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 .
Status of Claims
The claim set submitted on 03 JUNE 2024 is acknowledged and considered. In the claim set, the claim have status identifiers.
Current pending claims are Claim 1-20 and are considered on the merits below.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 26 AUGUST 2024 was filed. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Specification/Abstract
The abstract of the disclosure is objected to because the phrase "e.g." renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d).. A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b).
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1, 2, 3, 4, 5 and 7-9 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
In Claims 2, 3 and 4, there are steps of ‘determining’, which do not actually require or claim a detection or detecting steps itself and could be interpreted to be a mental process. The steps in Claim 1 are directed towards data gathering (pre-solution activities). Similarly, Claims 5 and 7; as well as 8 and 9 include a determining and analyzing step , which could be also interpreted to be a mental process.
This judicial exception is not integrated into a practical application because once the determining steps are made, there are no application at all. As stated above, the steps in the independent claim are directed toward data gathering (pre-solution activity), which is not a particular practical application, MPEP 2106.05(g). The eligibility of the claim as a whole under this step and prong, along with a discussion indicating whether any additional steps within the claim, including each of steps (a)-(c) do not transform the claim into something that integrates the abstract idea into a practical application of the abstract idea. Similarly, Claims 5 and 7, and 8 and 9 , once the determining steps are made, there are no application at all. As stated above, the steps in the independent claim are directed toward data gathering (pre-solution activity), which is not a particular practical application, MPEP 2106.05(g).
In addition, the claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because all of Claims 1-4 are well understood, routine and conventional. Moreover, Claims 6 and 10-20 do not include additional elements that are sufficient to amount to significantly more than the judicial exception.
Claim 6 merely recites repeating the data gathering steps.
Claim 10 is directed towards the analysis technique which is WURC and taught by the prior art.
Claims 11 is directed towards additional data gathering steps.
Claim 12 is directed towards an additional step for data gathering.
Claims 13-20 are directed towards parameters of the method which is known in the art, which do not add any practical application or any steps which are significantly more.
Claim Rejections - 35 USC § 112
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.
Claims 3 and 4 are 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 3 recites the limitation "the average number of labels" . There is insufficient antecedent basis for this limitation in the claim.
Claim 4 is also rejected under 112(b) as being dependent upon rejected Claim 3 under 112(b).
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1-15 and 17-20 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by WANG, Protein Footprinting Comes of Age: Mass Spectrometry for Biophysical Structure Assessment*, Molecular & Cellular Proteomics 16.5, as evidence by the Supplemental Material of WANG.
The applied reference has a common inventor with the instant application. Based upon the earlier effectively filed date of the reference, it constitutes prior art under 35 U.S.C. 102(a)(2). This rejection under 35 U.S.C. 102(a)(2) might be overcome by: (1) a showing under 37 CFR 1.130(a) that the subject matter disclosed in the reference was obtained directly or indirectly from the inventor or a joint inventor of this application and is thus not prior art in accordance with 35 U.S.C. 102(b)(2)(A); (2) a showing under 37 CFR 1.130(b) of a prior public disclosure under 35 U.S.C. 102(b)(2)(B) if the same invention is not being claimed; or (3) a statement pursuant to 35 U.S.C. 102(b)(2)(C) establishing that, not later than the effective filing date of the claimed invention, the subject matter disclosed in the reference and the claimed invention were either owned by the same person or subject to an obligation of assignment to the same person or subject to a joint research agreement.
Applicant’s invention is directed towards a method.
Regarding Claim 1, the WANG reference discloses a method of analyzing protein structure, abstract, page 706-707, ‘Description of Labeling Technologies, the method comprising:
(a) labeling a protein with a label to generate an intact labeled protein, abstract, wherein the label comprises a hydroxyl radical, abstract, page 706-707, ‘Description of Labeling Technologies;
(b) obtaining a mass spectrum of the intact labeled protein, abstract, page 707-709, Experimental Approaches; and
(c) analyzing the mass spectrum of the intact labeled protein, page 708-709, c. Prospects for automation.
Additional Disclosures Included are: Claim 2: wherein the method of claim 1, wherein analyzing the mass spectrum of the intact labeled protein comprising determining an average number of labels per protein molecule, page 707, a. Bottom-up Proteomics, Figure 2. ; Claim 3: wherein the method of claim 1, further comprising (d) determining a dose of the label based on the average number of labels per protein molecule, page 708, right column, Figure 2, page 709, left and right columns. ; Claim 4: wherein the method of claim 3, further comprising (e) repeating steps (a)-(d), in which the protein is labeled with the label according to the dose of the label, Figure 2, HRF dose curves are plotted. ; Claim 12: wherein the method of claim 1, wherein the protein is denatured prior to mass spectrometry, page 711, left column. ; Claim 13: wherein the method of claim 1, wherein the protein is at least 50 amino acids in length, Supplemental Material Table.; Claim 14: wherein the method of claim 1, wherein the protein is a lysozyme, Supplemental Material Table.; Claim 15: wherein the method of claim 1, wherein the label is a combination of a hydroxyl radical and at least one different radical, page 711, left column. ;
Claim 17: wherein the method of claim 1, wherein the label is a hydroxyl radical, page 711, c. Footprinting in Cells.; Claim 18: wherein the method of claim 1, wherein the label is generated by X-ray radiolysis, page 707, left column, page 713.
Applicant’s invention is directed towards a method.
Regarding Claim 5, the WANG reference discloses a method of determining a dose of hydroxyl radicals for protein labeling, abstract, Figure 2, page 708, right column, the method comprising:
labeling a protein with hydroxyl radicals to generate an intact labeled protein, abstract, page 706-707, ‘Description of Labeling Technologies;
obtaining a mass spectrum of the intact labeled protein, Figure 2B, page 708 ; and
analyzing the mass spectrum of the intact labeled protein to determine the dose of hydroxyl radicals, Figure 2B, page 708.
Additional Disclosures Included are: Claim 6: wherein the method of claim 5, further comprising: (iv) repeating (i)-(iii) to obtain a range of doses of hydroxyl radicals, Figure 2, HRF dose curves are plotted. ; Claim 7: wherein the method of claim 5, wherein (iii) analyzing the mass spectrum of the intact labeled protein to determine the dose of hydroxyl radicals comprises determining an average number of hydroxyl radicals per protein molecule, page 708, right column, Figure 2, page 709, left and right columns.
Applicant’s invention is directed towards a method.
Regarding Claim 8, the WANG reference discloses a method of labeling a protein, page 707-708, Experimental Approaches, abstract, the method comprising:
labeling a protein with a label to generate an intact labeled protein, wherein the label comprises a hydroxyl radical, abstract, page 706-707, ‘Description of Labeling Technologies;
subjecting the intact labeled protein to mass spectrometry, Figure 2B, page 708, thereby determining a dose of the label relative to the protein; and
further labeling the protein with the label according to the dose of the label, page 708, right column, Figure 2, page 709, left and right columns.
Applicant’s invention is directed towards a method.
Regarding Claim 9, the WANG reference discloses a method of performing protein footprinting, page 707-708, Experimental Approaches, abstract , the method comprising:
labeling a protein according to the method of claim 8 to generate a labeled protein sample, see Rejection of Claim 8 above; and
analyzing the labeled protein sample, thereby a structural character of the protein is determined, page 709-711, Use of Structural Mass Spectrometry Data for Structural Assessment.
Additional Disclosures Included are : Claim 10: wherein the method of claim 9, wherein the labeled protein sample is analyzed using mass spectrometry, abstract, Figure 2, page 708, right column. ; Claim 11: wherein the method of claim 9, wherein analyzing the labeled protein sample comprises: (i) analyzing the intact labeled protein in the labeled protein sample using mass spectrometry, (ii) digesting the intact labeled protein in the labeled protein sample into fragments and analyzing the fragments using mass spectrometry, or both, page 708, right column, page 711, left column .; Claim 19: wherein disclosed is an intact labeled protein produced by the method of claim 8, Figure 2.; and Claim 20: wherein the intact labeled protein of claim 19, which is an intact labeled lysozyme, Supplemental Material Table.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim 16 is rejected under 35 U.S.C. 103 as being unpatentable over WANG, Protein Footprinting Comes of Age: Mass Spectrometry for Biophysical Structure Assessment*, Molecular & Cellular Proteomics 16.5, as evidence by the Supplemental Material of WANG, and further in view of JAIN, et al., Multiplex Chemical Labeling of Amino Acids for Protein Footprinting Structure Assessment, Anal.Chem.2022,94,9819−9825.
Regarding Claim 16, the WANG reference discloses the claimed invention, but is silent in regards to label is combination of a hydroxyl radical and a trifluoromethyl radical.
The JAIN reference discloses a method of analyzing protein structure, abstract, page 4-5, Mass spectrometry analysis, the method comprising: (a) labeling a protein with a label to generate an intact labeled protein, wherein the label comprises a hydroxyl radical, abstract, page 2, page 3, last paragraph, ; (b) obtaining a mass spectrum of the intact labeled protein, page 4-5, Mass spectrometry analysis; and (c) analyzing the mass spectrum of the intact labeled protein, to wherein the label is a combination of a hydroxyl radical and at least one different radical, specifically the label is combination of a hydroxyl radical and a trifluoromethyl radical, page 5-6, Data Processing.
It would be obvious to one having ordinary skill in the art before the effective filing date to modify the label to be a combination with a hydroxyl radical and a trifluoromethyl radical to provide a “one-pot” reaction for multiplex labeling of protein side chains, page 2, page 3.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CHRISTINE T MUI whose telephone number is (571)270-3243. The examiner can normally be reached M-Th 5:30 -15:30 EST.
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CTM
/CHRISTINE T MUI/Primary Examiner, Art Unit 1797
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