enabling digestion of beta-caseins in the composition by the chymotrypsin;
(ii) obtaining an aqueous solution of beta-casein digestion peptides;
(iii) adding isotopically labeled peptides corresponding to the peptides: VYPFPGPIHN (SEQ ID NO: 1); and SLVYPFPGPIHN (SEQ ID NO: 2);
(iv) adding isotopically labeled peptides corresponding to the peptides: VYPFPGPIPN (SEQ ID NO: 5); and SLVYPFPGPIPN (SEQ ID NO: 6);
(v) performing liquid chromatograph-mass spectrometry on the solution to determine the concentrations of the peptides from (iii) present in the solution and the peptides present from (iv) in the solution; and
(vi) calculating the concentration of bovine A1-type beta-casein variants in the composition or the concentration of bovine A2-type beta-casein variants in the composition using the concentrations of the peptides determined in step (v).
CN485 discloses a mass spectrometry (MS) detection method for A1/A2 beta-casein [title].
Regarding claim 1 and the limitation of bovine A1-type and A2-type beta casein variants in milk or a product prepared from bovine milk, CN485 teaches a method for MS detection of A1/A2 beta-casein from milk [Claim 5], wherein the method is centered on bovine beta-casein as identified in definition of beta-casein as “encoded by the C2N2 gene on chromosome 6, a highly polymorphic gene … with A1 and A2 beta-casein being the most common forms of bovine beta-casein” [p 2, para 1 of “Background”].
Regarding claim 1 and the limitation of determining the amounts of A1- or A2- type beta-casein variants in a composition step (v), CN485 discloses a method for MS detection of A1 and A2 beta-casein that has high accuracy [abstract].
Regarding claim 1 and the limitations in step (i) of digesting beta-caseins with chymotrypsin and in step (ii) of obtaining an aqueous solution of beta-casein digestion peptides, CN485 teaches the method of MS detection of A1/A2 beta-casein from milk [Claim 5] wherein samples are cut using a specific enzymolysis method [Claim 1c], wherein the enzymolysis method performed using the protease trypsin [Claim 1] that produces characteristic peptide fragments of
IHPFAQTQSLVYPFPGPIHNSLPQNIPPLTQTPVVVPPFLQPEVMGVSK for A1 beta-casein, and
IHPFAQTQSLVYPFPGPIPNSLPQNIPPLTQTPVVVPPFLQPEVMGVSK for A2 beta-casein [Claim 1c], wherein the underlined amino acid represents position 67 of beta-casein to distinguish the variants. Additionally, the enzymolysis step of CN485 is understood to be carried out in an aqueous solution, and is therefore understood to produce an aqueous solution of digestion peptides.
Regarding claim 1 and the limitations in steps (iii)-(iv) of adding isotopically labeled peptides, step (v) of determining the concentrations of beta-casein digestion peptides present in the solution, and step (vi) of calculating the concentration of A1- and A2-type beta-casein variants in the composition using the concentrations of the beta-casein digestion peptides, CN485 teaches a method of MS detection of A1- and A2-type beta-casein peptide digestion fragments wherein isotope internal standard peptide fragments are used for quantitative analysis via multi-reaction monitoring (MRM) [Claim 1], and furthermore quantitative detection of A1 and A2 beta-casein in milk via multi-reaction monitoring (MRM) [Claim 5]. The quantitative detection as disclosed by CN485 is interpreted to encompass the calculation of concentration of the beta-casein variants as recited in the claim.
While CN485 teaches trypsin digestion of A1/A2 beta-casein from milk to produce polypeptide fragments whose concentrations are determined by comparing via LC-MS to isotopically labeled peptides that correspond to the trypsin digestion fragments, CN485 does not teach the use of chymotrypsin in step (i), and the isotopically labeled peptides corresponding to the digestion products from chymotrypsin in steps (iii)-(iv).
Giansanti discusses six alternative proteases for mass spectrometry-based proteomics beyond trypsin [title]. Regarding the limitation of using chymotrypsin, Giansanti teaches that protein digestion is largely performed using trypsin, but chymotrypsin is also used in proteomics and generates a different set of peptides [p 993, col 1, para 2], and the cleavage sites of chymotrypsin are C-terminal of F, Y, L, W, and M [Table 1].
Regarding claim 1 and the limitation in steps (iii)-(iv) of peptide digestion fragments, Giansanti teaches the use of chymotrypsin for protein digestion. In view of the teachings of Giansanti regarding the use of chymotrypsin and the disclosed cleavage sites of the protease, one of ordinary skill in the art in using the chymotrypsin of Giansanti in the method of CN485 to digest A1-type beta-casein with a sequence comprising:
IHPFAQTQSLVYPFPGPIHNSLPQNIPPLTQTPVVVPPFLQPEVMGVSK
would be reasonably expected to produce at least the fragments of
IHPF, AQTQSL, VY, PF, VYPFPGPIHNSL, PGPIHNSL, PQNIPPL, TQTPVVVPPF, L, QPEVM, and GVSK,
as well as numerous additional fragments as evidenced by CHYM-A1 that include VYPFPGPIHN and SLVYPFPGPIHN corresponding to SEQ ID NOs: 1-2 recited in the claims.
Furthermore, one of ordinary skill in the art in using the chymotrypsin of Giansanti in the method of CN485 to digest A2 beta-casein peptide of CN485 with a sequence comprising:
IHPFAQTQSLVYPFPGPIPNSLPQNIPPLTQTPVVVPPFLQPEVMGVSK
would be reasonably expected to produce at least the fragments of IHPF, AQTQSL, VY, PF, VYPFPGPIPNSL, PGPIPNSL, PQNIPPL, TQTPVVVPPF, L, QPEVM, and GVSK,
as well as numerous additional fragments as evidenced by CHYM-A2 that include VYPFPGPIPN and SLVYPFPGPIPN corresponding to SEQ ID NOs: 5-6 recited in the claims.
Regarding claim 1 and the limitations in steps (iii)-(iv), CN485 teaches the mixture of selected characteristic peptides corresponding to isotopically labeled peptide internal standards [Claim 1, and the Table on Page 4 of the machine translation] wherein the digestion of the A1 and A2 beta-casein peptides with the chymotrypsin taught by Giansanti would be expected to produce at least the peptide fragments as described above. As the method of CN485 includes the selection of peptide fragments for isotopically labeled internal standards, one of skill in the art would be reasonably expected to choose the corresponding fragments resulting from the digestion of beta-casein with the chymotrypsin of Giansanti as disclosed above. Considering that the claimed method is stated to “comprise” steps (i)-(v), the claimed method is interpreted to encompass undisclosed steps as well as undisclosed additions to steps (i)-(v) (see MPEP 2111.03.I), and therefore one of skill in the art in carrying out the method of CN485 with the chymotrypsin of Giansanti would have arrived at the claimed invention.
In view of the teachings of CN485 and Giansanti, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date to modify the method of CN485 by substituting chymotrypsin, as taught by Giansanti, to arrive at the claimed invention, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that both trypsin and chymotrypsin are proteases regularly used for digestion in peptide mass spectrometry protocols, and as such both are capable of being incorporated into the analysis methods as described by CN485 and Giansanti. Thus it would have been obvious to one of ordinary skill in the art to replace trypsin with chymotrypsin, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both CN485 and Giansanti discuss peptide digestion methods for peptide analysis via mass spectrometry.
Regarding claims 2-3, CN485 teaches the method described in the rejection of claim 1 above wherein the A1-type beta-casein variant comprises solely A1 beta-casein.
Regarding claims 4-5, CN485 teaches the method described in the rejection of claim 1 above wherein the A2-type beta-casein variant comprises solely A2 beta-casein.
Regarding claim 6, CN485 teaches the method described in the rejection of claim 1 above wherein the A1-type beta-casein variant comprises solely A1 beta-casein and the A2-type beta-casein variant comprises solely A2 beta-casein.
Regarding claim 7, CN485 teaches the method described in the rejection of claim 1 above wherein the digestion of the A2 beta-casein peptide with the chymotrypsin taught by Giansanti would cleave the beta-casein peptide to produce at least the peptide fragments of:
VYPFPGPIPN, SLVYPFPGPIPN, VYPFPGPIPNSLPQ, and SLVYPFPGPIPNSLPQ as evidenced by CHYM-A2.
Regarding claim 14, CN485 teaches the method of detection of A1/A2 beta-casein in milk [Claim 5] wherein the method is centered on bovine beta-casein as identified in definition of beta-casein as “encoded by the C2N2 gene on chromosome 6, a highly polymorphic gene … with A1 and A2 beta-casein being the most common forms of bovine beta-casein” [p 2, para 1 of “Background”]. Therefore the beta-casein and milk analyzed in the method of CN485 is interpreted to encompass bovine beta-casein and milk. CN485 further teaches the method described in the rejection of claim 1 above wherein the digestion of the A1 beta-casein peptide by the chymotrypsin taught by Giansanti would produce at least the peptide fragments of VYPFPGPIHN, SLVYPFPGPIHN, VYPFPGPIHNSLPQ, and SLVYPFPGPIHNSLPQ as evidenced by CHYM-A1, and the digestion of the A2 beta-casein peptide by the chymotrypsin taught by Giansanti would produce at least the peptide fragments of VYPFPGPIPN, SLVYPFPGPIPN, VYPFPGPIPNSLPQ, and SLVYPFPGPIPNSLPQ as evidenced by CHYM-A2.
Regarding claim 21, in view of the indefiniteness of the claim as discussed above, and for the sake of compact prosecution, the claim is being interpreted such that it is intended further limit steps (iii) and (iv) recited by claim 1.
CN485 teaches the method of detection of A1/A2 beta-casein in milk [Claim 5] wherein the method is centered on bovine beta-casein as identified in definition of beta-casein as “encoded by the C2N2 gene on chromosome 6, a highly polymorphic gene … with A1 and A2 beta-casein being the most common forms of bovine beta-casein” [p 2, para 1 of “Background”]. Therefore the beta-casein and milk analyzed in the method of CN485 is interpreted to encompass bovine beta-casein and milk. CN485 further teaches the method described in the rejection of claim 1 above wherein the digestion of the A1 beta-casein peptide by the chymotrypsin taught by Giansanti would produce at least the peptide fragments of VYPFPGPIHN, SLVYPFPGPIHN, VYPFPGPIHNSLPQ, and SLVYPFPGPIHNSLPQ corresponding to SEQ ID NOs: 1-4, respectively, as evidenced by CHYM-A1, and the digestion of the A2 beta-casein peptide by the chymotrypsin taught by Giansanti would produce at least the peptide fragments of VYPFPGPIPN, SLVYPFPGPIPN, VYPFPGPIPNSLPQ, and SLVYPFPGPIPNSLPQ corresponding to SEQ ID NOs: 5-8, respectively, as evidenced by CHYM-A2.
Therefore, the invention of claims 1-7, 14 and 21 would have been obvious to one of ordinary skill in the art before the effective filing date.
Claims 12-13 are rejected under 35 U.S.C. 103 as being unpatentable over CN485 and Giansanti as applied claims 1-7, 14 and 21 above, and further in view of Chen et al. (Biochim Biophys Acta, 2016, 1864:1122; cited on the Form PTO-892 mailed 04/03/2024; herein referred to as Chen).
The instant rejection is maintained from the previous Office Action and any newly recited portions are necessitated by claim amendment.
Claim 12 is drawn to the method of claim 1, wherein the isotopically labelled peptides correspond to the peptides disclosed in SEQ ID NOs: 10-13, which are the same sequences as SEQ ID NOs: 1-4 wherein the valine of SEQ ID NOs 1-2 and 4 is labeled corresponding to SEQ ID NOs: 10-11 and 13, respectively, and the leucine of SEQ ID NO: 3 is labeled corresponding to SEQ ID NO: 12. As
The teachings of CN485 and Giansanti as applied to claims 1-7, 14 and 21 are discussed above. These references do not teach the isotopic labeling of leucine.
Regarding the limitations of claim 12, CN485 teaches the mixture of isotopically labeled peptides [Claim 1, and the Table on Page 4 of the machine translation] in the method described in the rejection on claim 1 above, wherein the valine is labeled.
Chen describes methods for the quantification of beta-casein using LCMS methods based on isotope internal standards [title].
Regarding claim 12 and the labeling of leucine, Chen describes the production of a stable isotope labeled signature peptide of beta-casein using [13C6, 15N]-Leucine [p 1123, col 1, paras 2-3] to establish and validate a quantification method for beta-casein with MRM [p 1123, col 1, para 1]. Given the digestion peptides of A1 beta-casein with chymotrypsin discussed in the rejection of claim 14 above, one of ordinary skill in the art would have expected the isotopically labeled beta-casein variant would similarly produce the claimed digestion peptides that are isotopically labeled at the recited valine and leucine residues upon chymotrypsin digestion.
In view of Chen, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date to modify the combined method of CN485 and Giansanti by using isotopically labeled peptides, as taught by Chen, to arrive at the claimed invention. One of ordinary skill in the art would have been motivated to modify the combined method of CN485 and Giansanti by using the labeled peptides of Chen because Chen teaches the use of isotopically labeled leucine to establish and validate a quantification method for beta-casein with MRM. One of ordinary skill in the art would have had a reasonable expectation of success because CN485, Giansanti and Chen discuss peptide digestion methods for peptide analysis via mass spectrometry, and CN485 and Chen discuss quantification methods of beta-casein using isotopically labeled peptides with MRM.
Regarding claim 13, CN485 further teaches the mixture of isotopically labeled peptides [Claim 1, and the Table on Page 4 of the machine translation] in the method described in the rejection on claim 1 above, wherein the valine is labeled, and Chen teaches the use of isotopically labeled leucine as discussed in the rejection of claim 12 above. Given the digestion peptides of A2 beta-casein with chymotrypsin discussed in the rejection of claim 14 above, one of skill in the art would expect the isotopically labeled beta-casein variant would similarly produce the claimed digestion peptides that are isotopically labeled at the recited valine and leucine residues upon chymotrypsin digestion.
Therefore, the invention of claims 12-13 would have been obvious to one of ordinary skill in the art before the effective filing date.
Claim 19 is rejected under 35 U.S.C. 103 as being unpatentable over CN485 and Giansanti as applied claims 1-7, 14 and 21 above, and further in view of Nguyen et al. (J Food Comp Analysis, 2015, 44:102; cited on the Form PTO-892 mailed 04/03/2024; herein referred to as Nguyen).
The instant rejection is maintained from the previous Office Action and any newly recited portions are necessitated by claim amendment.
Claim 19 is drawn to the method of claim 1, wherein the milk is fresh milk, raw milk, milk powder, liquid milk reconstituted from powder, skim milk, homogenised milk, condensed milk, evaporated milk, flavoured milk, UHT milk, pasteurised milk, or non-pasteurised milk.
The teachings of CN485 and Giansanti as applied to claims 1-7, 14 and 21 are discussed above. These methods do not expressly teach the use of a composition wherein the milk comprises one of the specific types of milk recited in the claim.
Nguyen discusses the identification and quantification of native beta-casomorphins (BCMs) in milk using LCMS [title].
Regarding claim 19, Nguyen teaches a method of detecting BCMs in various types of pasteurized bovine milk [abstract, p 102, col 1, para 2], wherein pasteurized milk is shown to contain both beta-casein variants [Table 1].
In view of Nguyen, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date to modify the combined method of CN485 and Giansanti by using pasteurized bovine milk, as taught by Nguyen, to arrive at the claimed invention. One of ordinary skill in the art would have been motivated to modify the combined method of CN485 and Giansanti by using the pasteurized bovine milk because CN485 and Giansanti teach a method of quantifying A1 and A2 beta-casein variants, and Nguyen teaches that pasteurized bovine milk contains A1 and A2 beta-casein variants. One of ordinary skill in the art would have had a reasonable expectation of success because CN485, Giansanti and Nguyen discuss analysis methods of digested peptides via mass spectrometry, and CN485 and Nguyen discuss quantification methods of bovine milks.
Therefore, the invention of claim 19 would have been obvious to one of ordinary skill in the art before the effective filing date.
Response to Remarks: Beginning page 7 of Applicant’s response to the rejections under 35 USC 103 and the Declaration under 37 CFR 1.132; Applicant in summary contends there must be an articulated reason why one of skill in the art would make the proposed modification to establish a prima facie case of obviousness, as there is no teaching or suggestion of the particular selection of polypeptides to establish a prima facie case of obviousness; Applicant further contends there is no reason as to how or why one of ordinary skill in the art would arrive at the isotopically labeled peptides recited in claim 1, or why one of skill in the art would choose the claimed fragments out of the hundreds of possible fragments as there is no direction by the prior art for which fragments to choose; Applicant further contends the evidentiary references CHYM-A1 and CHYM-A2 are not prior art under 102, and as there is no evidence suggesting the information was available before the effective filing date of the claimed invention. Applicant further contends the claimed use of the isotopically labeled peptides in claim 1 amounts to a surprising discovery to render the method sufficient to quantify more than half of beta casein in a milk sample as described in the Declaration in paragraphs 4-5.
Applicant’s response and Declaration are considered and found not convincing.
The obviousness rejection of claim 1 set forth above and in previous Office actions is based on the simple substitution rationale, which does not necessarily rely on suggestions or motivations to combine prior art elements. MPEP 2143.I outlines multiple examples of rationales that may support a conclusion of obviousness, and includes the simple substitution of one known element for another to obtain predictable results, wherein MPEP 2143.I.B outlines the criteria for such a rationale that include:
(1) a finding that the prior art contained a device (method, product, etc.) which differed from the claimed device by the substitution of some components (step, element, etc.) with other components;
(2) a finding that the substituted components and their functions were known in the art;
(3) a finding that one of ordinary skill in the art could have substituted one known element for another, and the results of the substitution would have been predictable; and
(4) whatever additional findings based on the Graham factual inquiries may be necessary, in view of the facts of the case under consideration, to explain a conclusion of obviousness.
As described in the rejection above, the disclosure of CN485 satisfies item (1). As Giansanti discloses the use of various proteases for the purpose of digesting peptides for MS analysis, and as Giansanti further discloses the cleavage residues of chymotrypsin, it was known in the art that one could reasonably replace the trypsin of CN485 with the chymotrypsin of Giansanti, and that proteolysis of the target peptide would occur. Therefore Giansanti satisfies items (2)-(3), as it was known in the art the one could use any of the disclosed proteases to digest peptides for MS analysis.
Regarding the assertion that the prior art offers no guidance to select the isotopically labeled peptides recited in the claims, as stated in the rejection above, one of ordinary skill in the art in carrying out the modified method of CN485 using the chymotrypsin of Giansanti would have expected to produce multiple fragments as evidenced by CHYM-A1 and CHYM-A2, and therefore one of ordinary skill in the art in following the modified method of CN485 would generate isotopically labeled peptides corresponding to those peptides resulting from a chymotrypsin digest. While the claims recite adding two isotopically labeled fragments each which correspond to A1 and A2 beta-casein digestion peptides, the recitation of “comprising” to describe the method steps is inclusive and open-ended, and does not exclude additional unrecited elements or method steps (see MPEP 2111.03.I). Therefore, one of ordinary skill in the art would have been capable of generating isotopically labeled peptides corresponding to, for example, all predicted chymotrypsin digestion fragments, as the method of the prior art and the method of the claims do not exclusively limit the use of only two fragments per beta-casein variant.
Regarding the assertion that CHYM-A1 and CHYM-A2 were not known before the effective filing date, ExPASy, from which these evidentiary references originate, is an online predictive tool that aggregates publicly available bioinformatics resources that was established in 1994 as indicated on page 1, col 2, paragraph 1 of Artimo et al. (Nucleic Acids Res, 2012, 40:W597; cited on the attached Form PTO-892). Additionally, the chymotrypsin cut site frequency information which is evidenced by the CHYM-A1 and CHYM-A2 evidentiary references is also disclosed in the Giansanti reference used in the rejection above published in 2016 [see Figure 3]. As the information presented in Giansanti was available before the effective filing date, and ExPASy serves to aggregate publicly available bioinformatics resources for applications such as predicted protease digestions, the information presented in the rejection would therefore available to one of ordinary skill in the art before the effective filing date. Furthermore, the references CHYM-A1 and CHYM-A2 are evidentiary references, as stated in the rejection above and by Applicant, and as such they are not required to antedate the claimed invention, as they are considered references cited to show a universal fact, such as a characteristic or property (e.g., the cut sites) of the enzyme chymotrypsin, as chymotrypsin and its structure were known before the effective filing date, and the activity of chymotrypsin is presumed to be inherent to its structure (see MPEP 2112.I).
Regarding the assertion that the claimed use of isotopically labeled peptides in claim 1 amounts to a surprising discovery to render the method sufficient to quantify more than half of beta casein in a milk sample as described in the Declaration in paragraphs 4-5, Applicant’s assertion is being interpreted as an allegation of unexpected results.
MPEP 716.02(b) states that the burden is on Applicant to establish results are unexpected and significant, and the differences in results are in fact unexpected and unobvious and of both statistical and practical significance. The Declaration describes laboratory tests carried out by the Applicant to show that the tests of the Applicant could not initially produce a chymotrypsin digestion fragment that was predicted by PeptideCutter, and that the effective quantification of A1 and A2 variants was possible focusing on other chymotrypsin digestion fragments termed A1C-VQ14 (corresponding to SEQ ID NO: 3), A1C-VN10 (corresponding to SEQ ID NO: 1), A2C-VN10 (corresponding to SEQ ID NO: 5) and A2C-SN12 (corresponding to SEQ ID NO: 6) [paragraph 4]. Applicant further discloses in [paragraph 5] that the use of only VN(10) and SN(12) peptides corresponding to SEQ ID NOs: 1, 5 and 6 is considered quantitative, and the use of others are not necessary. As stated above in view of Giansanti and evidentiary references CHYM-A1 and CHYM-A2, the prior art indicates the digestion of the bovine A1 and A2 beta casein of CN485 would result in the peptide fragments corresponding to SEQ ID NOs: 1-8 recited in the claims. Therefore the results proffered by Applicant are not considered unexpected, and are not considered unobvious. Applicant’s allegations of unexpected results therefore do not satisfy the requirements of MPEP 716.02(b).
MPEP 716.02(e) states an affidavit or declaration under 37 CFR 1.132 must compare the claimed subject matter with the closest prior art to be effective to rebut a prima facie case of obviousness. As the Declaration describes laboratory tests carried out by the Applicant to show that the tests of the Applicant could not initially produce a predicted chymotrypsin digestion fragment from PeptideCutter, Applicant has not compared the claimed subject matter with the closest prior art. Applicant’s allegations of unexpected results therefore do not satisfy the requirements of MPEP 716.02(e).
MPEP 716.02(d) states that unexpected results must be commensurate in scope with the claimed invention. The data proffered by Applicant involves the quantification of fragments corresponding to SEQ ID NOs: 1 and 5-6, without the recitation or description of the steps involved in the carrying out of the cited laboratory tests. As the claims require the use of fragments corresponding to SEQ ID NOs: 1-2 and 5-6 to carry out the method described in steps (i)-(vi) of claim 1, the results proffered by Applicant are not commensurate in scope with the claimed invention. Applicant’s allegations of unexpected results therefore do not satisfy the requirements of MPEP 716.02(d).
Applicant’s Declaration under 37 CFR 1.132 has been fully considered, but Applicant’s allegations of unexpected results are considered insufficient to rebut a prima facie case of obviousness for the reasons stated above.
Conclusion
Status of the Application:
Claims 1-7, 12-14, 19 and 21 are pending.
Claims 1-7, 12-14, 19 and 21 are rejected.
No claim is in condition for allowance.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JOSEPH SPANGLER whose telephone number is (571)270-0314. The examiner can normally be reached M-F 7:30 am - 4:30 pm.
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/JOSEPH R SPANGLER/
Examiner
Art Unit 1656
/David Steadman/Primary Examiner, Art Unit 1656
Prosecution Insights