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 STATUS
Claims 1-20 were originally filed.
Claims 3-5, 7-14, and 17-19 were amended by the preliminary amendment filed 06 March 2024.
Claims 1, 5, 15-16, and 20 are currently amended.
Claims 1-20 are currently pending and have been examined herein.
RESPONSE TO APPLICANT’S AMENDMENTS/ARGUMENTS
– 35 USC § 112(a) –
Claims 1-19 were rejected under 35 USC § 112(a) in the previous Office Action.
Re claims 1-19, Applicant relies upon a fundamental misunderstanding of the rejection of record. More specifically, Applicant’s failure to properly address the fundamental basis of the analysis, namely ascertaining the full scope of the claimed invention, clearly shows Applicant’s lack of understanding with respect to the rejection. Applicant compounds this lack of understanding by arguing that an all-encompassing “processing” step is merely predictable in a computational environment and “not mysterious or unknowable”. The Examiner strenuously disagrees with this notion that black boxes do not exist in a computational environment. Moreover, despite asserting the Specification “provides detailed algorithmic sub-steps, scoring logic, threshold criteria, multiple flowcharts, and a concrete working example”, Applicant does not particularly point out where these details exist in the Specification.
Furthermore, the Examiner disagrees with the Applicant’s assertion that “if the Specification provides sufficient direction to enable the claimed method as recited in claim 20, it necessarily provides sufficient direction to enable the same method as recited in claims 1 and 15. This is nonsensical. If true, it would render the proper analysis of each claim moot. Claims 1 and 15 are significantly broader claim constructions than that of claim 20. What is particularly broadening are the “annotating” and “processing” steps of the method, as emphasized in the rejection. Because these are largely mathematical steps, their scope is incredibly broad, thus requiring significant disclosure to close the gap between what has been disclosed (e.g., claim 20) and the full scope. Applicant’s insinuation that the Examiner finds these steps “pure mathematics” and “infinite” are merely an exaggeration of the Examiner’s position. Accordingly, Applicant’s arguments are not persuasive and the rejections are maintained. Further still, should Applicant wish to maintain that the undeniably large gap between the scope of the claimed invention and the disclosure is merely within one of ordinary skill in the art and therefore enabling, the Examiner shall construe this as an admission that it is a factor weighing against eligibility under §101, as it lends weight to the notion that it is not sufficiently integrated into a practical application.
– 35 USC § 112(b) –
Claims 1-14 were rejected under 35 USC § 112(b) in the previous Office Action.
Re claims 1-14, the Examiner appreciates the Applicant’s prompt attention to these deficiencies and, in view of Applicant’s amendments, hereby withdraws such rejections.
– 35 USC § 101 –
Claims 1-20 were rejected under 35 USC § 101 in the previous Office Action.
Without conceding to the propriety of Applicant’s remarks, the Examiner appreciates the Applicant’s response to these deficiencies and hereby withdraws such rejections.
– Additional Remarks –
Applicant is reminded that in order to be entitled to reconsideration or further examination, the applicant or patent owner must reply to the Office action. The reply by the applicant or patent owner must be reduced to a writing which distinctly and specifically points out the supposed errors in the examiner’s action and must reply to every ground of objection and rejection in the prior Office action. The reply must present arguments pointing out the specific distinctions believed to render the claims, including any newly presented claims, patentable over any applied references. If the reply is with respect to an application, a request may be made that objections or requirements as to form not necessary to further consideration of the claims, be held in abeyance until allowable subject matter is indicated. The Applicant’s or patent owner’s reply must appear throughout to be a bona fide attempt to advance the application or the reexamination proceeding to final action. A general allegation that the claims define a patentable invention without specifically pointing out how the language of the claims patentably distinguishes them from the references does not comply with the requirements of this section1.
Should the Applicant believe that a telephone conference would expedite the prosecution of the instant application, Applicant is invited to call the Examiner.
CLAIM REJECTIONS - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. § 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 § U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-19 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, for failing to be fully enabled by the Applicant’s Specification.
Re claim 1, because the Specification, while being enabling for the steps of “introducing… analyzing… generating… assigning… grouping… (and) outputting…”, it does not reasonably provide enablement for the full scope of the steps, “annotating… (and) processing…”. In other words, the Specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims. More specifically, the following factors were considered by the Examiner and support the determination that Applicant’s claimed invention is not fully enabled:
(A) The breadth of the claims – since the claimed invention is largely mathematical, the generic steps mentioned become nearly infinite, thus favoring rejection.
(B) The nature of the invention – the claimed invention is a largely mathematical algorithm applied to mass spectrometry data, thus it is critical to define the scope of such algorithm. Pursuant to ‘A’ above, the pertinent steps leave a wide gap in breadth from what is disclosed and what is covered by the recited steps, thus favoring rejection.
(C) The state of the prior art – the prior art in the area is relatively robust, thus demanding clearly defined algorithms, particularly because it is mathematical. Here, Applicant has not done so, thus favoring rejection.
(D) The level of one of ordinary skill – mass spectrum analysis to identify analytes typical involves a relatively high level of skill in the art, thus favoring rejection pursuant to ‘A’.
(E) The level of predictability in the art – while mathematical algorithms in general are largely predictable, absent specificity in the claim itself or through explicit definition in the Specification, overly broad mathematical algorithms become black boxes, thus favoring rejection.
(F) The amount of direction provided by the inventor – the Applicant has provided sufficient direction in claim 20, which incorporates the particular algorithms for the pertinent steps mentioned above. For claims 1 and 15, the examiner suggests following the map of claim 20.
(G) The existence of working examples – n/a scope issue
(H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure – n/a scope issue
Re claims 2-14, Applicant recites limitations respectively dependent from claim 1, but that fail to cure the deficiencies discussed in the rejection above. Accordingly, claims 2-14 are rejected based at least upon the same rationale applied to claim 1.
Re claims 15-19, Applicant recites limitations that suffer from the same or substantially the same deficiencies noted above with respect to claims 1-14. Accordingly, claims 15-19 are rejected based at least upon the same rationale applied to claims 1-14.
Allowable Subject Matter
Claim 20 is allowable.
Claims 1-19 would be allowable if rewritten or amended to overcome the rejection(s) under 35 USC §112, set forth in this Office action.
Re claim 20, Applicant's claims encompass an invention that the prior art does not disclose, teach, or otherwise render obvious. More specifically, Applicant recites,
One or more non-transitory computer-readable media having computer-executable instructions embodied thereon that, when executed by at least one computing system, cause the at least one computing system to perform the one or more of the following operations:
receiving the plurality of a cycles of mass spectra for a sample to be analyzed, each spectrum comprising at least one peak and each sample comprising two or more analytes;
processing each cycle of mass spectra by:
generating a subset spectral peak list of the mass spectrum;
calculating one or more initial neutral masses;
finding neutral masses assuming absence of protonated peaks;
assigning mass difference relationships to the peaks;
updating a neutral mass value based on the finding and assignment;
assigning m/z errors and scores to spectral peak annotations;
annotating peaks in the mass spectrum based on their relationships;
resolving competing annotations based on mass error and commonality of individual annotations;
grouping complementary peaks by confirming complex ion types;
assigning best ion types to each peak; scoring each of the multiple peaks belonging to a group on a scale of 0 to 1, where peaks that have contradictory relationships have a score of 0 and peaks having the highest likelihood of being attributable to the same analyte have a score of 1;
qualifying results for each m/z ion as a function of time by grouping by consecutive cycles and scoring shape as a function of time, and consistency in ion types;
qualifying results for each neutral mass as a function of time to group neutral mass results by consecutive cycles and scoring shape, based on evidences and scores;
removing noise from single cycle, single member neutral mass groups;
identifying analytes based on the scores; grouping peaks that share a common neutral mass; and
outputting analytes identified in the sample. (emphasis added)
As best understood within the context of Applicant' s claimed invention as a whole, these limitations do not appear to be disclosed, taught, nor otherwise rendered obvious by the prior art.
For example, Wilhelm et al. (US20240266001, “WILHELM”) discloses a method of identifying analytes using mass spectrometry. However, WILHELM, as best understood by the Examiner, fails to disclose, teach, or otherwise render obvious the particular claim limitations highlighted above, in view of the claimed invention as a whole.
Furthermore, Shilov et al. (US20200217829, “SHILOV”) discloses a similar mass spectrometry method to identify analytes by generating an ion peak list. However, like WILHELM, SHILOV, as best understood by the Examiner, fails to disclose, teach, or otherwise render obvious the particular claim limitations highlighted above, in view of the claimed invention as a whole.
Further still, Pillai et al. (US 8975404, “PILLAI”) discloses another analyte identification system using mass spectrometry by analyzing peak ion intensity. However, like WILHELM and SHILOV, PILLAI, as best understood by the Examiner, fails to disclose, teach, or otherwise render obvious the particular claim limitations highlighted above, in view of the claimed invention as a whole.
Accordingly, independent claim 20 is deemed allowable over the prior art. Independent claims 1 and 15 encompass a similar scope as claim 1, and would be similarly allowable pending resolution of the rejections above. Dependent claims 1-14 and 16-19 are each allowable based at least on their respective dependency to claims 1 or 15.
Any comments considered necessary by Applicant must be submitted no later than the payment of the issue fee and, to avoid processing delays, should preferably accompany the issue fee. Such submissions should be clearly labeled “Comments on Statement of Reasons for Allowance”.
RELEVANT PRIOR ART
The Examiner would like to make Applicant aware of prior art references, not relied upon in this action, but pertinent to Applicant’s disclosure. They are as follows:
US20210375604, Gajadhar et al. – quantitation of a target analyte using mass spectrometer
CN107646089B, Richardson et al. – sample spectral analysis
US20150340216, Kwiecien et al. – analyte identification using mass spectrometry
US20140142865, Wright – product-ion analysis system using mass spectrometry
US20110143951, Thompson – determining analytes from neutral loss mass spectroscopy
CONCLUSION
THIS ACTION IS MADE FINAL. 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 extension fee 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 THOMAS M HAMMOND III whose telephone number is (571)272-2215. The Examiner can normally be reached on Mon-Fri 0800-1700.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner’s supervisor, Peter Macchiarolo can be reached on 571-272-2375. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000. For more information about the PAIR system, see: https://ppair-my.uspto.gov/pair/PrivatePair.
Respectfully,
/Thomas M Hammond III/Primary Examiner, GAU 2855
1 37 C.F.R. § 1.111(b)
Prosecution Insights