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 .
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.
Claim(s) 1-11 is/are rejected under 35 U.S.C. 103 as being unpatentable over Dekio et al. (Microorganisms, 2021) (Dekio).
Regarding claim 1, Dekio teaches a ribosomal protein judgement method (abstract), comprising:
an attribution step that involves comparing observed m/z values indicated by
peaks on a mass spectrum detected by mass spectrometry of a sample containing ribosomal proteins, with first calculated m/z values based on a database, and attributing at least some of the peaks thus detected to ribosomal proteins (page 6, par 3).
Dekio further teaches that “We could successfully assign the majority of the high-intensity peaks of MALDI–TOF spectra for Cutibacterium and Staphylococcus species by proteogenomic approaches, and this is the first report of such analysis for bacterial MALDI–TOF mass spectrometry. Our methodology includes a bottom-up approach by UPLC–MS/MS analysis, with gel excision and curation of amino acid sequences with genome data, and a top-down approach by protein-coding lesion analysis in a genome. In Cutibacterium spectra, only 2 out of 13 peaks were of ribosomal subunit proteins, making a striking contrast with Staphylococus spectra, in which 5 out of 11 peaks were of ribosomals. Our findings lead to a potential breakthrough for the development of a more precise and lighter database for MALDI–TOF microbial identification of bacterial species.” (page 12, par 1). Here, Dekio teaches that high intensity peaks are more likely to become meaningful ribosomal protein peaks. One can develop a more precise and lighter database for MALDI–TOF microbial identification of bacterial species by focusing on high intensity peaks. Thus, Dekio fairly suggest to one of ordinary skill in the art to presume a protein corresponding to a peak with a relative intensity from 50 to 150% relative to an approximate curve or an approximate straight line plotted with relative high intensities of the peaks attributed to ribosomal proteins, to be a ribosomal protein. The result is predictable.
Regarding claim 2, Dekio teaches that wherein the first calculated m/z values are calculated with consideration of post-translational modification (page 6, par 1).
Regarding claim 3, Dekio teaches that wherein the post-translational modification is N-terminal methionine cleavage (page 6, par 1).
Regarding claim 4, Dekio teaches that wherein the mass spectrometry is matrix-assisted laser desorption/ionization mass spectrometry (page 6, par 3).
Regarding claim 5, Dekio does not specifically teach that wherein the sample is of eukaryote origin. However, one of ordinary skill in the art would have appreciated that Dekio’s method can be applied on the sample of eukaryote origin.
Regarding claim 6, Dekio teaches that wherein the sample is a ribosomal protein fraction (gel excision) (Fig. 1, page 5).
Regarding claim 7, Dekio teaches that the ribosomal protein judgement method further comprising:
a verification step that involves calculating a second calculated m/z value of the protein presumed to be a ribosomal protein, with consideration of post-translational modification, and comparing the second calculated m/z value with the observed m/z values (page 6, par 1).
Regarding claim 8, Dekio teaches that wherein ribosomal proteins are judged by the ribosomal protein judgement method according to claim 1, and a species of a living thing that gives amino acid sequence information of the ribosomal proteins is identified (page 10, par 1).
Regarding claim 9, Dekio teaches that wherein the living thing is a microorganism (Staphylococcus strains) (page 10, par 1).
Regarding claim 10, Dekio discloses a mass spectrometry apparatus comprising:
a mass separation member that separates ions based on m/z values (page 3, par 2);
a detection member that detects the ions separated by the mass separation member (page 3, par 2);
a mass spectrum generation member that generates a mass spectrum based on the ions detected by the detection member (page 3, par 2); and
judgement member that determines, from the mass spectrum, peaks that are attributable to ribosomal proteins based on a database (page 6, par 3).
As has been discussed regarding claim 1 above, Dekio fairly suggest a judgement member that generates an approximate curve or an approximate straight line for relative intensities of the peaks, and selects a peak with a relative intensity from 50 to 150% relative to the approximate curve or the approximate straight line (page 12, par 1).
Regarding claim 11, Dekio discloses that the mass spectrometry apparatus comprising a verification member that attributes the peak thus selected, to a ribosomal protein, with further consideration of post-translational modification (page 6, par 1).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to XIAOYUN R XU, Ph. D. whose telephone number is (571)270-5560. The examiner can normally be reached M-F 8am-5pm.
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/XIAOYUN R XU, Ph.D./ Primary Examiner, Art Unit 1797