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 .
INFORMATION DISCLOSURE STATEMENT
The information disclosure statement (IDS) submitted on 26 July 2024 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the IDS has been considered by the Examiner herein.
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 1-20 are currently pending and have been examined herein.
INITIAL 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 section.
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.
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 1-14 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.
Re claim 1, Applicant recites first instances of the limitations, “with respect to the likely neutral mass related to the peak...” and “outputting the analyte neutral mass”. However, Applicant lacks antecedent basis for these limitations, thereby rendering them indefinite. In the interest of compact prosecution and for the purposes of examination, the Examiner will interpret these limitations as with respect to a likely neutral mass and outputting an analyte neutral mass.
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 on the same reasons applied to claim 1.
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 1-20 are rejected under 35 U.S.C. § 101 because the claimed invention is directed to an abstract idea without significantly more.
Following the 2024 Guidance Update on Patent Subject Matter Eligibility, Including on Artificial Intelligence (89 FR 58128 and MPEP § 2106, hereinafter 2024 GUIDANCE), the claim(s) appear to fall into one of the enumerated statutory categories and recites at least one judicial exception, as explained in the Step 2A, Prong I analysis below. Furthermore, the judicial exception(s) does/do not appear to be integrated into a practical application as explained in the Step 2A, Prong II analysis below. Further still, the claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception(s) as explained in the Step 2B analysis below.
STEP 2A, PRONG I:
Step 2A, prong I, of the 2024 GUIDANCE, first looks to whether the claimed invention recites any judicial exceptions, including certain groupings of abstract ideas (i.e., mathematical concepts, certain methods of organizing human activities such as a fundamental economic practice, or mental processes).
Re claim 1, Applicant recites the following limitations:
A method for identifying analytes in mass spectrometry data, the method comprising:
introducing a sample to a mass spectrometer;
analyzing the sample with the mass spectrometer in a plurality of cycles;
generating, for each cycle, a mass spectrum comprising at least one peak;
annotating peaks in the mass spectrum based on their relationships;
assigning best ion types to each peak;
processing each cycle of the mass spectrum to assign a score to each of the at least one peak thereof with respect to the likely neutral mass related to the peak;
grouping peaks that share a common neutral mass; and
outputting the analyte neutral mass.
The highlighted steps are directed to a mathematical concept, such as determining a mathematical relationship or performing a mathematical calculation, and/or a mental process. The 2024 GUIDANCE expressly recognizes such mathematical relationships/calculations and mental processes as constituting patent-ineligible abstract ideas. Accordingly, these limitations can reasonably be characterized as reciting a patent-ineligible abstract idea.
STEP 2A, PRONG II:
Step 2A, prong II, of the 2024 GUIDANCE, next analyzes whether the claimed invention recites additional elements that individually or in combination integrate the judicial exception into a practical application. In particular, the 2024 GUIDANCE identifies various considerations indicative of whether an additional element or combination of elements integrate the judicial exception into a practical application, such as an additional element reflecting an improvement in the functioning of a computer or an improvement to other technology or technical field.
Re claim 1, in addition to reciting the above-noted abstract idea(s), the judicial exception recited in the claim is not integrated into a practical application because the additional elements recited fail to integrate the judicial exception into a practical application. Specifically, these additional elements merely reflect insignificant extra-solution activity. An example such activity is a step of gathering data for use in a claimed process. Here, the “introducing… analyzing… and generating…” steps merely represent a form of data gathering particular to this technology at a very high level, while the “outputting” step merely represents insignificant post-solution activity. Furthermore, nothing in the claim reasonably indicates that anything other than a generic computer (i.e., “computer processor”) or simple mental processes need to be used to carry out the abstract idea.
STEP 2B:
Step 2B of the 2024 GUIDANCE, next analyzes whether the claimed invention adds any specific limitations beyond the judicial exception that, either alone or as an ordered combination, amount to more than “well-understood, routine, conventional” activity in the field.
Re claim 1, the additional limitation(s) recited above only generally link the judicial exception to a particular technological field. Furthermore, these additional elements do not appear to be sufficient to amount to significantly more than the judicial exception because they again merely reflect insignificant extra-solution activity, as described above, while only generally linking the judicial exception to a particular technological field (i.e., mass spectrometry). Further still, this/these additional limitation(s) does/do not, as an ordered combination, amount to more than “well-understood, routine, conventional” activity in the field.
Accordingly, claim 1 is rejected under 35 U.S.C. § 101 as being directed to patent-ineligible subject matter for at least these reasons.
Re claims 2-14, these claims do not cure the deficiencies noted above with regard to claim 1, from which they depend, as they merely add further mathematical processing steps and/or other extra-solution activity. Accordingly, they are rejected under the same or substantially similar analysis, as outlined above.
Re claims 15-20, Applicant recites language similar to claims 1-14, as discussed in the preceding paragraphs, and for reasons similar to those discussed above, claims 15-20 are also rejected under 35 USC § 101 as failing to recite patent-eligible subject matter.
Allowable Subject Matter
Claims 1-20 would be allowable if rewritten or amended to overcome the rejection(s) under 35 USC §112 and/or 35 USC §101, 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
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 Monday-Friday 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.
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Respectfully,
/Thomas M Hammond III/Primary Examiner, GAU 2855